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branch: rosetta:commits 「№20775」
Commited by: Rocco Moretti
GitHub Pull Request link: 「№426」
Merge: 「e6f643b81」← 「105e3c830」 code diff
Scheduled at: 2025-05-30 16:41:38.050632

	linux.clang	linux.gcc	linux.srlz	mac.clang
debug
release
unit

Pull Request №426 RosettaCommons/rosetta/main ← roccomoretti/rosetta/test_fixes Merge: e6f643b818cda63c8e00156a266c408faac3c3dd←105e3c830e83e5b070b4d758be28a04be01af44c Fixes for failing tests in main ---------------- Merge commit message: Fix documentation submodule regression.

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Test: linux.clang.build.debug

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Test: linux.clang.build.header

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

Failed sub-tests (click for more details):
replica_docking

Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):
ddG_of_mutation

Test: linux.clang.unit

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branch: rosetta:commits 「№20774」
Commited by: Rocco Moretti
GitHub Pull Request link: 「№426」
Merge: 「e6f643b81」← 「db533f771」 code diff
Scheduled at: 2025-05-30 14:45:06.173884

	linux.clang	linux.gcc	linux.srlz	mac.clang
debug
release
unit

Pull Request №426 RosettaCommons/rosetta/main ← roccomoretti/rosetta/test_fixes Merge: e6f643b818cda63c8e00156a266c408faac3c3dd←db533f77171895f80fd63ce315fa04aef8d58aaa Fixes for failing tests in main ---------------- Merge commit message: Attempt to turn off clang-tidy diagnostics related to external library headers.

Rosetta Benchmark 1 day
Tests for this revision was automatically canceled because newer set of tests for pull-request №426 was submitted!

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Test: ubuntu.clang.code_quality.clang_tidy

Failed sub-tests (click for more details):
src/ObjexxFCL/Cstring.cc src/ObjexxFCL/Dimension.cc src/ObjexxFCL/DimensionExpression.cc src/ObjexxFCL/DimensionExpressionRef.cc src/ObjexxFCL/DynamicIndexRange.cc src/ObjexxFCL/Fstring.cc src/ObjexxFCL/IndexRange.cc src/ObjexxFCL/Observer.cc src/ObjexxFCL/ObserverGraph.cc src/ObjexxFCL/ObserverMediator.cc src/ObjexxFCL/ObserverMulti.cc src/ObjexxFCL/Star.cc src/ObjexxFCL/Time_Date.cc src/ObjexxFCL/char.functions.cc src/ObjexxFCL/format.cc src/ObjexxFCL/string.functions.cc 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/AbinitioRelax.cc src/apps/public/DRRAFTER/drrafter_error_estimation.cc src/apps/public/DRRAFTER/fit_helix_in_map.cc src/apps/public/SymDock.cc src/apps/public/analysis/HDXEnergy.cc src/apps/public/analysis/InterfaceAnalyzer.cc src/apps/public/analysis/PeptideDeriver.cc src/apps/public/analysis/ResidueDisorder.cc src/apps/public/analysis/SID_ERMS_prediction.cc src/apps/public/analysis/atom_energy_breakdown.cc src/apps/public/analysis/batch_distances.cc src/apps/public/analysis/cl_complex_rescore.cc src/apps/public/analysis/contactMap.cc src/apps/public/analysis/cst_info.cc src/apps/public/analysis/ensemble_analysis.cc src/apps/public/analysis/fast_clustering.cc src/apps/public/analysis/interface_energy.cc src/apps/public/analysis/parcs_ccs_calc.cc src/apps/public/analysis/per_residue_energies.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/sc.cc src/apps/public/analysis/score.cc src/apps/public/analysis/score_jd2.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/antibody_graft.cc src/apps/public/antibody/antibody_legacy.cc src/apps/public/antibody/antibody_numbering_converter.cc src/apps/public/antibody/identify_cdr_clusters.cc src/apps/public/antibody/packing_angle.cc src/apps/public/antibody/snugdock.cc src/apps/public/backrub.cc src/apps/public/boinc/minirosetta.cc src/apps/public/boinc/minirosetta_graphics.cc src/apps/public/calculate_sasa.cc src/apps/public/carbohydrates/GlycanDock.cc src/apps/public/carbohydrates/dock_glycans.cc src/apps/public/carbohydrates/glycan_clash_check.cc src/apps/public/carbohydrates/glycan_info.cc src/apps/public/carbohydrates/pose_from_saccharide_sequence.cc src/apps/public/clustering/calibur.cc src/apps/public/clustering/cluster.cc src/apps/public/clustering/energy_based_clustering.cc src/apps/public/combine_silent.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/comparative_modeling/validate_silent.cc src/apps/public/constel.cc src/apps/public/coupled_moves/coupled_moves.cc src/apps/public/cyclic_peptide/count_cycpep_sequences.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/pmut_scan_parallel.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_prepack_protocol.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/dgdp.cc src/apps/public/electron_density/grower_prep.cc src/apps/public/electron_density/mr_protocols.cc src/apps/public/electron_density/sim_cryo.cc src/apps/public/enzdes/CstfileToTheozymePDB.cc src/apps/public/enzdes/enzyme_design.cc src/apps/public/extract_pdbs.cc src/apps/public/fiber_diffraction/FiberDiffractionFreeSet.cc src/apps/public/flexpep_docking/BuildPeptide.cc src/apps/public/flexpep_docking/FlexPepDocking.cc src/apps/public/fragment_picker.cc src/apps/public/helical_bundle/helical_bundle_predict.cc src/apps/public/hydrate/hydrate.cc src/apps/public/idealize_jd2.cc src/apps/public/interface_design/anchored_design/AnchorFinder.cc src/apps/public/interface_design/anchored_design/AnchoredDesign.cc src/apps/public/interface_design/anchored_design/AnchoredPDBCreator.cc src/apps/public/internal/generate_database_cache.cc src/apps/public/internal/validate_database.cc src/apps/public/legacy_sewing/sewing_hasher.cc src/apps/public/ligand_design/revold.cc src/apps/public/ligand_docking/extract_atomtree_diffs.cc src/apps/public/ligand_docking/ligand_dock.cc src/apps/public/ligand_docking/ligand_rpkmin.cc src/apps/public/ligand_docking/select_best_unique_ligand_poses.cc src/apps/public/loop_modeling/loodo.cc src/apps/public/loop_modeling/loopmodel.cc src/apps/public/loop_modeling/transform_loodo.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/helix_from_sequence.cc src/apps/public/membrane/mp_dock.cc src/apps/public/membrane/mp_dock_setup.cc src/apps/public/membrane/mp_domain_assembly.cc src/apps/public/membrane/mp_lipid_acc.cc src/apps/public/membrane/mp_mutate_relax.cc src/apps/public/membrane/mp_range_relax.cc src/apps/public/membrane/mp_seqrecov.cc src/apps/public/membrane/mp_span_from_pdb.cc src/apps/public/membrane/mp_symdock.cc src/apps/public/membrane/mp_transform.cc src/apps/public/membrane/mp_viewer.cc src/apps/public/membrane_abinitio/membrane_abinitio2.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_ligand_discovery/identify_ligand_motifs.cc src/apps/public/motif_ligand_discovery/ligand_discovery_search_protocol.cc src/apps/public/motif_tools/extract_motifs.cc src/apps/public/motif_tools/incorporate_motifs.cc src/apps/public/mutate.cc src/apps/public/ncaa_utilities/MakeRotLib.cc src/apps/public/ncaa_utilities/UnfoldedStateEnergyCalculator.cc src/apps/public/nmr/calc_nmr_tensor.cc src/apps/public/nmr/ligand_transform_with_pcs.cc src/apps/public/nmr/r_noe_assign.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/packstat.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/pose_sewing/MakeSegmentFile.cc src/apps/public/post-translational_modification/DNA_methylation.cc src/apps/public/post-translational_modification/N-terminal_acetylation.cc src/apps/public/post-translational_modification/glycosyltransfer.cc src/apps/public/post-translational_modification/phosphorylation.cc src/apps/public/recces/legacy/recces_turner.cc src/apps/public/recces/legacy/thermal_sampler.cc src/apps/public/recces/recces.cc src/apps/public/recon_design/recon.cc src/apps/public/relax.cc src/apps/public/remodel.cc src/apps/public/restype_converter.cc src/apps/public/rna/erraser/erraser2.cc src/apps/public/rna/erraser/erraser_minimizer.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_idealize.cc src/apps/public/rna/util/rna_minimize.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/rosettaDNA/rosettaDNA.cc src/apps/public/rosetta_scripts/multistage/multistage_rosetta_scripts.cc src/apps/public/rosetta_scripts/parse_rosetta_script.cc src/apps/public/rosetta_scripts/revert_design_to_native.cc src/apps/public/rosetta_scripts/rosetta_scripts.cc src/apps/public/rosetta_scripts/rosetta_scripts_jd3.cc src/apps/public/rosetta_scripts/validate_rosetta_script.cc src/apps/public/scenarios/FloppyTail.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/chemically_conjugated_docking/UBQ_Gp_LYX-Cterm.cc src/apps/public/scenarios/doug_dock_design_min_mod2_cal_cal.cc src/apps/public/sequence_tolerance.cc src/apps/public/sewing/edge_file_generator.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/struc_set_fragment_picker.cc src/apps/public/surface_docking/surface_docking.cc src/apps/public/tcr/tcrmodel.cc src/apps/public/trRosetta/trRosetta.cc src/apps/public/vip.cc src/apps/public/weight_optimization/optE_parallel.cc src/apps/public/weight_optimization/torsional_potential_corrections.cc src/apps/tests/test_C-terminal_conjugation.cc src/apps/tests/test_CCD_loop_closure.cc src/apps/tests/test_CarbohydrateInfo.cc src/apps/tests/test_EnergyMethodOptions.cc src/apps/tests/test_RingConformationMover.cc src/apps/tests/test_SiteConstraint.cc src/apps/tests/test_carbohydrate_docking.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/basic/ComparingTracer.cc src/basic/Emitter.cc src/basic/MemTracer.cc src/basic/MetricValueIO.cc src/basic/Tracer.cc src/basic/TracerImpl.cc src/basic/TracerToFile.cc src/basic/basic.cc src/basic/citation_manager/Citation.cc src/basic/citation_manager/CitationCollection.cc src/basic/citation_manager/CitationCollectionBase.cc src/basic/citation_manager/CitationManager.cc src/basic/citation_manager/UnpublishedModuleAuthor.cc src/basic/citation_manager/UnpublishedModuleInfo.cc src/basic/database/insert_statement_generator/InsertGenerator.cc src/basic/database/insert_statement_generator/RowData.cc src/basic/database/open.cc src/basic/database/schema_generator/Column.cc src/basic/database/schema_generator/Constraint.cc src/basic/database/schema_generator/DbDataType.cc src/basic/database/schema_generator/ForeignKey.cc src/basic/database/schema_generator/Index.cc src/basic/database/schema_generator/PrimaryKey.cc src/basic/database/schema_generator/Schema.cc src/basic/database/sql_utils.cc src/basic/datacache/BasicDataCache.cc src/basic/datacache/CacheableData.cc src/basic/datacache/CacheableResRotPairFloatMap.cc src/basic/datacache/CacheableString.cc src/basic/datacache/CacheableStringFloatMap.cc src/basic/datacache/CacheableStringIntegerMap.cc src/basic/datacache/CacheableStringMap.cc src/basic/datacache/CacheableUint64MathMatrixFloatMap.cc src/basic/datacache/ConstDataMap.cc src/basic/datacache/DataMap.cc src/basic/datacache/DataMapObj.cc src/basic/datacache/DiagnosticData.cc src/basic/datacache/HierarchicalDataMap.cc src/basic/datacache/WriteableCacheableData.cc src/basic/datacache/WriteableCacheableDataCreator.cc src/basic/datacache/WriteableCacheableDataFactory.cc src/basic/datacache/WriteableCacheableMap.cc src/basic/execute.cc src/basic/gpu/GPU.cc src/basic/gpu/Timer.cc src/basic/init.cc src/basic/interpolate.cc src/basic/mpi/DbMoverMessageListener.cc src/basic/mpi/MessageListenerFactory.cc src/basic/mpi/util.cc src/basic/options/PyRosettaFunctions.cc src/basic/options/after_opts.cc src/basic/options/keys/OptionKeys0.cc src/basic/options/keys/OptionKeys1.cc src/basic/options/keys/OptionKeys10.cc src/basic/options/keys/OptionKeys11.cc src/basic/options/keys/OptionKeys12.cc src/basic/options/keys/OptionKeys13.cc src/basic/options/keys/OptionKeys14.cc src/basic/options/keys/OptionKeys15.cc src/basic/options/keys/OptionKeys2.cc src/basic/options/keys/OptionKeys3.cc src/basic/options/keys/OptionKeys4.cc src/basic/options/keys/OptionKeys5.cc src/basic/options/keys/OptionKeys6.cc src/basic/options/keys/OptionKeys7.cc src/basic/options/keys/OptionKeys8.cc src/basic/options/keys/OptionKeys9.cc src/basic/options/option.cc src/basic/options/util.cc src/basic/prof.cc src/basic/pymol_chains.cc src/basic/random/RandomGeneratorSettings.cc src/basic/random/init_random_generator.cc src/basic/report.cc src/basic/resource_manager/ResourceLoader.cc src/basic/resource_manager/ResourceLoaderCreator.cc src/basic/resource_manager/ResourceLoaderFactory.cc src/basic/resource_manager/ResourceLocator.cc src/basic/resource_manager/ResourceLocatorCreator.cc src/basic/resource_manager/ResourceLocatorFactory.cc src/basic/resource_manager/ResourceManager.cc src/basic/resource_manager/ResourceManagerCreator.cc src/basic/resource_manager/ResourceManagerFactory.cc src/basic/resource_manager/loader_schemas.cc src/basic/resource_manager/locator/DatabaseResourceLocator.cc src/basic/resource_manager/locator/FileListResourceLocator.cc src/basic/resource_manager/locator/FileSystemResourceLocator.cc src/basic/resource_manager/locator/NullResourceLocator.cc src/basic/resource_manager/locator/StringResourceStream.cc src/basic/resource_manager/locator/locator_schemas.cc src/basic/sampling/orientations/QuaternionGrid.cc src/basic/svd/SVD_Solver.cc src/basic/tensorflow_manager/RosettaTensorflowManager.cc src/basic/tensorflow_manager/RosettaTensorflowProtocolBase.cc src/basic/tensorflow_manager/RosettaTensorflowSessionContainer.cc src/basic/tensorflow_manager/RosettaTensorflowTensorContainer.cc src/basic/tensorflow_manager/util.cc src/basic/thread_manager/RosettaThread.cc src/basic/thread_manager/RosettaThreadAllocation.cc src/basic/thread_manager/RosettaThreadAssignmentInfo.cc src/basic/thread_manager/RosettaThreadManager.cc src/basic/thread_manager/RosettaThreadManagerInitializationTracker.cc src/basic/thread_manager/RosettaThreadPool.cc src/core/chemical/AA.cc src/core/chemical/Adduct.cc src/core/chemical/Atom.cc src/core/chemical/AtomICoor.cc src/core/chemical/AtomProperties.cc src/core/chemical/AtomPropertiesManager.cc src/core/chemical/AtomProperty_mappings.cc src/core/chemical/AtomType.cc src/core/chemical/AtomTypeDatabaseIO.cc src/core/chemical/AtomTypeSet.cc src/core/chemical/Bond.cc src/core/chemical/CacheableResidueTypeSets.cc src/core/chemical/ChemicalManager.cc src/core/chemical/ElectronConfiguration.cc src/core/chemical/Element.cc src/core/chemical/ElementSet.cc src/core/chemical/Elements.cc src/core/chemical/GlobalResidueTypeSet.cc src/core/chemical/IdealBondLengthSet.cc src/core/chemical/MMAtomType.cc src/core/chemical/MMAtomTypeSet.cc src/core/chemical/Metapatch.cc src/core/chemical/MutableChiRecord.cc src/core/chemical/MutableICoorRecord.cc src/core/chemical/MutableResidueConnection.cc src/core/chemical/MutableResidueType.cc src/core/chemical/NucleotideTools.cc src/core/chemical/Orbital.cc src/core/chemical/Patch.cc src/core/chemical/PatchOperation.cc src/core/chemical/PatchOperationFactory.cc src/core/chemical/PoseResidueTypeSet.cc src/core/chemical/ResConnID.cc src/core/chemical/ResidueConnection.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/ResidueType.srlz.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/ResidueTypeSet.srlz.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/bcl/BCLFragmentHandler.cc src/core/chemical/bcl/util.cc src/core/chemical/bond_support.cc src/core/chemical/carbohydrates/CarbohydrateInfo.cc src/core/chemical/carbohydrates/CarbohydrateInfoManager.cc src/core/chemical/carbohydrates/database_io.cc src/core/chemical/gasteiger/GasteigerAtomTypeData.cc src/core/chemical/gasteiger/GasteigerAtomTypeSet.cc src/core/chemical/gasteiger/GasteigerAtomTyper.cc src/core/chemical/icoor_support.cc src/core/chemical/io/MergeAndSplitBehaviorManager.cc src/core/chemical/io/merge_and_split_behaviors_io.cc src/core/chemical/mainchain_potential/MainchainScoreTable.cc src/core/chemical/mainchain_potential/util.cc src/core/chemical/mmCIF/mmCIFParser.cc src/core/chemical/modifications/ChemistryBase.cc src/core/chemical/modifications/Reprotonate.cc src/core/chemical/modifications/ValenceHandler.cc src/core/chemical/orbitals/AssignOrbitals.cc src/core/chemical/orbitals/ICoorOrbitalData.cc src/core/chemical/orbitals/OrbitalType.cc src/core/chemical/orbitals/OrbitalTypeMapper.cc src/core/chemical/orbitals/OrbitalTypeSet.cc src/core/chemical/rdkit/RDMolToRestype.cc src/core/chemical/rdkit/RestypeToRDMol.cc src/core/chemical/rdkit/util.cc src/core/chemical/residue_io.cc src/core/chemical/residue_support.cc src/core/chemical/rings/RingConformerManager.cc src/core/chemical/rings/RingConformerSet.cc src/core/chemical/rings/ring_conformer_io.cc src/core/chemical/rings/util.cc src/core/chemical/rna/RNA_FittedTorsionInfo.cc src/core/chemical/rna/RNA_Info.cc src/core/chemical/rna/RNA_SamplerUtil.cc src/core/chemical/rna/util.cc src/core/chemical/rotamers/BasicRotamerLibrarySpecification.cc src/core/chemical/rotamers/CenrotRotamerLibrarySpecification.cc src/core/chemical/rotamers/DunbrackRotamerLibrarySpecification.cc src/core/chemical/rotamers/NCAARotamerLibrarySpecification.cc src/core/chemical/rotamers/PDBRotamerLibrarySpecification.cc src/core/chemical/rotamers/RotamerLibrarySpecification.cc src/core/chemical/rotamers/RotamerLibrarySpecificationFactory.cc src/core/chemical/rotamers/StoredRotamerLibrarySpecification.cc src/core/chemical/sdf/CtabV2000Parser.cc src/core/chemical/sdf/CtabV3000Parser.cc src/core/chemical/sdf/MolFileIOData.cc src/core/chemical/sdf/MolFileIOReader.cc src/core/chemical/sdf/SDFParser.cc src/core/chemical/sdf/mol_util.cc src/core/chemical/sdf/mol_writer.cc src/core/chemical/util.cc src/core/conformation/AbstractRotamerTrie.cc src/core/conformation/Atom.cc src/core/conformation/AtomGraph.cc src/core/conformation/Conformation.cc src/core/conformation/PointGraph.cc src/core/conformation/PointGraphData.cc src/core/conformation/PseudoBond.cc 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src/core/energy_methods/ImplicitMembraneElecEnergy.cc src/core/energy_methods/IntermolEnergy.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/LinearBranchEnergyCreator.cc src/core/energy_methods/LinearChainbreakEnergy.cc src/core/energy_methods/LinearChainbreakEnergyCreator.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 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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/RMS_Energy.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_CoarseDistEnergy.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_PartitionEnergy.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 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src/core/scoring/hbonds/NPDHBondSet.cc src/core/scoring/hbonds/graph/HBondGraph.cc src/core/scoring/hbonds/hbonds.cc src/core/scoring/hbonds/hbonds_geom.cc src/core/scoring/hbonds/hbtrie/HBAtom.cc src/core/scoring/hbonds/hbtrie/HBCPData.cc src/core/scoring/hbonds/hbtrie/HBCountPairFunction.cc src/core/scoring/hbonds/hbtrie/HBondsTrieVsTrieCachedDataContainer.cc src/core/scoring/hbonds/polynomial.cc src/core/scoring/hbonds/types.cc src/core/scoring/interface_/DDPlookup.cc src/core/scoring/interface_/DDPscore.cc src/core/scoring/lddt.cc src/core/scoring/lkball/LK_BallEnergy.cc src/core/scoring/lkball/LK_BallInfo.cc src/core/scoring/lkball/LK_DomeEnergy.cc src/core/scoring/lkball/LK_DomeInfo.cc src/core/scoring/lkball/lkbtrie/LKBAtom.cc src/core/scoring/lkball/lkbtrie/LKBTrieEvaluator.cc src/core/scoring/loop_graph/Loop.cc src/core/scoring/loop_graph/LoopCycle.cc src/core/scoring/loop_graph/LoopGraph.cc src/core/scoring/loop_graph/evaluator/GaussianChainFuncPotentialEvaluator.cc src/core/scoring/loop_graph/evaluator/LoopClosePotentialEvaluator.cc src/core/scoring/loop_graph/evaluator/SixDTransRotPotential.cc src/core/scoring/loop_graph/evaluator/SixDTransRotPotentialEvaluator.cc src/core/scoring/loop_graph/util.cc src/core/scoring/magnesium/MgKnowledgeBasedPotential.cc src/core/scoring/magnesium/util.cc src/core/scoring/memb_etable/MembEtable.cc src/core/scoring/membrane/MPNonHelixPenalty.cc src/core/scoring/membrane/MPTMProjPenalty.cc src/core/scoring/membrane/MPTerminiPenalty.cc src/core/scoring/membrane/MembraneData.cc src/core/scoring/methods/ContextDependentLRTwoBodyEnergy.cc src/core/scoring/methods/ContextDependentOneBodyEnergy.cc src/core/scoring/methods/ContextDependentTwoBodyEnergy.cc src/core/scoring/methods/ContextIndependentLRTwoBodyEnergy.cc src/core/scoring/methods/ContextIndependentOneBodyEnergy.cc src/core/scoring/methods/ContextIndependentTwoBodyEnergy.cc src/core/scoring/methods/EnergyMethod.cc src/core/scoring/methods/EnergyMethodOptions.cc src/core/scoring/methods/FreeDOF_Options.cc src/core/scoring/methods/LongRangeTwoBodyEnergy.cc src/core/scoring/methods/MMBondAngleEnergy.cc src/core/scoring/methods/MMBondLengthEnergy.cc src/core/scoring/methods/MMLJEnergyInter.cc src/core/scoring/methods/MMLJEnergyIntra.cc src/core/scoring/methods/MMTorsionEnergy.cc src/core/scoring/methods/OneBodyEnergy.cc src/core/scoring/methods/ShortRangeTwoBodyEnergy.cc src/core/scoring/methods/TwoBodyEnergy.cc src/core/scoring/methods/WholeStructureEnergy.cc src/core/scoring/methods/branch_energy_util.cc 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/MHCEpitopePredictor.cc src/core/scoring/mhc_epitope_energy/MHCEpitopePredictorExternal.cc src/core/scoring/mhc_epitope_energy/MHCEpitopePredictorMatrix.cc src/core/scoring/mhc_epitope_energy/MHCEpitopePredictorPreLoaded.cc src/core/scoring/mhc_epitope_energy/MHCEpitopePredictorSVM.cc src/core/scoring/mm/MMBondAngleLibrary.cc src/core/scoring/mm/MMBondAngleResidueTypeParam.cc src/core/scoring/mm/MMBondAngleResidueTypeParamSet.cc src/core/scoring/mm/MMBondAngleScore.cc src/core/scoring/mm/MMBondLengthLibrary.cc src/core/scoring/mm/MMBondLengthScore.cc src/core/scoring/mm/MMLJEnergyTable.cc src/core/scoring/mm/MMLJLibrary.cc src/core/scoring/mm/MMLJScore.cc src/core/scoring/mm/MMTorsionLibrary.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/NMRDataFactory.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/NMRTensor.cc src/core/scoring/nmr/pcs/PCSData.cc src/core/scoring/nmr/pcs/PCSMultiSet.cc src/core/scoring/nmr/pcs/PCSSingle.cc src/core/scoring/nmr/pcs/PCSSingleSet.cc src/core/scoring/nmr/pcs/PCSTensor.cc src/core/scoring/nmr/pre/PREData.cc src/core/scoring/nmr/pre/PREMultiSet.cc src/core/scoring/nmr/pre/PRESingle.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/RDCSingle.cc src/core/scoring/nmr/rdc/RDCSingleSet.cc src/core/scoring/nmr/rdc/RDCTensor.cc src/core/scoring/nmr/util.cc src/core/scoring/nv/NVlookup.cc src/core/scoring/nv/NVscore.cc src/core/scoring/orbitals/OrbitalsLookup.cc src/core/scoring/orbitals/OrbitalsScore.cc src/core/scoring/orbitals/OrbitalsStatistics.cc src/core/scoring/packing/HolesEnergyRes.cc src/core/scoring/packing/HolesParamsRes.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/AtomRadiusMap.cc src/core/scoring/packstat/CavityBall.cc src/core/scoring/packstat/LeeRichards.cc src/core/scoring/packstat/PackingScore.cc src/core/scoring/packstat/SimplePDB.cc src/core/scoring/packstat/SimplePDB_Atom.cc src/core/scoring/packstat/compute_sasa.cc src/core/scoring/packstat/io.cc src/core/scoring/packstat/packing_score_params.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_EnergyMethodOptions.cc src/core/scoring/rna/RNA_LowResolutionPotential.cc src/core/scoring/rna/RNA_Motif.cc src/core/scoring/rna/RNA_ScoringInfo.cc src/core/scoring/rna/RNA_ScoringUtil.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 src/core/scoring/rna/data/util.cc src/core/scoring/rna/util.cc src/core/scoring/sasa.cc src/core/scoring/sasa/LeGrandSasa.cc src/core/scoring/sasa/SasaCalc.cc src/core/scoring/sasa/SasaMethod.cc src/core/scoring/sasa/SasaMethodFactory.cc src/core/scoring/sasa/util.cc src/core/scoring/saxs/FormFactor.cc src/core/scoring/saxs/FormFactorManager.cc src/core/scoring/saxs/SinXOverX.cc src/core/scoring/sc/ContactMolecularSurfaceCalculator.cc src/core/scoring/sc/ElectrostaticComplementarityCalculator.cc src/core/scoring/sc/ElectrostaticSimilarityCalculator.cc src/core/scoring/sc/MolecularSurfaceCalculator.cc src/core/scoring/sc/ShapeComplementarityCalculator.cc src/core/scoring/sc/ShapeSimilarityCalculator.cc src/core/scoring/solid_surface/SurfaceEnergies.cc src/core/scoring/sym_e/symE.cc src/core/scoring/symmetry/SymmetricEnergies.cc src/core/scoring/trie/CPDataCorrespondence.cc src/core/scoring/trie/TrieCollection.cc src/core/scoring/trie/TrieCountPairBase.cc src/core/scoring/trie/TrieVsTrieCachedDataContainerBase.cc src/core/scoring/trie/trie_vs_path.cc src/core/scoring/trie/trie_vs_trie.cc src/core/scoring/util.cc src/core/scoring/vdwaals/VDWTrie.cc src/core/scoring/vdwaals/VDW_Energy.cc src/core/scoring/xml_util.cc src/core/select/jump_selector/AndJumpSelector.cc src/core/select/jump_selector/ExclusivelySharedJumpSelector.cc src/core/select/jump_selector/InterchainJumpSelector.cc src/core/select/jump_selector/JumpForResidue.cc src/core/select/jump_selector/JumpIndexSelector.cc src/core/select/jump_selector/JumpSelector.cc src/core/select/jump_selector/JumpSelectorFactory.cc src/core/select/jump_selector/NotJumpSelector.cc src/core/select/jump_selector/OrJumpSelector.cc src/core/select/jump_selector/util.cc src/core/select/movemap/MoveMapFactory.cc src/core/select/movemap/util.cc src/core/select/residue_selector/AndResidueSelector.cc src/core/select/residue_selector/AsymmetricUnitSelector.cc src/core/select/residue_selector/BFactorSelector.cc src/core/select/residue_selector/BinSelector.cc src/core/select/residue_selector/BlockSelector.cc src/core/select/residue_selector/BondedResidueSelector.cc src/core/select/residue_selector/CachedResidueSubset.cc src/core/select/residue_selector/ChainSelector.cc src/core/select/residue_selector/CloseContactResidueSelector.cc src/core/select/residue_selector/ConfluentSelector.cc src/core/select/residue_selector/DensityFitResidueSelector.cc src/core/select/residue_selector/FalseResidueSelector.cc src/core/select/residue_selector/FractionSelector.cc src/core/select/residue_selector/GlycanLayerSelector.cc src/core/select/residue_selector/GlycanPositionSelector.cc src/core/select/residue_selector/GlycanResidueSelector.cc src/core/select/residue_selector/GlycanSequonsSelector.cc src/core/select/residue_selector/InterGroupInterfaceByVectorSelector.cc src/core/select/residue_selector/JumpDownstreamSelector.cc src/core/select/residue_selector/JumpUpstreamSelector.cc src/core/select/residue_selector/LayerSelector.cc src/core/select/residue_selector/LogicResidueSelector.cc src/core/select/residue_selector/NeighborhoodResidueSelector.cc src/core/select/residue_selector/NotResidueSelector.cc src/core/select/residue_selector/NumNeighborsSelector.cc src/core/select/residue_selector/OrResidueSelector.cc src/core/select/residue_selector/PhiSelector.cc src/core/select/residue_selector/PrimarySequenceNeighborhoodSelector.cc src/core/select/residue_selector/RandomGlycanFoliageSelector.cc src/core/select/residue_selector/RandomResidueSelector.cc src/core/select/residue_selector/ResidueInMembraneSelector.cc src/core/select/residue_selector/ResidueInSequenceMotifSelector.cc src/core/select/residue_selector/ResidueIndexSelector.cc src/core/select/residue_selector/ResidueNameSelector.cc src/core/select/residue_selector/ResiduePDBInfoHasLabelSelector.cc src/core/select/residue_selector/ResiduePropertySelector.cc src/core/select/residue_selector/ResidueRanges.cc src/core/select/residue_selector/ResidueSelector.cc src/core/select/residue_selector/ResidueSelectorFactory.cc src/core/select/residue_selector/ResidueSpanSelector.cc src/core/select/residue_selector/ResidueVector.cc src/core/select/residue_selector/ReturnResidueSubsetSelector.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/SelectorLogicParser.cc src/core/select/residue_selector/SimpleMetricSelector.cc src/core/select/residue_selector/SliceResidueSelector.cc src/core/select/residue_selector/SymmetricalResidueSelector.cc src/core/select/residue_selector/TrueResidueSelector.cc src/core/select/residue_selector/VirtualResidueSelector.cc src/core/select/residue_selector/util.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/Aligner.cc src/core/sequence/AlignerFactory.cc src/core/sequence/AnnotatedSequence.cc src/core/sequence/BasicSequenceCreators.cc src/core/sequence/ChemicalShiftScoringScheme.cc src/core/sequence/ChemicalShiftSequence.cc src/core/sequence/CompassScoringScheme.cc src/core/sequence/CompositeScoringScheme.cc src/core/sequence/CompositeSequence.cc src/core/sequence/DPScoringScheme.cc src/core/sequence/DP_Matrix.cc src/core/sequence/DerivedSequenceMapping.cc src/core/sequence/L1ScoringScheme.cc src/core/sequence/MCAligner.cc src/core/sequence/MatrixScoringScheme.cc src/core/sequence/NWAligner.cc src/core/sequence/PairScoringScheme.cc src/core/sequence/ProfSimScoringScheme.cc src/core/sequence/SSManager.cc src/core/sequence/SWAligner.cc src/core/sequence/ScoringScheme.cc src/core/sequence/ScoringSchemeFactory.cc src/core/sequence/Sequence.cc src/core/sequence/SequenceAlignment.cc src/core/sequence/SequenceCoupling.cc src/core/sequence/SequenceCreator.cc src/core/sequence/SequenceFactory.cc src/core/sequence/SequenceProfile.cc src/core/sequence/SimpleScoringScheme.cc src/core/sequence/sequence_motif.cc src/core/sequence/util.cc src/core/simple_metrics/CompositeRealMetric.cc src/core/simple_metrics/CompositeStringMetric.cc src/core/simple_metrics/PerResidueProbabilitiesMetric.cc src/core/simple_metrics/PerResidueRealMetric.cc src/core/simple_metrics/PerResidueStringMetric.cc src/core/simple_metrics/RealMetric.cc src/core/simple_metrics/SimpleMetric.cc src/core/simple_metrics/SimpleMetricData.cc src/core/simple_metrics/SimpleMetricFactory.cc src/core/simple_metrics/StringMetric.cc src/core/simple_metrics/composite_metrics/BestMutationsFromProbabilitiesMetric.cc src/core/simple_metrics/composite_metrics/CompositeEnergyMetric.cc src/core/simple_metrics/composite_metrics/ElectrostaticComplementarityMetric.cc src/core/simple_metrics/composite_metrics/ElectrostaticSimilarityMetric.cc src/core/simple_metrics/composite_metrics/ProtocolSettingsMetric.cc src/core/simple_metrics/metrics/AverageProbabilitiesMetric.cc src/core/simple_metrics/metrics/CalculatorMetric.cc src/core/simple_metrics/metrics/CustomRealValueMetric.cc src/core/simple_metrics/metrics/CustomStringValueMetric.cc src/core/simple_metrics/metrics/DihedralDistanceMetric.cc src/core/simple_metrics/metrics/InteractionEnergyMetric.cc src/core/simple_metrics/metrics/RMSDMetric.cc src/core/simple_metrics/metrics/ResidueSummaryMetric.cc src/core/simple_metrics/metrics/SasaMetric.cc src/core/simple_metrics/metrics/SecondaryStructureMetric.cc src/core/simple_metrics/metrics/SelectedResidueCountMetric.cc src/core/simple_metrics/metrics/SelectedResiduesMetric.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/ShapeSimilarityMetric.cc src/core/simple_metrics/metrics/TimingProfileMetric.cc src/core/simple_metrics/metrics/TotalEnergyMetric.cc src/core/simple_metrics/per_residue_metrics/CurrentProbabilityMetric.cc src/core/simple_metrics/per_residue_metrics/HbondMetric.cc src/core/simple_metrics/per_residue_metrics/LoadedProbabilitiesMetric.cc src/core/simple_metrics/per_residue_metrics/PerResidueBfactorMetric.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/PerResidueSasaMetric.cc src/core/simple_metrics/per_residue_metrics/ProbabilityConservationMetric.cc src/core/simple_metrics/per_residue_metrics/SidechainNeighborCountMetric.cc src/core/simple_metrics/per_residue_metrics/WaterMediatedHbondMetric.cc src/core/simple_metrics/test_classes.cc src/core/simple_metrics/util.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/numeric/Calculator.cc src/numeric/ClusteringTreeNode.cc src/numeric/DiscreteIntervalEncodingTree.cc src/numeric/HomogeneousTransform.srlz.cc src/numeric/MathMatrix.srlz.cc src/numeric/MathVector.srlz.cc src/numeric/MultiDimensionalHistogram.cc src/numeric/agglomerative_hierarchical_clustering.cc src/numeric/alignment/rmsd_calc.cc src/numeric/color_util.cc src/numeric/constants.cc src/numeric/crick_equations/BundleParams.cc src/numeric/crick_equations/HelixParams.cc src/numeric/cubic_polynomial.cc src/numeric/cyclic_coordinate_descent.cc src/numeric/expression_parser/Arithmetic.cc src/numeric/fourier/FFT.cc src/numeric/fourier/SHT.cc src/numeric/fourier/kiss_fft.cc src/numeric/fourier/kiss_fft_state.cc src/numeric/geometry/BoundingBox.srlz.cc src/numeric/geometry/hashing/MinimalClashHash.cc src/numeric/geometry/hashing/SixDHasher.cc src/numeric/geometry/hashing/xyzStripeHash.cc src/numeric/geometry/projection_area.cc src/numeric/geometry/ring_plane.functions.cc src/numeric/interpolation/Histogram.srlz.cc src/numeric/interpolation/spline/BicubicSpline.cc src/numeric/interpolation/spline/CompoundInterpolator.cc src/numeric/interpolation/spline/CubicSpline.cc src/numeric/interpolation/spline/Interpolator.cc src/numeric/interpolation/spline/PolycubicSpline.cc src/numeric/interpolation/spline/SimpleInterpolator.cc src/numeric/interpolation/spline/SplineGenerator.cc src/numeric/interpolation/spline/TricubicSpline.cc src/numeric/interpolation/spline/spline_functions.cc src/numeric/interpolation/util.cc src/numeric/kdtree/HyperRectangle.cc src/numeric/kdtree/KDNode.cc src/numeric/kdtree/KDPoint.cc src/numeric/kdtree/KDPointList.cc src/numeric/kdtree/KDTree.cc src/numeric/kdtree/calc_distance.cc src/numeric/kdtree/construct_kdtree.cc src/numeric/kdtree/nearest_neighbors.cc src/numeric/kdtree/util.cc src/numeric/kinematic_closure/bridgeObjects.cc src/numeric/kinematic_closure/bridgeObjects_nonredundant.cc src/numeric/kinematic_closure/closure.cc src/numeric/kinematic_closure/dixon.cc src/numeric/kinematic_closure/kinematic_closure_helpers.cc src/numeric/kinematic_closure/sturm.cc src/numeric/kinematic_closure/vector.cc src/numeric/linear_algebra/EllipseParameters.cc src/numeric/linear_algebra/minimum_bounding_ellipse.cc src/numeric/linear_algebra/rgg.cc src/numeric/linear_algebra/singular_value_decomposition.cc src/numeric/model_quality/RmsData.cc src/numeric/model_quality/functions.cc src/numeric/model_quality/maxsub.cc src/numeric/model_quality/rms.cc src/numeric/nls/lmmin.cc src/numeric/polynomial.cc src/numeric/prob_util.cc src/numeric/random/WeightedSampler.cc src/numeric/random/random.cc src/numeric/random/random_xyz.cc src/numeric/roc_curve.cc src/numeric/statistics/functions.cc src/numeric/util.cc src/numeric/xyz.serialization.cc src/numeric/zscores.cc src/protocols/RotamerDump/RotamerDumpMover.cc src/protocols/aa_composition/AddCompositionConstraintMover.cc src/protocols/aa_composition/AddHelixSequenceConstraintsMover.cc src/protocols/aa_composition/AddMHCEpitopeConstraintMover.cc src/protocols/aa_composition/AddNetChargeConstraintMover.cc src/protocols/aa_composition/ClearCompositionConstraintsMover.cc src/protocols/aa_composition/util.cc src/protocols/abinitio/AbrelaxApplication.cc src/protocols/abinitio/AbrelaxMover.cc src/protocols/abinitio/BrokerMain.cc src/protocols/abinitio/ClassicAbinitio.cc src/protocols/abinitio/ConstraintFragmentSampler.cc src/protocols/abinitio/DomainAssembly.cc src/protocols/abinitio/DoubleLayerKinematicAbinitio.cc src/protocols/abinitio/FoldConstraints.cc src/protocols/abinitio/FragmentSampler.cc src/protocols/abinitio/HedgeArchive.cc src/protocols/abinitio/IterativeAbrelax.cc src/protocols/abinitio/IterativeBase.cc src/protocols/abinitio/IterativeCentroid.cc src/protocols/abinitio/IterativeFullatom.cc src/protocols/abinitio/KinematicAbinitio.cc src/protocols/abinitio/KinematicControl.cc src/protocols/abinitio/KinematicTaskControl.cc src/protocols/abinitio/LoopJumpFoldCst.cc src/protocols/abinitio/MembraneAbinitio.cc src/protocols/abinitio/PairingStatistics.cc src/protocols/abinitio/Protocol.cc src/protocols/abinitio/ResolutionSwitcher.cc src/protocols/abinitio/StrandConstraints.cc src/protocols/abinitio/Template.cc src/protocols/abinitio/TemplateJumpSetup.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/JumpSampleData.cc src/protocols/abinitio/abscript/RigidChunkCM.cc src/protocols/abinitio/abscript/StagePreparer.cc src/protocols/abinitio/abscript/StructPerturberCM.cc src/protocols/abinitio/util.cc src/protocols/abinitio/vs_test.cc src/protocols/analysis/GlycanInfoMover.cc src/protocols/analysis/InterfaceAnalyzerMover.cc src/protocols/analysis/LoopAnalyzerFilter.cc src/protocols/analysis/LoopAnalyzerMover.cc src/protocols/analysis/PackStatMover.cc src/protocols/analysis/burial_metrics/PolarGroupBurialPyMolStringMetric.cc src/protocols/analysis/simple_metrics/ConstraintsMetric.cc src/protocols/analysis/simple_metrics/RunSimpleMetricsMover.cc src/protocols/analysis/simple_metrics/SequenceRecoveryMetric.cc src/protocols/anchored_design/Anchor.cc src/protocols/anchored_design/AnchorMovers.cc src/protocols/anchored_design/AnchorMoversData.cc src/protocols/antibody/Ab_TemplateInfo.cc src/protocols/antibody/AntibodyCDRGrafter.cc src/protocols/antibody/AntibodyEnumManager.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/AntibodyNumberingParser.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/CDRClusterEnumManager.cc src/protocols/antibody/clusters/CDRClusterFeatures.cc src/protocols/antibody/clusters/CDRClusterFeaturesCreator.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/database/CDRSetOptions.cc src/protocols/antibody/database/CDRSetOptionsParser.cc src/protocols/antibody/design/AntibodyDesignEnumManager.cc src/protocols/antibody/design/AntibodyDesignMover.cc src/protocols/antibody/design/AntibodySeqDesignTFCreator.cc src/protocols/antibody/design/CDRGraftDesignOptions.cc src/protocols/antibody/design/CDRSeqDesignOptions.cc src/protocols/antibody/design/GeneralAntibodyModeler.cc src/protocols/antibody/design/MutateFrameworkForCluster.cc src/protocols/antibody/design/NativeAntibodySeq.cc src/protocols/antibody/design/ResnumFromStringsWithRangesSelector.cc src/protocols/antibody/design/util.cc src/protocols/antibody/grafting/antibody_sequence.cc src/protocols/antibody/grafting/cdr_detection.cc src/protocols/antibody/grafting/chothia_numberer.cc src/protocols/antibody/grafting/grafter.cc src/protocols/antibody/grafting/json_based_cdr_detection.cc src/protocols/antibody/grafting/regex_based_cdr_detection.cc src/protocols/antibody/grafting/regex_manager.cc src/protocols/antibody/grafting/scs_blast.cc src/protocols/antibody/grafting/scs_functor.cc src/protocols/antibody/grafting/scs_helper.cc src/protocols/antibody/grafting/scs_multi_template.cc src/protocols/antibody/grafting/scs_subst_mat.cc src/protocols/antibody/grafting/util.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/backbone_moves/local_backbone_mover/GapCloser.cc src/protocols/backbone_moves/local_backbone_mover/LocalBackboneMover.cc src/protocols/backbone_moves/local_backbone_mover/free_peptide_movers/CircularPermuteFreePeptideMover.cc src/protocols/backbone_moves/local_backbone_mover/free_peptide_movers/FreePeptideMover.cc src/protocols/backbone_moves/local_backbone_mover/free_peptide_movers/LongAxisRotationFreePeptideMover.cc src/protocols/backbone_moves/local_backbone_mover/free_peptide_movers/ShearFreePeptideMover.cc src/protocols/backbone_moves/local_backbone_mover/free_peptide_movers/TranslationFreePeptideMover.cc src/protocols/backbone_moves/local_backbone_mover/gap_solution_pickers/GapSolutionPicker.cc src/protocols/backbone_moves/local_backbone_mover/gap_solution_pickers/RandomGapSolutionPicker.cc src/protocols/backbone_moves/local_backbone_mover/util.cc src/protocols/backrub/BackrubMover.cc src/protocols/backrub/BackrubProtocol.cc src/protocols/backrub/BackrubSegment.cc src/protocols/backrub/BackrubSidechainMover.cc src/protocols/backrub/util.cc src/protocols/boinc/BoincPoseObserver.cc src/protocols/boinc/boinc.cc src/protocols/boinc/util.cc src/protocols/boinc/watchdog.cc src/protocols/branch_angle/BranchAngleOptimizer.cc src/protocols/buns/BuriedUnsatHbondFilter2.cc src/protocols/buns/BuriedUnsatisfiedPolarsCalculator2.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/BiasEnergy.cc src/protocols/canonical_sampling/BiasedMonteCarlo.cc src/protocols/canonical_sampling/CanonicalSamplingApplication.cc src/protocols/canonical_sampling/CanonicalSamplingMover.cc src/protocols/canonical_sampling/DbTrajectoryRecorder.cc src/protocols/canonical_sampling/HamiltonianExchange.cc src/protocols/canonical_sampling/MetricRecorder.cc src/protocols/canonical_sampling/MetropolisHastingsMover.cc src/protocols/canonical_sampling/MultiTemperatureTrialCounter.cc src/protocols/canonical_sampling/PDBTrajectoryRecorder.cc src/protocols/canonical_sampling/ParallelTempering.cc src/protocols/canonical_sampling/ProgressBarObserver.cc src/protocols/canonical_sampling/SidechainMetropolisHastingsMover.cc src/protocols/canonical_sampling/SilentTrajectoryRecorder.cc src/protocols/canonical_sampling/SimulatedTempering.cc src/protocols/canonical_sampling/TemperatureController.cc src/protocols/canonical_sampling/TemperingBase.cc src/protocols/canonical_sampling/ThermodynamicMover.cc src/protocols/canonical_sampling/ThermodynamicObserver.cc src/protocols/canonical_sampling/TrajectoryRecorder.cc src/protocols/canonical_sampling/TrialCounterObserver.cc src/protocols/canonical_sampling/WTEBiasEnergy.cc src/protocols/canonical_sampling/mc_convergence_checks/HPool.cc src/protocols/canonical_sampling/mc_convergence_checks/HierarchicalLevel.cc src/protocols/canonical_sampling/mc_convergence_checks/MPIBPool_ConvergenceCheck.cc src/protocols/canonical_sampling/mc_convergence_checks/MPIHPool_ConvergenceCheck.cc src/protocols/canonical_sampling/mc_convergence_checks/MPIPool_ConvergenceCheck.cc src/protocols/canonical_sampling/mc_convergence_checks/Pool_ConvergenceCheck.cc src/protocols/canonical_sampling/mc_convergence_checks/pool_util.cc src/protocols/canonical_sampling/mc_convergence_checks/util.cc src/protocols/carbohydrates/CreateGlycanSequonMover.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/checkpoint/CheckPointer.cc src/protocols/checkpoint/Checkpoint.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/chemistries/ChemistryCreators.cc src/protocols/chemistries/ChemistryFactory.cc src/protocols/chemistries/ChemistryLoader.cc src/protocols/chemistries/PatchChemistry.cc src/protocols/chemistries/WrappedChemistries.cc src/protocols/chemistries/util.cc src/protocols/chromophore/ChromophoreDataReader.cc src/protocols/chromophore/ReadResidueCoordinatesFromPDB.cc src/protocols/cluster/APCluster.cc src/protocols/cluster/calibur/AdjacentList.cc src/protocols/cluster/calibur/Clustering.cc src/protocols/cluster/calibur/InitCluster.cc src/protocols/cluster/calibur/PreloadedPDB.cc src/protocols/cluster/calibur/SimPDB.cc src/protocols/cluster/calibur/cubic.cc src/protocols/cluster/calibur/jacobi.cc src/protocols/cluster/calibur/pdb_util.cc src/protocols/cluster/calibur/rmsd.cc src/protocols/cluster/cluster.cc src/protocols/comparative_modeling/AlignRmsdTargetEvaluatorCreator.cc src/protocols/comparative_modeling/Align_RmsdEvaluator.cc src/protocols/comparative_modeling/Align_RotamerEvaluator.cc src/protocols/comparative_modeling/AlignmentClustering.cc src/protocols/comparative_modeling/AlignmentSet.cc src/protocols/comparative_modeling/ExtraThreadingMover.cc src/protocols/comparative_modeling/GenericJobInputter.cc src/protocols/comparative_modeling/IgnoreSubsetConstraintSet.cc src/protocols/comparative_modeling/LoopRelaxThreadingMover.cc src/protocols/comparative_modeling/MultiThreadingMover.cc src/protocols/comparative_modeling/PartialThreadingMover.cc src/protocols/comparative_modeling/RecoverSideChainsMover.cc src/protocols/comparative_modeling/StealLigandMover.cc src/protocols/comparative_modeling/StealSideChainsMover.cc src/protocols/comparative_modeling/ThreadingJob.cc src/protocols/comparative_modeling/ThreadingJobInputter.cc src/protocols/comparative_modeling/ThreadingMover.cc src/protocols/comparative_modeling/cm_main.cc src/protocols/comparative_modeling/coord_util.cc src/protocols/comparative_modeling/features/ResidueFeature.cc src/protocols/comparative_modeling/features/ResidueFeatureFactory.cc src/protocols/comparative_modeling/features/SSFeature.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/ExcludedFilter.cc src/protocols/constel/FilterByProxTerm.cc src/protocols/constel/FilterBySASA.cc src/protocols/constel/InterfaceFilter.cc src/protocols/constel/MasterFilter.cc src/protocols/constel/NeighTeller.cc src/protocols/constel/PairConstelFilters.cc src/protocols/constel/Primitives.cc src/protocols/constel/ResidueMask.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/ConstraintScoreFilter.cc src/protocols/constraint_filters/SavePoseConstraintToFileFilter.cc src/protocols/constraint_filters/ShowConstraintsFilter.cc src/protocols/constraint_generator/AddConstraints.cc src/protocols/constraint_generator/AtomPairConstraintGenerator.cc src/protocols/constraint_generator/ConstraintGenerator.cc src/protocols/constraint_generator/ConstraintGeneratorFactory.cc src/protocols/constraint_generator/ConstraintsManager.cc src/protocols/constraint_generator/ConstraintsMap.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/RemoveConstraints.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/ClearConstraintsMover.cc src/protocols/constraint_movers/ConstraintSetMover.cc src/protocols/constraint_movers/CstInfoMover.cc src/protocols/constraint_movers/ResidueTypeConstraintMover.cc src/protocols/constraints_additional/AdditionalConstraintCreators.cc src/protocols/constraints_additional/AmbiguousMultiConstraint.cc src/protocols/constraints_additional/BindingSiteConstraint.cc src/protocols/constraints_additional/COMCoordinateConstraint.cc src/protocols/constraints_additional/CombinedConstraintEvaluator.cc src/protocols/constraints_additional/CombinedConstraintEvaluatorCreator.cc src/protocols/constraints_additional/ConstraintEvaluator.cc src/protocols/constraints_additional/ConstraintEvaluatorCreator.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/spacegroup_symmops1.cc src/protocols/cryst/spacegroup_symmops2.cc src/protocols/cryst/spacegroup_symmops3.cc src/protocols/cryst/spacegroup_symmops4.cc src/protocols/cryst/wallpaper.cc src/protocols/cutoutdomain/CutOutDomain.cc src/protocols/cyclic_peptide/CrankshaftFlipMover.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/CycpepRigidBodyPermutationMover.cc src/protocols/cyclic_peptide/CycpepSymmetryFilter.cc src/protocols/cyclic_peptide/FlipChiralityMover.cc src/protocols/cyclic_peptide/OversaturatedHbondAcceptorFilter.cc src/protocols/cyclic_peptide/PeptideCyclizeMover.cc src/protocols/cyclic_peptide/PeptideInternalHbondsFilter.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/1_4_BBMB_Helper.cc src/protocols/cyclic_peptide/crosslinker/CrosslinkerMoverHelper.cc src/protocols/cyclic_peptide/crosslinker/Lanthionine_Helper.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/Thioether_Helper.cc src/protocols/cyclic_peptide/crosslinker/TrigonalPlanarMetal_Helper.cc src/protocols/cyclic_peptide/crosslinker/TrigonalPyramidalMetal_Helper.cc src/protocols/cyclic_peptide/crosslinker/lanthionine_util.cc src/protocols/cyclic_peptide/crosslinker/thioether_util.cc src/protocols/cyclic_peptide_predict/HierarchicalHybridJDApplication.cc src/protocols/cyclic_peptide_predict/HierarchicalHybridJD_JobResultsSummary.cc src/protocols/cyclic_peptide_predict/HierarchicalHybridJD_PNearToArbitraryStateSummary.cc src/protocols/cyclic_peptide_predict/HierarchicalHybridJD_RMSDToBestSummary.cc src/protocols/cyclic_peptide_predict/HierarchicalHybridJD_ResultsSummaryBase.cc src/protocols/cyclic_peptide_predict/HierarchicalHybridJD_SASASummary.cc src/protocols/cyclic_peptide_predict/PNearCalculator.cc src/protocols/cyclic_peptide_predict/SimpleCycpepPredictApplication.cc src/protocols/cyclic_peptide_predict/SimpleCycpepPredictApplication_MPI.cc src/protocols/cyclic_peptide_predict/util.cc src/protocols/ddg/CartesianddG.cc src/protocols/ddg/ddGData.cc src/protocols/ddg/ddGMover.cc src/protocols/ddg/ddG_main.cc src/protocols/denovo_design/architects/BetaSheetArchitect.cc src/protocols/denovo_design/architects/BlueprintArchitect.cc src/protocols/denovo_design/architects/CompoundArchitect.cc src/protocols/denovo_design/architects/DeNovoArchitect.cc src/protocols/denovo_design/architects/DeNovoArchitectFactory.cc src/protocols/denovo_design/architects/HelixArchitect.cc src/protocols/denovo_design/architects/MotifArchitect.cc src/protocols/denovo_design/architects/PoseArchitect.cc src/protocols/denovo_design/architects/StrandArchitect.cc src/protocols/denovo_design/architects/StructureArchitect.cc src/protocols/denovo_design/architects/util.cc src/protocols/denovo_design/calculators/CavityCalculator.cc src/protocols/denovo_design/components/DivideAndConqueror.cc src/protocols/denovo_design/components/ExtendedPoseBuilder.cc src/protocols/denovo_design/components/FoldGraph.cc src/protocols/denovo_design/components/IdealAbegoGenerator.cc src/protocols/denovo_design/components/NullPoseFolder.cc src/protocols/denovo_design/components/Picker.cc src/protocols/denovo_design/components/PoseFolder.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/SegmentPairing.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/components/StructureDataPerturber.cc src/protocols/denovo_design/connection/ConnectionArchitect.cc src/protocols/denovo_design/connection/util.cc src/protocols/denovo_design/constraints/FileConstraintGenerator.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/AddSegmentDataMover.cc src/protocols/denovo_design/movers/AlignResiduesMover.cc src/protocols/denovo_design/movers/BridgeChainsMover.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/FoldArchitectMover.cc src/protocols/denovo_design/movers/FoldTreeFromFoldGraphMover.cc src/protocols/denovo_design/movers/MakeAsymmetricStructureDataMover.cc src/protocols/denovo_design/movers/RotateSegmentMover.cc src/protocols/denovo_design/movers/SealFoldTreeMover.cc src/protocols/denovo_design/movers/SetResidueAliasMover.cc src/protocols/denovo_design/residue_selectors/NamedSegmentSelector.cc src/protocols/denovo_design/residue_selectors/PairedSheetResidueSelector.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/design_opt/Supercharge.cc src/protocols/dna/DNAParameters.cc src/protocols/dna/DesignProteinBackboneAroundDNA.cc src/protocols/dna/DnaChains.cc src/protocols/dna/DnaDesignDef.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/DockFilters.cc src/protocols/docking/DockMCMCycle.cc src/protocols/docking/DockMCMProtocol.cc src/protocols/docking/DockMinMover.cc src/protocols/docking/DockSetupMover.cc src/protocols/docking/DockTaskFactory.cc src/protocols/docking/DockingEnsemble.cc src/protocols/docking/DockingEnsemblePrepackProtocol.cc src/protocols/docking/DockingHighRes.cc src/protocols/docking/DockingHighResFactory.cc src/protocols/docking/DockingHighResLegacy.cc src/protocols/docking/DockingInitialPerturbation.cc src/protocols/docking/DockingLowRes.cc src/protocols/docking/DockingLowResEnsemble.cc src/protocols/docking/DockingPrepackProtocol.cc src/protocols/docking/DockingProtocol.cc src/protocols/docking/EllipsoidalRandomizationMover.cc src/protocols/docking/EnsureExclusivelySharedJumpMover.cc src/protocols/docking/RigidBodyInfo.cc src/protocols/docking/SidechainMinMover.cc src/protocols/docking/TemperedDocking.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/CombineChainsMover.cc src/protocols/domain_assembly/PostDockAssemblyScorer.cc src/protocols/drug_design/ApplyChemistryMover.cc src/protocols/drug_design/AtomExistsFilter.cc src/protocols/drug_design/ChemicalReaction.cc src/protocols/drug_design/ConformationSelectionToRDMol.cc src/protocols/drug_design/DrugDesignMover.cc src/protocols/drug_design/DrugPolishMover.cc src/protocols/drug_design/HeteroHeteroBondFilter.cc src/protocols/drug_design/LigandLocationFilter.cc src/protocols/drug_design/NChiFilter.cc src/protocols/drug_design/RDKitMetric.cc src/protocols/drug_design/RDKitMetricFilter.cc src/protocols/drug_design/RDKitMetricsMover.cc src/protocols/drug_design/RandomFragmentLigand.cc src/protocols/drug_design/ReactionBasedAnalogSampler.cc src/protocols/drug_design/ReactionChemistry.cc src/protocols/drug_design/ReactionFragment.cc src/protocols/drug_design/ReactionGrow.cc src/protocols/drug_design/ReactionMultiTransform.cc src/protocols/drug_design/SAScoreFilter.cc src/protocols/drug_design/SubstituentReplace.cc src/protocols/drug_design/SubstructureReplace.cc src/protocols/drug_design/bcl/BCLFragmentBaseMover.cc src/protocols/drug_design/bcl/BCLFragmentMutateMover.cc src/protocols/drug_design/bcl/BCLReferenceSDFilesManager.cc src/protocols/drug_design/bcl/BCLSampleConfsManager.cc src/protocols/drug_design/substitution_support.cc src/protocols/drug_design/util.cc src/protocols/electron_density/BfactorFittingMover.cc src/protocols/electron_density/DensitySymmInfo.cc src/protocols/electron_density/DensityZscores.cc src/protocols/electron_density/DockFragmentsIntoDensityMover.cc src/protocols/electron_density/DockIntoDensityUtils.cc src/protocols/electron_density/DockPDBIntoDensityMover.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/EnergyBasedClusteringOptions.cc src/protocols/energy_based_clustering/EnergyBasedClusteringProtocol.cc src/protocols/environment/AutoCutData.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/BrokerElements.cc src/protocols/environment/claims/ClaimStrength.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/DesignVsNativeComparison.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/EnzdesJobInputter.cc src/protocols/enzdes/EnzdesJobOutputter.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/GlycosyltransferaseMover.cc src/protocols/enzymatic_movers/KinaseMover.cc src/protocols/enzymatic_movers/NTerminalAcetyltransferaseMover.cc src/protocols/esm_perplexity/EsmPerplexityTensorflowProtocol.cc src/protocols/esm_perplexity/PerResidueEsmProbabilitiesMetric.cc src/protocols/esm_perplexity/PseudoPerplexityMetric.cc src/protocols/evaluation/AlignEvaluator.cc src/protocols/evaluation/EvaluatorFactory.cc src/protocols/evaluation/PCA.cc src/protocols/evaluation/PoseEvaluator.cc src/protocols/evaluation/TimeEvaluator.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/AtomAtomPairFeaturesCreator.cc src/protocols/features/AtomInResidueAtomInResiduePairFeatures.cc src/protocols/features/AtomInResidueAtomInResiduePairFeaturesCreator.cc src/protocols/features/AtomTypesFeatures.cc src/protocols/features/AtomTypesFeaturesCreator.cc src/protocols/features/BatchFeatures.cc src/protocols/features/BetaTurnDetection.cc src/protocols/features/BetaTurnDetectionFeatures.cc src/protocols/features/BetaTurnDetectionFeaturesCreator.cc src/protocols/features/ChargeChargeFeatures.cc src/protocols/features/ChargeChargeFeaturesCreator.cc src/protocols/features/DatabaseFilters.cc src/protocols/features/DatabaseJobInputter.cc src/protocols/features/DatabaseJobOutputter.cc src/protocols/features/DatabaseStatements.cc src/protocols/features/DdGFeatures.cc src/protocols/features/DdGFeaturesCreator.cc src/protocols/features/FeaturesReporter.cc src/protocols/features/FeaturesReporterFactory.cc src/protocols/features/GeometricSolvationFeatures.cc src/protocols/features/GeometricSolvationFeaturesCreator.cc src/protocols/features/HBondFeatures.cc src/protocols/features/HBondFeaturesCreator.cc src/protocols/features/HBondParameterFeatures.cc src/protocols/features/HBondParameterFeaturesCreator.cc src/protocols/features/HelixCapFeatures.cc src/protocols/features/HelixCapFeaturesCreator.cc src/protocols/features/InterfaceDdGMover.cc src/protocols/features/InterfaceDdGMoverCreator.cc src/protocols/features/InterfaceFeatures.cc src/protocols/features/InterfaceFeaturesCreator.cc src/protocols/features/JobDataFeatures.cc src/protocols/features/JobDataFeaturesCreator.cc src/protocols/features/LoopAnchorFeatures.cc src/protocols/features/LoopAnchorFeaturesCreator.cc src/protocols/features/ModelFeatures.cc src/protocols/features/OrbitalsFeatures.cc src/protocols/features/OrbitalsFeaturesCreator.cc src/protocols/features/PairFeatures.cc src/protocols/features/PairFeaturesCreator.cc src/protocols/features/PdbDataFeatures.cc src/protocols/features/PdbDataFeaturesCreator.cc src/protocols/features/PoseCommentsFeatures.cc src/protocols/features/PoseCommentsFeaturesCreator.cc src/protocols/features/PoseConformationFeatures.cc src/protocols/features/PoseConformationFeaturesCreator.cc src/protocols/features/ProteinBackboneAtomAtomPairFeatures.cc src/protocols/features/ProteinBackboneAtomAtomPairFeaturesCreator.cc src/protocols/features/ProteinBackboneTorsionAngleFeatures.cc src/protocols/features/ProteinBackboneTorsionAngleFeaturesCreator.cc src/protocols/features/ProteinBondGeometryFeatures.cc src/protocols/features/ProteinBondGeometryFeaturesCreator.cc src/protocols/features/ProteinRMSDFeatures.cc src/protocols/features/ProteinRMSDFeaturesCreator.cc src/protocols/features/ProteinRMSDNoSuperpositionFeatures.cc src/protocols/features/ProteinRMSDNoSuperpositionFeaturesCreator.cc src/protocols/features/ProteinResidueConformationFeatures.cc src/protocols/features/ProteinResidueConformationFeaturesCreator.cc src/protocols/features/ProteinSilentReport.cc src/protocols/features/ProtocolFeatures.cc src/protocols/features/RadiusOfGyrationFeatures.cc src/protocols/features/RadiusOfGyrationFeaturesCreator.cc src/protocols/features/Report.cc src/protocols/features/ReportToDB.cc src/protocols/features/ResidueBurialFeatures.cc src/protocols/features/ResidueBurialFeaturesCreator.cc src/protocols/features/ResidueConformationFeatures.cc src/protocols/features/ResidueConformationFeaturesCreator.cc src/protocols/features/ResidueFeatures.cc src/protocols/features/ResidueFeaturesCreator.cc src/protocols/features/ResidueGridScoresFeatures.cc src/protocols/features/ResidueScoresFeatures.cc src/protocols/features/ResidueScoresFeaturesCreator.cc src/protocols/features/ResidueSecondaryStructureFeatures.cc src/protocols/features/ResidueSecondaryStructureFeaturesCreator.cc src/protocols/features/ResidueTotalScoresFeatures.cc src/protocols/features/ResidueTotalScoresFeaturesCreator.cc src/protocols/features/ResidueTypesFeatures.cc src/protocols/features/ResidueTypesFeaturesCreator.cc src/protocols/features/RotamerBoltzmannWeightFeatures.cc src/protocols/features/RotamerBoltzmannWeightFeaturesCreator.cc src/protocols/features/RotamerFeatures.cc src/protocols/features/RotamerFeaturesCreator.cc src/protocols/features/RotamerRecoveryFeatures.cc src/protocols/features/RotamerRecoveryFeaturesCreator.cc src/protocols/features/RuntimeFeatures.cc src/protocols/features/SaltBridgeFeatures.cc src/protocols/features/SaltBridgeFeaturesCreator.cc src/protocols/features/ScoreFunctionFeatures.cc src/protocols/features/ScoreFunctionFeaturesCreator.cc src/protocols/features/ScoreTypeFeatures.cc src/protocols/features/ScoreTypeFeaturesCreator.cc src/protocols/features/ScreeningFeatures.cc src/protocols/features/ScreeningFeaturesCreator.cc src/protocols/features/SecondaryStructureSegmentFeatures.cc src/protocols/features/SecondaryStructureSegmentFeaturesCreator.cc src/protocols/features/SimpleMetricFeatures.cc src/protocols/features/SimpleMetricFeaturesCreator.cc src/protocols/features/SmotifFeatures.cc src/protocols/features/SmotifFeaturesCreator.cc src/protocols/features/StructureFeatures.cc src/protocols/features/StructureFeaturesCreator.cc src/protocols/features/StructureScoresFeatures.cc src/protocols/features/StructureScoresFeaturesCreator.cc src/protocols/features/TaskOperationFeatures.cc src/protocols/features/TaskOperationFeaturesCreator.cc src/protocols/features/TotalScoreFeatures.cc src/protocols/features/TrajectoryMapFeatures.cc src/protocols/features/TrajectoryMapFeaturesCreator.cc src/protocols/features/TrajectoryReportToDB.cc src/protocols/features/UnrecognizedAtomFeatures.cc src/protocols/features/UnrecognizedAtomFeaturesCreator.cc src/protocols/features/WaterFeatures.cc src/protocols/features/WaterFeaturesCreator.cc src/protocols/features/feature_schemas.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/helixAssembly/HelixBundleFeaturesCreator.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/StrandBundleFeaturesCreator.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/SetupForFibrilMover.cc src/protocols/fibril/fibril_util.cc src/protocols/filters/BasicFilters.cc src/protocols/filters/CalculatorFilter.cc src/protocols/filters/ContingentFilter.cc src/protocols/filters/Filter.cc src/protocols/filters/FilterCreator.cc src/protocols/filters/FilterFactory.cc src/protocols/filters/FilterValueMetric.cc src/protocols/filters/ReplicateFilter.cc src/protocols/filters/TimeFilter.cc src/protocols/filters/VectorPoseFilter.cc src/protocols/filters/filter_schemas.cc src/protocols/filters/util.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/SheetRemodelConstraintGenerator.cc src/protocols/fldsgn/filters/CoreDunbrackFilter.cc src/protocols/fldsgn/filters/FragQualFilter.cc src/protocols/fldsgn/filters/HSSTripletFilter.cc src/protocols/fldsgn/filters/HelixBendFilter.cc src/protocols/fldsgn/filters/HelixKinkFilter.cc src/protocols/fldsgn/filters/HelixPairingFilter.cc src/protocols/fldsgn/filters/InterlockingAromaFilter.cc src/protocols/fldsgn/filters/NcontactsFilter.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/filters/StrandHelixGeometryFilter.cc src/protocols/fldsgn/potentials/AACompositionEnergy.cc src/protocols/fldsgn/potentials/SetAACompositionPotential.cc src/protocols/fldsgn/potentials/SetSecStructEnergies.cc src/protocols/fldsgn/potentials/sspot/HSPairPotential.cc src/protocols/fldsgn/potentials/sspot/NatbiasHelicesSheetPotential.cc src/protocols/fldsgn/potentials/sspot/NatbiasHelixPairPotential.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/BetaAlphaBetaMotif.cc src/protocols/fldsgn/topology/DimerPairing.cc src/protocols/fldsgn/topology/HSSTriplet.cc src/protocols/fldsgn/topology/HelixPairing.cc src/protocols/fldsgn/topology/SS_Info2.cc src/protocols/fldsgn/topology/Sheet.cc src/protocols/fldsgn/topology/SheetFoldTypeManager.cc src/protocols/fldsgn/topology/StrandPairing.cc src/protocols/fldsgn/topology/util.cc src/protocols/flexpack/FlexPacker.cc src/protocols/flexpack/OtherContextScoreFunction.cc src/protocols/flexpack/annealer/FlexbbSimAnnealer.cc src/protocols/flexpack/interaction_graph/FlexbbIGFactory.cc src/protocols/flexpack/interaction_graph/FlexbbInteractionGraph.cc src/protocols/flexpack/interaction_graph/MinimalistFlexbbInteractionGraph.cc src/protocols/flexpack/interaction_graph/OTFFlexbbInteractionGraph.cc src/protocols/flexpack/interaction_graph/PrecomputedFlexbbInteractionGraph.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/FilterStructs.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/ConstraintFulfilmentFilter.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/MoveMapFactoryToNamedMoveMapMover.cc src/protocols/fold_from_loops/movers/NubInitioLoopClosureMover.cc src/protocols/fold_from_loops/movers/ReleaseConstraintFromResidueMover.cc src/protocols/fold_from_loops/movers/ResidueLabelsToPymolSelectionMover.cc src/protocols/fold_from_loops/movers/SavePDBInfoMover.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/RelativeConnectRight.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/constraints/InvrotTreeRCG.cc src/protocols/forge/constraints/NtoCConstraintGenerator.cc src/protocols/forge/constraints/RemoveRemodelCsts.cc src/protocols/forge/methods/chainbreak_eval.cc src/protocols/forge/methods/fold_tree_functions.cc src/protocols/forge/methods/fragment_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/RemodelConstraintGenerator.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/forge/remodel/ResidueVicinityRCG.cc src/protocols/frag_picker/BestTotalScoreSelector.cc src/protocols/frag_picker/CS2ndShift.cc src/protocols/frag_picker/CSTalosIO.cc src/protocols/frag_picker/CompositeFragmentSelector.cc src/protocols/frag_picker/ContactTypes.cc src/protocols/frag_picker/CustomScoreSelector.cc src/protocols/frag_picker/DiversifyCrmsdByClustering.cc src/protocols/frag_picker/DiversifyCrmsdSelector.cc src/protocols/frag_picker/DiversifyDihedralsSelector.cc src/protocols/frag_picker/Faraggi_SA.cc src/protocols/frag_picker/FragmentCandidate.cc src/protocols/frag_picker/FragmentPicker.cc src/protocols/frag_picker/FragmentScoreFilter.cc src/protocols/frag_picker/JCouplingIO.cc src/protocols/frag_picker/LAMBEGO_IO.cc src/protocols/frag_picker/PdbIdChunkFilter.cc src/protocols/frag_picker/PhiPsiTalosIO.cc src/protocols/frag_picker/SidechainContactDistCutoff.cc src/protocols/frag_picker/TorsionBinIO.cc src/protocols/frag_picker/VallChunk.cc src/protocols/frag_picker/VallProvider.cc src/protocols/frag_picker/VallResidue.cc src/protocols/frag_picker/nonlocal/NonlocalFrags.cc src/protocols/frag_picker/nonlocal/NonlocalFragsMain.cc src/protocols/frag_picker/quota/ABEGO_SS_Config.cc src/protocols/frag_picker/quota/ABEGO_SS_Map.cc src/protocols/frag_picker/quota/ABEGO_SS_Pool.cc src/protocols/frag_picker/quota/QuotaCollector.cc src/protocols/frag_picker/quota/QuotaConfig.cc src/protocols/frag_picker/quota/QuotaSelector.cc src/protocols/frag_picker/quota/SecondaryStructurePool.cc src/protocols/frag_picker/scores/ABEGO_SS_Score.cc src/protocols/frag_picker/scores/AdaptiveScoreHistogram.cc src/protocols/frag_picker/scores/AmbigCSScore.cc src/protocols/frag_picker/scores/AtomBasedConstraintsScore.cc src/protocols/frag_picker/scores/AtomPairConstraintsScore.cc src/protocols/frag_picker/scores/BFactor.cc src/protocols/frag_picker/scores/CSScore.cc src/protocols/frag_picker/scores/DihedralConstraintsScore.cc src/protocols/frag_picker/scores/DisulfideDistance.cc src/protocols/frag_picker/scores/DisulfideIdentity.cc src/protocols/frag_picker/scores/FourAtomsConstraintData.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/FragmentScoreManager.cc src/protocols/frag_picker/scores/GunnCost.cc src/protocols/frag_picker/scores/GunnCostScore.cc src/protocols/frag_picker/scores/HydrophobicityProfileSimilarity.cc src/protocols/frag_picker/scores/HydrophobicitySimilarity.cc src/protocols/frag_picker/scores/InterbondAngleScore.cc src/protocols/frag_picker/scores/JCoupling.cc src/protocols/frag_picker/scores/LAMBEGO_Similarity.cc src/protocols/frag_picker/scores/MidPhiOut.cc src/protocols/frag_picker/scores/MidPsiOut.cc src/protocols/frag_picker/scores/PCS_FragDistance.cc src/protocols/frag_picker/scores/PValuedFragmentScoreManager.cc src/protocols/frag_picker/scores/PartialSecondarySimilarity.cc src/protocols/frag_picker/scores/Phi.cc src/protocols/frag_picker/scores/PhiPsiRmsd.cc src/protocols/frag_picker/scores/PhiPsiSquareWell.cc src/protocols/frag_picker/scores/ProfileScore.cc src/protocols/frag_picker/scores/ProfileScoreBlosum62.cc src/protocols/frag_picker/scores/ProfileScoreDistWeight.cc src/protocols/frag_picker/scores/ProfileScoreL1.cc src/protocols/frag_picker/scores/ProfileScoreStructL1.cc src/protocols/frag_picker/scores/ProfileScoreSubMatrix.cc src/protocols/frag_picker/scores/ProlinePhiScore.cc src/protocols/frag_picker/scores/Psi.cc src/protocols/frag_picker/scores/RDCScore.cc src/protocols/frag_picker/scores/RamaScore.cc src/protocols/frag_picker/scores/ScoreEValuator.cc src/protocols/frag_picker/scores/SecondaryIdentity.cc src/protocols/frag_picker/scores/SecondarySimilarity.cc src/protocols/frag_picker/scores/SequenceIdentity.cc src/protocols/frag_picker/scores/SolventAccessibility.cc src/protocols/frag_picker/scores/TalosSSSimilarity.cc src/protocols/frag_picker/scores/TorsionBinSimilarity.cc src/protocols/frag_picker/scores/fragment_scoring_utilities.cc src/protocols/frags/TorsionFragment.cc src/protocols/frags/VallData.cc src/protocols/frags/heap.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/genetic_algorithm/Entity.cc src/protocols/genetic_algorithm/EntityRandomizer.cc src/protocols/genetic_algorithm/GeneticAlgorithm.cc src/protocols/genetic_algorithm/Mutate1Randomizer.cc src/protocols/glycan_docking/GlycanDockProtocol.cc src/protocols/glycan_docking/util.cc src/protocols/glycopeptide_docking/GlycopeptideDockingFlags.cc src/protocols/glycopeptide_docking/GlycopeptideDockingHighResRefinement.cc src/protocols/glycopeptide_docking/GlycopeptideDockingLowResRefinement.cc src/protocols/glycopeptide_docking/GlycopeptideDockingProtocol.cc src/protocols/glycopeptide_docking/utils.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/InsertPoseIntoPoseMover.cc src/protocols/grafting/simple_movers/KeepRegionMover.cc src/protocols/grafting/simple_movers/ReplaceRegionMover.cc src/protocols/grafting/util.cc src/protocols/hbnet/HBNet.cc src/protocols/hbnet/HBNetScore.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_FinalFullatomRefinementMoveGenerator.cc src/protocols/helical_bundle_predict/HBP_HelixCoilMoveGenerator.cc src/protocols/helical_bundle_predict/HBP_MoveGenerator.cc src/protocols/helical_bundle_predict/HBP_SigmoidalTemperatureScheduleGenerator.cc src/protocols/helical_bundle_predict/HBP_TemperatureScheduleGenerator.cc src/protocols/helical_bundle_predict/HelicalBundlePredictApplication.cc src/protocols/helical_bundle_predict/HelicalBundlePredictApplication_MPI.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/SearchPattern.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/TemplateHistory.cc src/protocols/hybridization/WeightedFragmentSmoothTrialMover.cc src/protocols/hybridization/WeightedFragmentTrialMover.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/BinaryFragmentStoreBackend.cc src/protocols/indexed_structure_store/DirStructureStoreBackend.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/H5FragmentStoreBackend.cc src/protocols/indexed_structure_store/H5StructureStoreBackend.cc src/protocols/indexed_structure_store/JSONStructureStoreBackend.cc src/protocols/indexed_structure_store/SSHashedFragmentStore.cc src/protocols/indexed_structure_store/SegmentSequenceProfile.cc src/protocols/indexed_structure_store/SilentStructureStoreBackend.cc src/protocols/indexed_structure_store/StructureStore.cc src/protocols/indexed_structure_store/StructureStoreManager.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/search/QueryDatabase.cc src/protocols/indexed_structure_store/utility.cc src/protocols/init/init.cc src/protocols/init/register1.cc src/protocols/init/register2.cc src/protocols/init/register3.cc src/protocols/init/register4.cc src/protocols/interface/util.cc src/protocols/inverse_folding/MIFST.cc src/protocols/inverse_folding/MIFSTProbabilitiesMetric.cc src/protocols/inverse_folding/util.cc src/protocols/jd2/AtomTreeDiffJobInputter.cc src/protocols/jd2/AtomTreeDiffJobOutputter.cc src/protocols/jd2/BOINCJobDistributor.cc src/protocols/jd2/BatchJobInputter.cc src/protocols/jd2/EmptyPoseJobInputter.cc src/protocols/jd2/EnsembleJobInputter.cc src/protocols/jd2/FileJobOutputter.cc src/protocols/jd2/FileSystemJobDistributor.cc src/protocols/jd2/InnerJob.cc src/protocols/jd2/InnerMultiThreadingJob.cc src/protocols/jd2/Job.cc src/protocols/jd2/JobDistributor.cc src/protocols/jd2/JobDistributorFactory.cc src/protocols/jd2/JobInputter.cc src/protocols/jd2/JobInputterCreator.cc src/protocols/jd2/JobInputterFactory.cc src/protocols/jd2/JobOutputter.cc src/protocols/jd2/JobOutputterCreator.cc src/protocols/jd2/JobOutputterFactory.cc src/protocols/jd2/JobsContainer.cc src/protocols/jd2/LargeNstructJobInputter.cc src/protocols/jd2/LazySilentFileJobInputter.cc src/protocols/jd2/MPIFileBufJobDistributor.cc src/protocols/jd2/MPIMultiCommJobDistributor.cc src/protocols/jd2/MPIWorkPartitionJobDistributor.cc src/protocols/jd2/MPIWorkPoolJobDistributor.cc src/protocols/jd2/MpiFileBuffer.cc src/protocols/jd2/MultiThreadingJob.cc src/protocols/jd2/NoOutputJobOutputterCreator.cc src/protocols/jd2/PDBJobInputter.cc src/protocols/jd2/PDBJobOutputter.cc src/protocols/jd2/PoseInputStreamJobInputter.cc src/protocols/jd2/RNA_DeNovoJobOutputter.cc src/protocols/jd2/ScoreOnlyJobOutputter.cc src/protocols/jd2/ScreeningJobInputter.cc src/protocols/jd2/SerializedPoseJobInputter.cc src/protocols/jd2/SerializedPoseJobOutputter.cc src/protocols/jd2/ShuffleJobDistributor.cc src/protocols/jd2/SilentFileJobInputter.cc src/protocols/jd2/SilentFileJobOutputter.cc src/protocols/jd2/SingleFileBuffer.cc src/protocols/jd2/VectorPoseJobDistributor.cc src/protocols/jd2/archive/ArchiveBase.cc src/protocols/jd2/archive/ArchiveManager.cc src/protocols/jd2/archive/EvaluatedArchive.cc src/protocols/jd2/archive/MPIArchiveJobDistributor.cc src/protocols/jd2/archive/NormalizedEvaluatedArchive.cc src/protocols/jd2/archive/VarianceStatisticsArchive.cc src/protocols/jd2/internal_util.cc src/protocols/jd2/mmCIFJobOutputter.cc src/protocols/jd2/mmtfJobOutputter.cc src/protocols/jd2/util.cc src/protocols/jd2/wwPDBJobOutputter.cc src/protocols/jd3/InnerLarvalJob.cc src/protocols/jd3/InputSource.cc src/protocols/jd3/Job.cc src/protocols/jd3/JobDigraph.cc src/protocols/jd3/JobDistributor.cc src/protocols/jd3/JobDistributorFactory.cc src/protocols/jd3/JobGenealogist.cc src/protocols/jd3/JobOutputIndex.cc src/protocols/jd3/JobQueen.cc src/protocols/jd3/JobResult.cc src/protocols/jd3/JobSummary.cc src/protocols/jd3/JobTracker.cc src/protocols/jd3/LarvalJob.cc src/protocols/jd3/chunk_library/ChunkLibraryInnerLarvalJob.cc src/protocols/jd3/chunk_library/ChunkLibraryJobQueen.cc src/protocols/jd3/chunk_library/MoverAndChunkLibraryJob.cc src/protocols/jd3/chunk_library_inputters/ChunkLibraryInputSource.cc src/protocols/jd3/chunk_library_inputters/ChunkLibraryInputter.cc src/protocols/jd3/chunk_library_inputters/ChunkLibraryInputterFactory.cc src/protocols/jd3/chunk_library_inputters/PDBChunkLibraryInputter.cc src/protocols/jd3/chunk_library_inputters/chunk_library_inputter_schemas.cc src/protocols/jd3/dag_node_managers/EvenlyPartitionedNodeManager.cc src/protocols/jd3/dag_node_managers/NodeManager.cc src/protocols/jd3/dag_node_managers/NodeManagerStorageMatrix.cc src/protocols/jd3/dag_node_managers/SimpleNodeManager.cc src/protocols/jd3/deallocation/DeallocationMessage.cc src/protocols/jd3/deallocation/InputPoseDeallocationMessage.cc src/protocols/jd3/deallocation/ResourceDeallocationMessage.cc src/protocols/jd3/full_model/FullModelInnerLarvalJob.cc src/protocols/jd3/full_model/FullModelJobQueen.cc src/protocols/jd3/full_model_inputters/FullModelInputSource.cc src/protocols/jd3/full_model_inputters/FullModelInputter.cc src/protocols/jd3/full_model_inputters/FullModelInputterFactory.cc src/protocols/jd3/full_model_inputters/PDBFullModelInputter.cc src/protocols/jd3/full_model_inputters/SilentFileFullModelInputter.cc src/protocols/jd3/full_model_inputters/full_model_inputter_schemas.cc src/protocols/jd3/job_distributors/JobExtractor.cc src/protocols/jd3/job_distributors/MPIWorkPoolJobDistributor.cc src/protocols/jd3/job_distributors/MultiThreadedJobDistributor.cc src/protocols/jd3/job_distributors/VanillaJobDistributor.cc src/protocols/jd3/job_results/PoseJobResult.cc src/protocols/jd3/job_summaries/EnergyJobSummary.cc src/protocols/jd3/job_summaries/StandardPoseJobSummary.cc src/protocols/jd3/jobs/MoverJob.cc src/protocols/jd3/output/MultipleOutputSpecification.cc src/protocols/jd3/output/MultipleOutputter.cc src/protocols/jd3/output/OutputSpecification.cc src/protocols/jd3/output/ResultOutputter.cc src/protocols/jd3/pose_inputters/PDBPoseInputter.cc src/protocols/jd3/pose_inputters/PDBPoseInputterCreator.cc src/protocols/jd3/pose_inputters/PoseInputSource.cc src/protocols/jd3/pose_inputters/PoseInputter.cc src/protocols/jd3/pose_inputters/PoseInputterCreator.cc src/protocols/jd3/pose_inputters/PoseInputterFactory.cc src/protocols/jd3/pose_inputters/SilentFilePoseInputter.cc src/protocols/jd3/pose_inputters/SilentFilePoseInputterCreator.cc src/protocols/jd3/pose_inputters/pose_inputter_schemas.cc src/protocols/jd3/pose_outputters/DeNovoSilentFilePoseOutputter.cc src/protocols/jd3/pose_outputters/DeNovoSilentFilePoseOutputterCreator.cc src/protocols/jd3/pose_outputters/PDBPoseOutputSpecification.cc src/protocols/jd3/pose_outputters/PDBPoseOutputter.cc src/protocols/jd3/pose_outputters/PDBPoseOutputterCreator.cc src/protocols/jd3/pose_outputters/PoseOutputSpecification.cc src/protocols/jd3/pose_outputters/PoseOutputter.cc src/protocols/jd3/pose_outputters/PoseOutputterCreator.cc src/protocols/jd3/pose_outputters/PoseOutputterFactory.cc src/protocols/jd3/pose_outputters/ScoreFileOutputSpecification.cc src/protocols/jd3/pose_outputters/ScoreFileOutputter.cc src/protocols/jd3/pose_outputters/SecondaryPoseOutputter.cc src/protocols/jd3/pose_outputters/SilentFilePoseOutputSpecification.cc src/protocols/jd3/pose_outputters/SilentFilePoseOutputter.cc src/protocols/jd3/pose_outputters/SilentFilePoseOutputterCreator.cc src/protocols/jd3/pose_outputters/mmTFPoseOutputSpecification.cc src/protocols/jd3/pose_outputters/mmTFPoseOutputter.cc src/protocols/jd3/pose_outputters/mmTFPoseOutputterCreator.cc src/protocols/jd3/pose_outputters/pose_outputter_schemas.cc src/protocols/jd3/standard/PreliminaryLarvalJob.cc src/protocols/jd3/standard/PreliminaryLarvalJobTracker.cc src/protocols/jd3/standard/StandardInnerLarvalJob.cc src/protocols/jd3/standard/StandardJobQueen.cc src/protocols/jd3/strong_types.cc src/protocols/jd3/util.cc src/protocols/jobdist/JobDistributors.cc src/protocols/jobdist/Jobs.cc src/protocols/jobdist/not_universal_main.cc src/protocols/jobdist/standard_mains.cc src/protocols/jumping/DisulfPairingLibrary.cc src/protocols/jumping/DisulfPairingsList.cc src/protocols/jumping/JumpSample.cc src/protocols/jumping/JumpSetup.cc src/protocols/jumping/MembraneJump.cc src/protocols/jumping/PairingLibrary.cc src/protocols/jumping/RandomSheetBuilder.cc src/protocols/jumping/ResiduePairJump.cc src/protocols/jumping/ResiduePairJumpSetup.cc src/protocols/jumping/SameStrand.cc src/protocols/jumping/SheetBuilder.cc src/protocols/jumping/util.cc src/protocols/kinematic_closure/BalancedKicMover.cc src/protocols/kinematic_closure/ClosureProblem.cc src/protocols/kinematic_closure/ClosureSolution.cc src/protocols/kinematic_closure/KicMover.cc src/protocols/kinematic_closure/internal.cc src/protocols/kinematic_closure/perturbers/BondAnglePerturber.cc src/protocols/kinematic_closure/perturbers/FragmentPerturber.cc src/protocols/kinematic_closure/perturbers/IdealizeNonPhiPsi.cc src/protocols/kinematic_closure/perturbers/LogFilePerturber.cc src/protocols/kinematic_closure/perturbers/OmegaPerturber.cc src/protocols/kinematic_closure/perturbers/Perturber.cc src/protocols/kinematic_closure/perturbers/PerturberSet.cc src/protocols/kinematic_closure/perturbers/Rama2bPerturber.cc src/protocols/kinematic_closure/perturbers/RamaPerturber.cc src/protocols/kinematic_closure/perturbers/UniformPerturber.cc src/protocols/kinematic_closure/perturbers/VicinityPerturber.cc src/protocols/kinematic_closure/perturbers/WalkingBondAnglePerturber.cc src/protocols/kinematic_closure/perturbers/WalkingPerturber.cc src/protocols/kinematic_closure/pivot_pickers/EndToEndPivots.cc src/protocols/kinematic_closure/pivot_pickers/FixedOffsetPivots.cc src/protocols/kinematic_closure/pivot_pickers/FixedOffsetsPivots.cc src/protocols/kinematic_closure/pivot_pickers/FixedPivots.cc src/protocols/kinematic_closure/pivot_pickers/LoopPivots.cc src/protocols/kinematic_closure/pivot_pickers/StandardPivots.cc src/protocols/kinematic_closure/solution_pickers/FilteredSolutions.cc src/protocols/kinematic_closure/solution_pickers/RandomSolutions.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/hashing/Hasher.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/LegacyRequirementFactory.cc src/protocols/legacy_sewing/sampling/requirements/LegacyRequirementSet.cc src/protocols/legacy_sewing/sampling/requirements/LegacyResidueRetentionRequirement.cc src/protocols/legacy_sewing/sampling/requirements/LegacySegmentDsspRequirement.cc src/protocols/legacy_sewing/sampling/requirements/LegacySegmentLengthRequirement.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/DistributionMap.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/MCSAligner.cc src/protocols/ligand_docking/GALigandDock/RotamerData.cc src/protocols/ligand_docking/GALigandDock/TorsionSampler.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/LigandArea.cc src/protocols/ligand_docking/LigandBaseProtocol.cc src/protocols/ligand_docking/LigandDesign.cc src/protocols/ligand_docking/LigandDockProtocol.cc src/protocols/ligand_docking/LigandDockingLoaders.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/UnconstrainedTorsionsMover.cc src/protocols/ligand_docking/WriteLigandMolFile.cc src/protocols/ligand_docking/grid_functions.cc src/protocols/ligand_docking/ligand_dock_impl.cc src/protocols/ligand_docking/ligand_functions.cc src/protocols/ligand_docking/ligand_options/Interface.cc src/protocols/ligand_docking/ligand_options/interface_distance_functions.cc src/protocols/ligand_docking/ligand_scores.cc src/protocols/ligand_docking/rdf/RDFFunctionFactory.cc src/protocols/ligand_docking/rdf/StandardRDFFunctions.cc src/protocols/ligand_docking/util.cc src/protocols/ligand_evolution/EvolutionManager.cc src/protocols/ligand_evolution/EvolutionOptions.cc src/protocols/ligand_evolution/FragmentLibrary.cc src/protocols/ligand_evolution/Individual.cc src/protocols/ligand_evolution/Population.cc src/protocols/ligand_evolution/Scorer.cc src/protocols/ligand_evolution/WorkManager.cc src/protocols/ligand_evolution/offspring_factory/Crossover.cc src/protocols/ligand_evolution/offspring_factory/IdentityFactory.cc src/protocols/ligand_evolution/offspring_factory/Mutator.cc src/protocols/ligand_evolution/selectors/ElitistSelector.cc src/protocols/ligand_evolution/selectors/RouletteSelector.cc src/protocols/ligand_evolution/selectors/TournamentSelector.cc src/protocols/loop_build/LoopBuild.cc src/protocols/loop_build/LoopBuildMover.cc src/protocols/loop_build/LoopMover_SlidingWindow.cc src/protocols/loop_build/LoopMover_SlidingWindowCreator.cc src/protocols/loop_build/LoopmodelWrapper.cc src/protocols/loop_grower/DensSkeleton.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_modeler/perturbers/LoopHashPerturber.cc src/protocols/loop_modeling/LoopBuilder.cc src/protocols/loop_modeling/LoopMover.cc src/protocols/loop_modeling/LoopProtocol.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/samplers/LegacyKicSampler.cc src/protocols/loop_modeling/utilities/AcceptanceCheck.cc src/protocols/loop_modeling/utilities/LoopFilter.cc src/protocols/loop_modeling/utilities/LoopMoverGroup.cc src/protocols/loop_modeling/utilities/PrepareForCentroid.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/LoopHashLibraryLoader.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_Emperor.cc src/protocols/loophash/MPI_LoopHashRefine_Master.cc src/protocols/loophash/Mover_LoopHashRefine.cc src/protocols/loophash/WorkUnit_LoopHash.cc src/protocols/loops/FoldTreeFromLoopsWrapper.cc src/protocols/loops/Loop.cc src/protocols/loops/LoopMoverFactory.cc src/protocols/loops/Loops.cc src/protocols/loops/LoopsFileIO.cc src/protocols/loops/LoopsFileLoader.cc src/protocols/loops/loop_closure/ccd/CCDLoopClosureMover.cc src/protocols/loops/loop_closure/ccd/LoopClosure.cc src/protocols/loops/loop_closure/ccd/RamaCheck.cc src/protocols/loops/loop_closure/ccd/ShortLoopClosure.cc src/protocols/loops/loop_closure/ccd/SlidingWindowLoopClosure.cc src/protocols/loops/loop_closure/ccd/WidthFirstSlidingWindowLoopClosure.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_closure/kinematic_closure/KinematicWrapper.cc src/protocols/loops/loop_mover/IndependentLoopMover.cc src/protocols/loops/loop_mover/LoopCM.cc src/protocols/loops/loop_mover/LoopMover.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/LoopsDatabaseDefiner.cc src/protocols/loops/loops_definers/LoopsDatabaseDefinerCreator.cc src/protocols/loops/loops_definers/LoopsDefinerFactory.cc src/protocols/loops/loops_definers/LoopsDefinerLoader.cc src/protocols/loops/loops_definers/LoopsExplicitDefiner.cc src/protocols/loops/loops_definers/LoopsExplicitDefinerCreator.cc src/protocols/loops/loops_definers/LoopsFileDefiner.cc src/protocols/loops/loops_definers/LoopsFileDefinerCreator.cc src/protocols/loops/loops_definers/LoopsStringDefiner.cc src/protocols/loops/loops_definers/util.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/mainchain_potential/GenerateMainchainPotentialOptions.cc src/protocols/make_rot_lib/MakeRotLibJob.cc src/protocols/make_rot_lib/MakeRotLibJobInputter.cc src/protocols/make_rot_lib/MakeRotLibMover.cc src/protocols/make_rot_lib/MakeRotLibOptionsData.cc src/protocols/make_rot_lib/RotData.cc src/protocols/match/BumpGrid.cc src/protocols/match/Hit.cc src/protocols/match/MatchPositionModifiers.cc src/protocols/match/MatchSet.cc src/protocols/match/Matcher.cc src/protocols/match/MatcherMover.cc src/protocols/match/MatcherTask.cc src/protocols/match/OccupiedSpaceHash.cc src/protocols/match/VoxelSetIterator.cc src/protocols/match/downstream/ActiveSiteGrid.cc src/protocols/match/downstream/ClassicMatchAlgorithm.cc src/protocols/match/downstream/DownstreamAlgorithm.cc src/protocols/match/downstream/DownstreamBuilder.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/SecMatchEvaluatorFactory.cc src/protocols/match/downstream/SecMatchResiduePairEvaluator.cc src/protocols/match/downstream/SecondaryMatcherToDownstreamResidue.cc src/protocols/match/downstream/SecondaryMatcherToUpstreamResidue.cc src/protocols/match/output/DownstreamRMSEvaluator.cc src/protocols/match/output/LimitHitsPerRotamerFilter.cc src/protocols/match/output/MatchConsolidator.cc src/protocols/match/output/MatchEvaluator.cc src/protocols/match/output/MatchFilter.cc src/protocols/match/output/MatchGrouper.cc src/protocols/match/output/MatchOutputter.cc src/protocols/match/output/MatchProcessor.cc src/protocols/match/output/MatchScoreWriter.cc src/protocols/match/output/OutputWriter.cc src/protocols/match/output/PDBWriter.cc src/protocols/match/output/PoseInserter.cc src/protocols/match/output/ProcessorFactory.cc src/protocols/match/output/SameChiBinComboGrouper.cc src/protocols/match/output/SameRotamerComboGrouper.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/ScaffoldBuildPoint.cc src/protocols/match/upstream/UpstreamBuilder.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/SymDofMoverSampler.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/MedalMain.cc src/protocols/medal/MedalMover.cc src/protocols/medal/util.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/ElectricfieldLipidlayer.cc src/protocols/membrane/scoring/FaWaterToBilayerEnergy.cc src/protocols/membrane/scoring/MEnvAtomParams.cc src/protocols/membrane/scoring/MEnvElectroAtomParams.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/MetalSiteResidue.cc src/protocols/metal_interface/RemoveMetalConnectionsMover.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/SaneMinMover.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/SymPackRotamersMover.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/monte_carlo/MonteCarloInterface.cc src/protocols/monte_carlo/MonteCarloRecover.cc src/protocols/monte_carlo/MonteCarloReset.cc src/protocols/monte_carlo/MonteCarloTest.cc src/protocols/monte_carlo/ResetBaselineMover.cc src/protocols/motif_grafting/movers/MotifGraftMover.cc src/protocols/motifs/BuildPosition.cc src/protocols/motifs/IRCollection.cc src/protocols/motifs/IdentifyLigandMotifs.cc src/protocols/motifs/LigandDiscoverySearch.cc src/protocols/motifs/LigandMotifSearch.cc src/protocols/motifs/Motif.cc src/protocols/motifs/MotifDnaPacker.cc src/protocols/motifs/MotifHit.cc src/protocols/motifs/MotifLibrary.cc src/protocols/motifs/MotifSearch.cc src/protocols/motifs/SingleMotif.cc src/protocols/motifs/motif_utils.cc src/protocols/moves/CompositionMover.cc src/protocols/moves/CyclicMover.cc src/protocols/moves/DsspMover.cc src/protocols/moves/DualMonteCarlo.cc src/protocols/moves/FilterMover.cc src/protocols/moves/FilterReportAsPoseExtraScoresMover.cc src/protocols/moves/FilterReporterMover.cc src/protocols/moves/IfMover.cc src/protocols/moves/IteratedConvergenceMover.cc src/protocols/moves/JumpOutMover.cc src/protocols/moves/MixedMonteCarlo.cc src/protocols/moves/MonteCarlo.cc src/protocols/moves/MonteCarloStatus.cc src/protocols/moves/MoveMapMover.cc src/protocols/moves/Mover.cc src/protocols/moves/MoverApplyingMover.cc src/protocols/moves/MoverContainer.cc src/protocols/moves/MoverCreator.cc src/protocols/moves/MoverFactory.cc src/protocols/moves/MoverForPoseList.cc src/protocols/moves/MoverStatistics.cc src/protocols/moves/MoverStatus.cc src/protocols/moves/NullMover.cc src/protocols/moves/OutputMovers.cc src/protocols/moves/PyMOLMover.cc src/protocols/moves/RampingMover.cc src/protocols/moves/RepeatMover.cc src/protocols/moves/ReplicaExchangeMC.cc src/protocols/moves/ResId.cc src/protocols/moves/SimulatedTempering.cc src/protocols/moves/StructureRestrictor.cc src/protocols/moves/TrialCounter.cc src/protocols/moves/TrialMover.cc src/protocols/moves/VectorPoseMover.cc src/protocols/moves/WhileMover.cc src/protocols/moves/mover_schemas.cc src/protocols/moves/util.cc src/protocols/mpi_refinement/Clusterer.cc src/protocols/mpi_refinement/MPI_Refine_Emperor.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/MRSJob.cc src/protocols/multistage_rosetta_scripts/MRSJobQueen.cc src/protocols/multistage_rosetta_scripts/MRSJobQueenChecker.cc src/protocols/multistage_rosetta_scripts/MRSJobSummary.cc src/protocols/multistage_rosetta_scripts/TagManager.cc src/protocols/multistage_rosetta_scripts/cluster/ClusterMetric.cc src/protocols/multistage_rosetta_scripts/cluster/ClusterMetricFactory.cc src/protocols/multistage_rosetta_scripts/cluster/KMedoids.cc src/protocols/multistage_rosetta_scripts/cluster/KMedoidsOnTheFly.cc src/protocols/multistage_rosetta_scripts/cluster/metrics/JumpMetric.cc src/protocols/multistage_rosetta_scripts/cluster/metrics/SequenceMetric.cc src/protocols/multistage_rosetta_scripts/cluster/util.cc src/protocols/multistate_design/MetricCalculatorFitnessFunction.cc src/protocols/multistate_design/MultiStateAggregateFunction.cc src/protocols/multistate_design/MultiStateEntity.cc src/protocols/multistate_design/MultiStateFitnessFunction.cc src/protocols/multistate_design/MultiStatePacker.cc src/protocols/multistate_design/PackingState.cc src/protocols/multistate_design/PartitionAggregateFunction.cc src/protocols/multistate_design/SingleState.cc src/protocols/multistate_design/SingleStateEntityData.cc src/protocols/multistate_design/SingleStateFitnessFunction.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/network/cloud.cc src/protocols/network/hal.cc src/protocols/network/ui_mover.cc src/protocols/network/util.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/pcs/PCSTensorOptimizer.cc src/protocols/nmr/pre/PREEnergy.cc src/protocols/nmr/pre/PREMover.cc src/protocols/nmr/rdc/RDCEnergy.cc src/protocols/noesy_assign/CovalentCompliance.cc src/protocols/noesy_assign/CrossPeak.cc src/protocols/noesy_assign/CrossPeakInfo.cc src/protocols/noesy_assign/CrossPeakList.cc src/protocols/noesy_assign/DistanceScoreMover.cc src/protocols/noesy_assign/FloatingResonance.cc src/protocols/noesy_assign/FragsToAtomDist.cc src/protocols/noesy_assign/LabelResonance.cc src/protocols/noesy_assign/MethylNames.cc src/protocols/noesy_assign/NoesyModule.cc src/protocols/noesy_assign/PeakAssignment.cc src/protocols/noesy_assign/PeakAssignmentParameters.cc src/protocols/noesy_assign/PeakAssignmentResidueMap.cc src/protocols/noesy_assign/PeakCalibrator.cc src/protocols/noesy_assign/PeakFileFormat.cc src/protocols/noesy_assign/PeakFileFormat_Sparky.cc src/protocols/noesy_assign/PeakFileFormat_xpk.cc src/protocols/noesy_assign/ProtonResonance.cc src/protocols/noesy_assign/Resonance.cc src/protocols/noesy_assign/ResonanceList.cc src/protocols/noesy_assign/StructureDependentPeakCalibrator.cc src/protocols/noesy_assign/StructureIndependentPeakCalibrator.cc src/protocols/noesy_assign/util.cc src/protocols/nonlocal/BiasedFragmentMover.cc src/protocols/nonlocal/Chunk.cc src/protocols/nonlocal/HelixRotate.cc src/protocols/nonlocal/PolicyFactory.cc src/protocols/nonlocal/Region.cc src/protocols/nonlocal/SheetTranslate.cc src/protocols/nonlocal/SimpleTreeBuilder.cc src/protocols/nonlocal/SingleFragmentMover.cc src/protocols/nonlocal/SingleFragmentMoverCreator.cc src/protocols/nonlocal/SmoothPolicy.cc src/protocols/nonlocal/StarTreeBuilder.cc src/protocols/nonlocal/TreeBuilderFactory.cc src/protocols/nonlocal/UniformPolicy.cc src/protocols/nonlocal/util.cc src/protocols/normalmode/NormalMode.cc src/protocols/normalmode/NormalModeMinimizer.cc src/protocols/normalmode/NormalModeMultiFunc.cc src/protocols/normalmode/NormalModeRelaxMover.cc src/protocols/optimize_weights/DDGBindOptEData.cc src/protocols/optimize_weights/DGBindOptEData.cc src/protocols/optimize_weights/IterativeOptEDriver.cc src/protocols/optimize_weights/NestedEnergyTermOptEData.cc src/protocols/optimize_weights/OptEData.cc src/protocols/optimize_weights/OptEMultifunc.cc src/protocols/optimize_weights/PNatLigPoseOptEData.cc src/protocols/pack_daemon/DynamicAggregateFunction.cc src/protocols/pack_daemon/EntityCorrespondence.cc src/protocols/pack_daemon/MultistateAggregateFunction.cc src/protocols/pack_daemon/MultistateFitnessFunction.cc src/protocols/pack_daemon/PackDaemon.cc src/protocols/pack_daemon/util.cc src/protocols/pack_interface/ProteinProteinInterfaceUpweighterTaskOperation.cc src/protocols/parser/BluePrint.cc src/protocols/parser/ConstraintGeneratorLoader.cc src/protocols/parser/DataLoader.cc src/protocols/parser/DataLoaderCreator.cc src/protocols/parser/DataLoaderFactory.cc src/protocols/parser/DatabaseSessionLoader.cc src/protocols/parser/FragSetLoader.cc src/protocols/parser/FragmentReader.cc src/protocols/parser/JumpSelectorLoader.cc src/protocols/parser/MonteCarloLoader.cc src/protocols/parser/MoveMapFactoryLoader.cc src/protocols/parser/PackerPaletteLoader.cc src/protocols/parser/ResLvlTaskOperationLoader.cc src/protocols/parser/ResidueSelectorLoader.cc src/protocols/parser/ScoreFunctionLoader.cc src/protocols/parser/SimpleMetricLoader.cc src/protocols/parser/TaskOperationLoader.cc src/protocols/pb_potential/SetupPoissonBoltzmannPotential.cc src/protocols/pdbinfo_manipulations/AlignPDBInfoToSequences.cc src/protocols/pdbinfo_manipulations/AlignPDBInfoToSequencesUtil.cc src/protocols/peptide_deriver/PeptideDeriverBasicStreamOutputter.cc src/protocols/peptide_deriver/PeptideDeriverFilter.cc src/protocols/peptide_deriver/PeptideDeriverFilterCreator.cc src/protocols/peptide_deriver/PeptideDeriverMarkdownStreamOutputter.cc src/protocols/peptide_deriver/PeptideDeriverOutputter.cc src/protocols/peptide_deriver/PeptideDeriverOutputterContainer.cc src/protocols/peptide_deriver/PeptideDeriverPoseOutputter.cc src/protocols/pmut_scan/AlterSpecDisruptionDriver.cc src/protocols/pmut_scan/Mutant.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/ExtendedPoseMoverCreator.cc src/protocols/pose_creation/HelixFromSequence.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/PoseFromSequenceMover.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/DecomposeAndReweightEnergiesCalculator.cc src/protocols/pose_metric_calculators/FragQualCalculator.cc src/protocols/pose_metric_calculators/HPatchCalculator.cc src/protocols/pose_metric_calculators/InterGroupNeighborsCalculator.cc src/protocols/pose_metric_calculators/MetricValueGetter.cc src/protocols/pose_metric_calculators/NeighborhoodByDistanceCalculator.cc src/protocols/pose_metric_calculators/NeighborsByDistanceCalculator.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/ResidueDecompositionCalculator.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/pose_selectors/ClusterPoseSelector.cc src/protocols/pose_sewing/data_storage/DsspShiftArray.cc src/protocols/pose_sewing/data_storage/PoseSegment.cc src/protocols/pose_sewing/data_storage/PoseWithTerminalSegmentsOfKnownDSSP.cc src/protocols/pose_sewing/data_storage/SegmentEnvelope.cc src/protocols/pose_sewing/data_storage/TerminalDSSPSortedPoseVector.cc src/protocols/pose_sewing/filters/CoreScorer.cc src/protocols/pose_sewing/filters/HasDisulfideFilter.cc src/protocols/pose_sewing/movers/AddFlankingVirtualResiduesMover.cc src/protocols/pose_sewing/movers/BlockwiseAnalysisMover.cc src/protocols/pose_sewing/movers/OmnibusDisulfideAnalysisLabelerMover.cc 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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 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src/protocols/qsar/RenderGridsToKinemage.cc src/protocols/qsar/qsarMap.cc src/protocols/qsar/qsarMover.cc src/protocols/qsar/qsarOptFunc.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/GridCreator.cc src/protocols/qsar/scoring_grid/GridFactory.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/LipidMemGrid.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/ScoringGridLoader.cc src/protocols/qsar/scoring_grid/ShapeGrid.cc src/protocols/qsar/scoring_grid/SingleGrid.cc 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src/protocols/recces/options/RECCES_Options.cc src/protocols/recces/params/RECCES_Parameters.cc src/protocols/recces/sampler/MC_Any.cc src/protocols/recces/sampler/MC_Comb.cc src/protocols/recces/sampler/MC_Loop.cc src/protocols/recces/sampler/MC_OneTorsion.cc src/protocols/recces/sampler/rna/MC_RNA_KIC_Sampler.cc src/protocols/recces/sampler/rna/MC_RNA_MultiSuite.cc src/protocols/recces/sampler/rna/MC_RNA_OneJump.cc src/protocols/recces/sampler/rna/MC_RNA_Sugar.cc src/protocols/recces/sampler/rna/MC_RNA_Suite.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/stdev_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/RelaxScriptManager.cc src/protocols/relax/RepeatProteinRelax.cc src/protocols/relax/WorkUnit_BatchRelax.cc src/protocols/relax/cst_util.cc src/protocols/relax/loop/LoopRelaxMover.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/relax_main.cc src/protocols/relax/util.cc src/protocols/residue_optimization/MetapatchEnumeration.cc src/protocols/residue_selectors/HBondSelector.cc src/protocols/residue_selectors/LigandMetalContactSelector.cc src/protocols/residue_selectors/NativeSelector.cc src/protocols/residue_selectors/StoreResidueSubsetMover.cc src/protocols/residue_selectors/StoredResidueSubsetSelector.cc src/protocols/residue_selectors/TaskSelector.cc src/protocols/rigid/PoseMembraneRigidBodyMover.cc src/protocols/rigid/RB_geometry.cc src/protocols/rigid/RigidBodyMotionMover.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/rigid/rigid_body_moves.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 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src/protocols/rosetta_scripts/AdditionalOutputWrapper.cc src/protocols/rosetta_scripts/MultipleOutputWrapper.cc src/protocols/rosetta_scripts/MultiplePoseMover.cc src/protocols/rosetta_scripts/ParsedProtocol.cc src/protocols/rosetta_scripts/PosePropertyReporter.cc src/protocols/rosetta_scripts/PosePropertyReporterCreator.cc src/protocols/rosetta_scripts/PosePropertyReporterFactory.cc src/protocols/rosetta_scripts/PoseSelector.cc src/protocols/rosetta_scripts/PoseSelectorCreator.cc src/protocols/rosetta_scripts/PoseSelectorFactory.cc src/protocols/rosetta_scripts/RosettaScriptsJobQueen.cc src/protocols/rosetta_scripts/RosettaScriptsParser.cc src/protocols/rosetta_scripts/RosettaScriptsSchemaValidator.cc src/protocols/rosetta_scripts/SavePoseMover.cc src/protocols/rosetta_scripts/XmlObjects.cc src/protocols/rosetta_scripts/util.cc src/protocols/rotamer_gen/FragmentRotamers.cc src/protocols/rotamer_gen/RDKitRotamers.cc src/protocols/rotamer_recovery/RRComparer.cc src/protocols/rotamer_recovery/RRComparerAutomorphicRMSD.cc src/protocols/rotamer_recovery/RRComparerElecDensDiff.cc src/protocols/rotamer_recovery/RRProtocol.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/RRReporter.cc src/protocols/rotamer_recovery/RRReporterHuman.cc src/protocols/rotamer_recovery/RRReporterSQLite.cc src/protocols/rotamer_recovery/RotamerRecovery.cc src/protocols/rotamer_recovery/RotamerRecoveryCreator.cc src/protocols/rotamer_recovery/RotamerRecoveryFactory.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/ResidualDipolarCouplingRigidSegments.cc src/protocols/scoring/VDW_CachedRepScreenInfo.cc src/protocols/scoring/VDW_GridEnergy.cc src/protocols/scoring/methods/EnsembleEnergy.cc src/protocols/scoring/methods/InterchainEnvEnergy.cc src/protocols/scoring/methods/InterchainPairEnergy.cc src/protocols/scoring/methods/ResidualDipolarCouplingEnergyRigidSegments.cc src/protocols/scoring/methods/SpecialRotamerEnergy.cc src/protocols/scoring/methods/TargetClashEnergy.cc src/protocols/scoring/methods/pcs/GridSearchIterator.cc src/protocols/scoring/methods/pcs/PseudocontactShiftData.cc src/protocols/scoring/methods/pcs/PseudocontactShiftEnergy.cc 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src/protocols/scoring/methods/pcs2/PcsTensor.cc src/protocols/scoring/methods/pcs2/TensorsOptimizer.cc src/protocols/scoring/methods/pcs2/TensorsOptimizerFix.cc src/protocols/scoring/methods/pcs2/TensorsOptimizerSvd.cc src/protocols/scoring/methods/pcsTs1/GridSearchIterator.cc src/protocols/scoring/methods/pcsTs1/PseudocontactShiftData.cc src/protocols/scoring/methods/pcsTs1/PseudocontactShiftEnergy.cc src/protocols/scoring/methods/pcsTs1/PseudocontactShiftInput.cc src/protocols/scoring/methods/pcsTs1/PseudocontactShiftTensor.cc src/protocols/scoring/methods/pcsTs1/TensorsOptimizer.cc src/protocols/scoring/methods/pcsTs2/GridSearchIterator.cc src/protocols/scoring/methods/pcsTs2/PseudocontactShiftData.cc src/protocols/scoring/methods/pcsTs2/PseudocontactShiftEnergy.cc src/protocols/scoring/methods/pcsTs2/PseudocontactShiftInput.cc src/protocols/scoring/methods/pcsTs2/PseudocontactShiftTensor.cc src/protocols/scoring/methods/pcsTs2/TensorsOptimizer.cc src/protocols/scoring/methods/pcsTs3/GridSearchIterator.cc src/protocols/scoring/methods/pcsTs3/PseudocontactShiftData.cc src/protocols/scoring/methods/pcsTs3/PseudocontactShiftEnergy.cc src/protocols/scoring/methods/pcsTs3/PseudocontactShiftInput.cc src/protocols/scoring/methods/pcsTs3/PseudocontactShiftTensor.cc src/protocols/scoring/methods/pcsTs3/TensorsOptimizer.cc src/protocols/scoring/methods/pcsTs4/GridSearchIterator.cc src/protocols/scoring/methods/pcsTs4/PseudocontactShiftData.cc src/protocols/scoring/methods/pcsTs4/PseudocontactShiftEnergy.cc src/protocols/scoring/methods/pcsTs4/PseudocontactShiftInput.cc src/protocols/scoring/methods/pcsTs4/PseudocontactShiftTensor.cc src/protocols/scoring/methods/pcsTs4/TensorsOptimizer.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/seeded_abinitio/util.cc src/protocols/sewing/data_storage/Basis.cc src/protocols/sewing/data_storage/HashedSmartAssembly.cc src/protocols/sewing/data_storage/LigandResidue.cc src/protocols/sewing/data_storage/LigandSegment.cc src/protocols/sewing/data_storage/SmartAssembly.cc src/protocols/sewing/data_storage/SmartSegment.cc src/protocols/sewing/data_storage/SmartSewingResidue.cc src/protocols/sewing/hashing/AlignmentFileGeneratorMover.cc src/protocols/sewing/hashing/AlignmentGenerator.cc src/protocols/sewing/hashing/BasisMapGenerator.cc src/protocols/sewing/hashing/EdgeMapGenerator.cc src/protocols/sewing/hashing/Hasher.cc src/protocols/sewing/hashing/LigandBindingResPlacer.cc src/protocols/sewing/hashing/ModelFileReader.cc src/protocols/sewing/movers/AppendAssemblyMover.cc src/protocols/sewing/movers/AssemblyMover.cc src/protocols/sewing/movers/LigandBindingAssemblyMover.cc src/protocols/sewing/requirements/AssemblyRequirementFactory.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/LigandAssemblyRequirement.cc src/protocols/sewing/requirements/LigandClashRequirement.cc src/protocols/sewing/requirements/NonTerminalStartingSegmentRequirement.cc src/protocols/sewing/requirements/SizeInSegmentsRequirement.cc src/protocols/sewing/scoring/AssemblyScorerFactory.cc src/protocols/sewing/scoring/InterModelMotifScorer.cc src/protocols/sewing/scoring/IntraDesignTerminusMotifScorer.cc src/protocols/sewing/scoring/LigandAssemblyScorer.cc src/protocols/sewing/scoring/LigandScorer.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/BatchNrEvaluator.cc src/protocols/simple_filters/BuriedSurfaceAreaFilter.cc src/protocols/simple_filters/BuriedUnsatHbondFilter.cc src/protocols/simple_filters/COFilter.cc src/protocols/simple_filters/CamShiftEvaluator.cc src/protocols/simple_filters/CamShiftEvaluatorCreator.cc src/protocols/simple_filters/ChainBreakFilter.cc src/protocols/simple_filters/ChainCountFilter.cc src/protocols/simple_filters/ChiWellRmsdEvaluator.cc src/protocols/simple_filters/ChiWellRmsdEvaluatorCreator.cc src/protocols/simple_filters/ContactMapEvaluator.cc src/protocols/simple_filters/ContactMapEvaluatorCreator.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/ExpiryFilter.cc src/protocols/simple_filters/ExternalEvaluator.cc src/protocols/simple_filters/ExtraScoreEvaluatorCreator.cc src/protocols/simple_filters/FileExistFilter.cc src/protocols/simple_filters/FileRemoveFilter.cc src/protocols/simple_filters/HelixHelixAngleFilter.cc src/protocols/simple_filters/HolesFilter.cc src/protocols/simple_filters/InterRepeatContactFilter.cc src/protocols/simple_filters/InterfaceHbondsFilter.cc src/protocols/simple_filters/InterfaceHydrophobicResidueContactsFilter.cc src/protocols/simple_filters/InterfaceSasaFilter.cc src/protocols/simple_filters/IntraRepeatContactFilter.cc src/protocols/simple_filters/JScoreEvaluator.cc src/protocols/simple_filters/JScoreEvaluatorCreator.cc src/protocols/simple_filters/JumpEvaluator.cc src/protocols/simple_filters/JumpNrEvaluatorCreator.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/PDDFScoreFilter.cc src/protocols/simple_filters/PackStatFilter.cc src/protocols/simple_filters/PackerNeighborGraphFilter.cc src/protocols/simple_filters/PalesEvaluator.cc src/protocols/simple_filters/PalesEvaluatorCreator.cc src/protocols/simple_filters/PoolEvaluatorCreator.cc src/protocols/simple_filters/PoseCommentFilter.cc src/protocols/simple_filters/PoseInfoFilter.cc src/protocols/simple_filters/PredictedBurialEvaluator.cc src/protocols/simple_filters/PredictedBurialFnEvaluatorCreator.cc src/protocols/simple_filters/RDC_Evaluator.cc src/protocols/simple_filters/RGFilter.cc src/protocols/simple_filters/RangeFilter.cc src/protocols/simple_filters/RdcEvaluatorCreator.cc src/protocols/simple_filters/RdcSelectEvaluatorCreator.cc src/protocols/simple_filters/RdcTargetEvaluatorCreator.cc src/protocols/simple_filters/ReadPoseExtraScoreFilter.cc src/protocols/simple_filters/RepeatParameterFilter.cc src/protocols/simple_filters/ReportFilter.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/RmsdEvaluator.cc src/protocols/simple_filters/RmsdEvaluatorCreator.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/ScoreEvaluator.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/StructureSimilarityEvaluatorCreator.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_filters/Worst9merFilter.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/AddSapConstraintMover.cc src/protocols/simple_moves/AddSapMathConstraintMover.cc src/protocols/simple_moves/AlignChainMover.cc src/protocols/simple_moves/BBConRotMover.cc src/protocols/simple_moves/BBDihedralSamplerMover.cc src/protocols/simple_moves/BBGaussianMover.cc src/protocols/simple_moves/BackboneMover.cc src/protocols/simple_moves/ChainSplitMover.cc src/protocols/simple_moves/ChangeAndResetFoldTreeMover.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/DEEROptimizeCoordsMover.cc src/protocols/simple_moves/DME_FilterMover.cc src/protocols/simple_moves/DOFHistogramRecorder.cc src/protocols/simple_moves/DeclareBond.cc src/protocols/simple_moves/DeleteChainMover.cc src/protocols/simple_moves/DeleteChainsMover.cc src/protocols/simple_moves/DisulfideInsertionMover.cc src/protocols/simple_moves/DisulfideInsertionMoverCreator.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/FavorSymmetricSequence.cc src/protocols/simple_moves/FoldTreeFromMotif.cc src/protocols/simple_moves/FragmentMover.cc src/protocols/simple_moves/GunnCost.cc src/protocols/simple_moves/LoadUnboundRotMover.cc src/protocols/simple_moves/MembraneTopology.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/PoseFromPoseResourceMover.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/ResetFullModelInfoMover.cc src/protocols/simple_moves/ReturnSidechainMover.cc src/protocols/simple_moves/RingConformationMover.cc src/protocols/simple_moves/SampleSequenceFromProbabilities.cc src/protocols/simple_moves/SaveProbabilitiesMetricMover.cc src/protocols/simple_moves/SaveSequenceToCommentsMover.cc src/protocols/simple_moves/ScoreMover.cc src/protocols/simple_moves/SequenceProfileMover.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/SixDoFGridDockMover.cc src/protocols/simple_moves/SmoothFragmentMover.cc src/protocols/simple_moves/StorePoseSnapshot.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/SymmetricFragmentMover.cc src/protocols/simple_moves/TailsScoreMover.cc src/protocols/simple_moves/TorsionDOFMover.cc src/protocols/simple_moves/TorsionSetMover.cc src/protocols/simple_moves/Tumble.cc src/protocols/simple_moves/UniformPositionMover.cc src/protocols/simple_moves/VirtualRootMover.cc src/protocols/simple_moves/WobbleMover.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/asym_fold_and_dock/AsymFoldandDockRbTrialMover.cc src/protocols/simple_moves/bb_sampler/BBDihedralSampler.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/rational_mc/RationalMonteCarlo.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/InterfaceTaskOperation.cc src/protocols/simple_task_operations/RestrictToInterface.cc src/protocols/simple_task_operations/RestrictToLoops.cc src/protocols/simple_task_operations/RestrictToLoopsAndNeighbors.cc src/protocols/sparta/ANN.cc src/protocols/sparta/ChemicalShiftEvaluator.cc src/protocols/sparta/ChemicalShiftEvaluatorCreator.cc src/protocols/sparta/GDB.cc src/protocols/sparta/PDB.cc src/protocols/sparta/Sparta.cc src/protocols/sparta/SpartaUtil.cc src/protocols/sparta/util.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/ss_prediction/SS_predictor.cc src/protocols/star/Extender.cc src/protocols/star/StarAbinitio.cc src/protocols/star/StarAbinitioMain.cc src/protocols/star/util.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/ProteinAtrRepScreener.cc src/protocols/stepwise/legacy/screener/RNA_AtrRepScreener.cc src/protocols/stepwise/legacy/screener/SimplePoseSelection.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/StepWiseBasicModelerOptions.cc src/protocols/stepwise/modeler/options/StepWiseModelerOptions.cc src/protocols/stepwise/modeler/options/StepWiseProteinModelerOptions.cc src/protocols/stepwise/modeler/options/StepWiseRNA_ModelerOptions.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/MainChainTorsionSet.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/StepWiseProteinCCD_MultiPoseCloser.cc src/protocols/stepwise/modeler/protein/loop_close/StepWiseProteinKIC_LoopBridger.cc src/protocols/stepwise/modeler/protein/loop_close/util.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/PhosphateMove.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/scoring_util.cc src/protocols/stepwise/modeler/util.cc src/protocols/stepwise/modeler/working_parameters/StepWiseBasicWorkingParameters.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/StepWiseMove.cc src/protocols/stepwise/monte_carlo/mover/StepWiseMoveSelector.cc src/protocols/stepwise/monte_carlo/mover/TransientCutpointHandler.cc src/protocols/stepwise/monte_carlo/mover/VaryLoopLengthMover.cc src/protocols/stepwise/monte_carlo/mover/options/StepWiseMoveSelectorOptions.cc src/protocols/stepwise/monte_carlo/options/StepWiseMonteCarloOptions.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/monte_carlo/util.cc src/protocols/stepwise/options/StepWiseBasicOptions.cc src/protocols/stepwise/sampler/StepWiseSamplerComb.cc src/protocols/stepwise/sampler/StepWiseSamplerOneDOF.cc src/protocols/stepwise/sampler/StepWiseSamplerOneTorsion.cc src/protocols/stepwise/sampler/StepWiseSamplerOneValue.cc src/protocols/stepwise/sampler/StepWiseSamplerOneValueComb.cc src/protocols/stepwise/sampler/StepWiseSamplerRingConformer.cc src/protocols/stepwise/sampler/StepWiseSamplerSized.cc src/protocols/stepwise/sampler/StepWiseSamplerSizedAny.cc src/protocols/stepwise/sampler/StepWiseSamplerSizedComb.cc src/protocols/stepwise/sampler/copy_dofs/CopyDofStepWiseSampler.cc src/protocols/stepwise/sampler/copy_dofs/ResidueAlternativeSet.cc src/protocols/stepwise/sampler/copy_dofs/ResidueAlternativeStepWiseSampler.cc src/protocols/stepwise/sampler/copy_dofs/ResidueAlternativeStepWiseSamplerComb.cc src/protocols/stepwise/sampler/copy_dofs/ResidueListStepWiseSampler.cc src/protocols/stepwise/sampler/input_streams/InputStreamStepWiseSampler.cc src/protocols/stepwise/sampler/jump/JumpStepWiseSampler.cc src/protocols/stepwise/sampler/protein/ProteinBetaAntiParallelStepWiseSampler.cc src/protocols/stepwise/sampler/protein/ProteinFragmentStepWiseSampler.cc src/protocols/stepwise/sampler/protein/ProteinMainChainStepWiseSampler.cc src/protocols/stepwise/sampler/protein/util.cc src/protocols/stepwise/sampler/rigid_body/EulerAngles.cc src/protocols/stepwise/sampler/rigid_body/RigidBodyStepWiseSampler.cc src/protocols/stepwise/sampler/rigid_body/RigidBodyStepWiseSamplerValueRange.cc src/protocols/stepwise/sampler/rigid_body/RigidBodyStepWiseSamplerWithResidueAlternatives.cc src/protocols/stepwise/sampler/rigid_body/RigidBodyStepWiseSamplerWithResidueList.cc src/protocols/stepwise/sampler/rna/RNA_ChiStepWiseSampler.cc src/protocols/stepwise/sampler/rna/RNA_KIC_Sampler.cc src/protocols/stepwise/sampler/rna/RNA_KinematicCloser.cc src/protocols/stepwise/sampler/rna/RNA_NucleosideStepWiseSampler.cc src/protocols/stepwise/sampler/rna/RNA_SugarStepWiseSampler.cc src/protocols/stepwise/sampler/rna/RNA_SuiteStepWiseSampler.cc src/protocols/stepwise/sampler/rna/util.cc src/protocols/stepwise/sampler/screener/RNA_TorsionScreener.cc src/protocols/stepwise/screener/AlignRMSD_Screener.cc src/protocols/stepwise/screener/AnchorSugarScreener.cc src/protocols/stepwise/screener/BaseBinMapUpdater.cc src/protocols/stepwise/screener/BaseCentroidScreener.cc src/protocols/stepwise/screener/BulgeApplier.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/O2PrimeScreener.cc src/protocols/stepwise/screener/PackScreener.cc src/protocols/stepwise/screener/PartitionContactScreener.cc src/protocols/stepwise/screener/PhosphateScreener.cc src/protocols/stepwise/screener/PoseSelectionScreener.cc src/protocols/stepwise/screener/ProteinCCD_ClosureScreener.cc src/protocols/stepwise/screener/RNA_ChainClosableGeometryResidueBasedScreener.cc src/protocols/stepwise/screener/RNA_ChainClosableGeometryScreener.cc src/protocols/stepwise/screener/RNA_ChainClosableGeometryStubBasedScreener.cc src/protocols/stepwise/screener/RNA_ChainClosureScreener.cc src/protocols/stepwise/screener/ResidueContactScreener.cc src/protocols/stepwise/screener/SampleApplier.cc src/protocols/stepwise/screener/Scorer.cc src/protocols/stepwise/screener/StepWiseResiduePairScreener.cc src/protocols/stepwise/screener/StepWiseScreener.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/stepwise/setup/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/surface_docking/SurfaceOrientMover.cc src/protocols/surface_docking/SurfaceParameters.cc src/protocols/surface_docking/SurfaceVectorLoader.cc src/protocols/switches/GraftSwitchMover.cc src/protocols/symmetric_docking/SymDockBaseProtocol.cc src/protocols/symmetric_docking/SymDockProtocol.cc src/protocols/symmetric_docking/SymDockingHiRes.cc src/protocols/symmetric_docking/SymDockingLowRes.cc src/protocols/symmetric_docking/SymFoldandDockMoveRbJumpMover.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/SetupForSequenceSymmetryMover.cc src/protocols/symmetry/SetupForSymmetryMover.cc src/protocols/symmetry/SetupNCSMover.cc src/protocols/symmetry/SymDockingInitialPerturbation.cc src/protocols/symmetry/SymShakeStructureMover.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/ProteinCoreResFilter.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/RestrictAAsFromProbabilities.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/RestrictOperationsBase.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/TCRloopRefine.cc src/protocols/tcr/TCRmodel.cc src/protocols/tcr/TCRseqInfo.cc src/protocols/tcr/grafting_util.cc src/protocols/tcr/modeling_util.cc src/protocols/tcr/template_util.cc src/protocols/tcr/util.cc src/protocols/testing/BenchmarkBuildRotamersMover.cc src/protocols/toolbox/CalcInterNeighborGroup.cc src/protocols/toolbox/Cluster.cc src/protocols/toolbox/DecoySetEvaluation.cc src/protocols/toolbox/EnergyLandscapeEvaluator.cc src/protocols/toolbox/IGEdgeReweighters.cc src/protocols/toolbox/InteratomicVarianceMatrix.cc src/protocols/toolbox/KCluster.cc src/protocols/toolbox/NetworkAlgorithms.cc src/protocols/toolbox/PyReturnValuePolicyTest.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/EnzdesLoopsFile.cc src/protocols/toolbox/match_enzdes_util/EnzdesSeqRecoveryCache.cc src/protocols/toolbox/match_enzdes_util/ExternalGeomSampler.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/BasicJumpClaimer.cc src/protocols/topology_broker/ClaimerMessage.cc src/protocols/topology_broker/ConstraintClaimer.cc src/protocols/topology_broker/ConstraintEvaluatorWrapper.cc src/protocols/topology_broker/ConstraintEvaluatorWrapperCreator.cc src/protocols/topology_broker/CoordConstraintClaimer.cc src/protocols/topology_broker/CutBiasClaimer.cc src/protocols/topology_broker/DensityScoringClaimer.cc src/protocols/topology_broker/DisulfJumpClaimer.cc src/protocols/topology_broker/FibrilModelingClaimer.cc src/protocols/topology_broker/FoldandDockClaimer.cc src/protocols/topology_broker/FragmentClaimer.cc src/protocols/topology_broker/FragmentJumpClaimer.cc src/protocols/topology_broker/LoopFragmentClaimer.cc src/protocols/topology_broker/MembraneTopologyClaimer.cc src/protocols/topology_broker/MetalloClaimer.cc src/protocols/topology_broker/PcsEnergyController.cc src/protocols/topology_broker/PseudocontactShiftEnergyController.cc src/protocols/topology_broker/PseudocontactShiftEnergyController_Ts1.cc src/protocols/topology_broker/PseudocontactShiftEnergyController_Ts2.cc src/protocols/topology_broker/PseudocontactShiftEnergyController_Ts3.cc src/protocols/topology_broker/PseudocontactShiftEnergyController_Ts4.cc src/protocols/topology_broker/RigidBodyRandomTMHMover.cc src/protocols/topology_broker/RigidChunkClaimer.cc src/protocols/topology_broker/SequenceClaimer.cc src/protocols/topology_broker/SequenceNumberResolver.cc src/protocols/topology_broker/StartStructClaimer.cc src/protocols/topology_broker/SymmetryClaimer.cc src/protocols/topology_broker/TMHTopologySamplerClaimer.cc src/protocols/topology_broker/TemplateFragmentClaimer.cc src/protocols/topology_broker/TemplateJumpClaimer.cc src/protocols/topology_broker/TopologyBroker.cc src/protocols/topology_broker/TopologyClaimer.cc src/protocols/topology_broker/TopologyClaimerFactory.cc src/protocols/topology_broker/claims/DofClaim.cc src/protocols/topology_broker/util.cc src/protocols/trRosetta/trRosettaMultipleSequenceAlignment.cc src/protocols/trRosetta/trRosettaOutputsBase.cc src/protocols/trRosetta/trRosettaOutputs_v1.cc src/protocols/trRosetta/trRosettaProtocolBase.cc src/protocols/trRosetta/trRosettaProtocol_v1.cc src/protocols/trRosetta_protocols/constraint_generators/trRosettaConstraintGenerator.cc src/protocols/trRosetta_protocols/movers/trRosettaProtocolMover.cc src/protocols/trajectory/DbTrajectoryReader.cc src/protocols/trajectory/DbTrajectoryWriter.cc src/protocols/unfolded_state_energy_calculator/UnfoldedStateEnergyCalculatorJobDistributor.cc src/protocols/unfolded_state_energy_calculator/UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor.cc src/protocols/unfolded_state_energy_calculator/UnfoldedStateEnergyCalculatorMover.cc src/protocols/unfolded_state_energy_calculator/UnfoldedStateEnergyCalculatorUtil.cc src/protocols/vardist_solaccess/VarSolDRotamerDots.cc src/protocols/viewer/ConformationViewer.cc src/protocols/viewer/SilentObserver.cc src/protocols/viewer/marchingCubes.cc src/protocols/viewer/triangleIterator.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/vip/VIP_Utils.cc src/protocols/wum/DatabaseEntryWorkUnit.cc src/protocols/wum/MPI_WorkUnitManager.cc src/protocols/wum/MPI_WorkUnitManager_Slave.cc src/protocols/wum/MoverList.cc src/protocols/wum/SilentStructStore.cc src/protocols/wum/WorkUnitBase.cc src/protocols/wum/WorkUnitList.cc src/protocols/wum/WorkUnitManager.cc src/utility/Binary_Util.cc src/utility/CSI_Sequence.cc src/utility/LexicographicalIterator.cc src/utility/SimulateMPI.cc src/utility/VirtualBase.srlz.cc src/utility/backtrace.cc src/utility/boinc/boinc_util.cc src/utility/crash_report.cc src/utility/curl.cc src/utility/dating.cc src/utility/excn/Exceptions.cc src/utility/exit.cc src/utility/file/FileName.cc src/utility/file/PathName.cc src/utility/file/file_sys_util.cc src/utility/file/gzip_util.cc src/utility/graph/ArrayPool.cc src/utility/graph/Digraph.cc src/utility/graph/DisjointSets.cc src/utility/graph/Graph.cc src/utility/graph/LowMemGraph.cc src/utility/graph/graph_util.cc src/utility/heap.cc src/utility/inline_file_provider.cc src/utility/integer_mapping.cc src/utility/io/FileContentsMap.cc src/utility/io/GeneralFileManager.cc src/utility/io/base64.cc src/utility/io/icstream.cc src/utility/io/izstream.cc src/utility/io/ocstream.cc src/utility/io/ozstream.cc src/utility/io/tarparser.cc src/utility/io/util.cc src/utility/json_spirit/json_spirit_reader.cc src/utility/json_spirit/json_spirit_tools.cc src/utility/json_spirit/json_spirit_value.cc src/utility/json_spirit/json_spirit_writer.cc src/utility/json_utilities.cc src/utility/keys/Key.cc src/utility/keys/Key2Tuple.srlz.cc src/utility/keys/Key3Tuple.srlz.cc src/utility/keys/Key4Tuple.srlz.cc src/utility/libsvm/Svm_rosetta.cc src/utility/mpi_util.cc src/utility/options/BooleanOption.cc src/utility/options/BooleanVectorOption.cc src/utility/options/FileOption.cc src/utility/options/FileVectorOption.cc src/utility/options/IntegerOption.cc src/utility/options/IntegerVectorOption.cc src/utility/options/Option.cc src/utility/options/OptionCollection.cc src/utility/options/PathOption.cc src/utility/options/PathVectorOption.cc src/utility/options/RealOption.cc src/utility/options/RealVectorOption.cc src/utility/options/ResidueChainVectorOption.cc src/utility/options/ScalarOption.cc src/utility/options/StringOption.cc src/utility/options/StringVectorOption.cc src/utility/options/VectorOption.cc src/utility/options/keys/AnyOptionKey.cc src/utility/options/keys/AnyVectorOptionKey.cc src/utility/options/keys/BooleanOptionKey.cc src/utility/options/keys/BooleanVectorOptionKey.cc src/utility/options/keys/FileOptionKey.cc src/utility/options/keys/FileVectorOptionKey.cc src/utility/options/keys/IntegerOptionKey.cc src/utility/options/keys/IntegerVectorOptionKey.cc src/utility/options/keys/OptionKey.cc src/utility/options/keys/OptionKeyList.cc src/utility/options/keys/OptionKeys.cc src/utility/options/keys/PathOptionKey.cc src/utility/options/keys/PathVectorOptionKey.cc src/utility/options/keys/RealOptionKey.cc src/utility/options/keys/RealVectorOptionKey.cc src/utility/options/keys/ResidueChainVectorOptionKey.cc src/utility/options/keys/ScalarOptionKey.cc src/utility/options/keys/StringOptionKey.cc src/utility/options/keys/StringVectorOptionKey.cc src/utility/options/keys/VectorOptionKey.cc src/utility/options/mpi_stderr.cc src/utility/py/PyExitCallback.cc src/utility/recent_history_queue.cc src/utility/serialization/ObjexxFCL/DynamicIndexRange.srlz.cc src/utility/serialization/ObjexxFCL/FArray1D.srlz.cc src/utility/serialization/ObjexxFCL/FArray2D.srlz.cc src/utility/serialization/ObjexxFCL/FArray3D.srlz.cc src/utility/serialization/ObjexxFCL/ubyte.srlz.cc src/utility/serialization/serialization.cc src/utility/sql_database/DatabaseSessionManager.cc src/utility/sql_database/types.cc src/utility/static_database.cc src/utility/string_util.cc src/utility/sys_util.cc src/utility/tag/Tag.cc src/utility/tag/XMLSchemaGeneration.cc src/utility/tag/XMLSchemaValidation.cc src/utility/tag/util.cc src/utility/thread/ReadWriteMutex.cc src/utility/vector0.srlz.cc src/utility/vector1.srlz.cc src/utility/xsd_util/util.cc

Test: linux.clang.code_quality.submodule_regression

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

Failed sub-tests (click for more details):
replica_docking

Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):
ddG_of_mutation

branch: rosetta:commits 「№20773」
Commited by: Andrew Muenks
GitHub Pull Request link: 「№425」
Merge: 「e6f643b81」← 「d4c0d6840」 code diff
Scheduled at: 2025-05-30 13:58:03.735939

	linux.clang	linux.gcc	linux.srlz	mac.clang
debug
release
unit

Pull Request №425 RosettaCommons/rosetta/main ← agmuenks/rosetta/ligand_density_id Merge: e6f643b818cda63c8e00156a266c408faac3c3dd←d4c0d6840059f421dd35cb7bb28ce28a1b7f8de8 Updates to cryoEM ligand identification in GALigandDock ---------------- Merge commit message: added comments for ligand ID values and changed math.h to cmath

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Test: linux.gcc.code_quality.beautification

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Test: ubuntu.gcc.code_quality.merge_size

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

Failed sub-tests (click for more details):
replica_docking

Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):
ddG_of_mutation

Test: mac.clang.python39.integration

Failed sub-tests (click for more details):
revold

Test: windows.cl.windows.build.debug

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branch: rosetta:commits 「№20772」
Commited by: Ari Benjamin Ginsparg
GitHub Pull Request link: 「№428」
Merge: 「cdd8f4763」← 「80a92ffab」 code diff
Scheduled at: 2025-05-30 13:57:17.218744

	linux.clang	linux.gcc	linux.srlz	mac.clang
debug
release
unit

Pull Request №428 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/ag_post_lds_quick_fix Merge: cdd8f4763dd711a4aa6b38a8552c98401fe5a0ed←80a92ffab8ebd1f800e6aa202b1560366aeb6a34 Fixing gcc errors from LigandDiscoverySearch merge ---------------- Merge commit message: Initializing bp_xyz values to avoid gcc test errors

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Test: linux.clang.bcl.static.build.release

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Test: linux.gcc.bcl.static.build.release

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

Failed sub-tests (click for more details):
backbonegridsampler_nstruct_mode mpi_simple_cycpep_predict mpi_simple_cycpep_predict_4level mpi_simple_cycpep_predict_computing_pnear_to_all recon_design_mpi replica_docking threefold_symm_peptide_design

Test: mac.clang.python39.integration

Failed sub-tests (click for more details):
mp_f19_relax revold

branch: rosetta:commits 「№20771」
Commited by: Ari Benjamin Ginsparg
GitHub commit link: 「80a92ffab8ebd1f8」
Difference from previous tested commit: code diff
Commit date: 2025-05-30 17:36:36

	linux.clang	linux.gcc	linux.srlz	mac.clang
debug
release
unit

Initializing bp_xyz values to avoid gcc test errors

Summary

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branch: rosetta:commits 「№20770」
Commited by: Rocco Moretti
GitHub Pull Request link: 「№426」
Merge: 「e6f643b81」← 「65e6dc6d4」 code diff
Scheduled at: 2025-05-29 17:01:59.689491

	linux.clang	linux.gcc	linux.srlz	mac.clang
debug
release
unit

Pull Request №426 RosettaCommons/rosetta/main ← roccomoretti/rosetta/test_fixes Merge: e6f643b818cda63c8e00156a266c408faac3c3dd←65e6dc6d4806da11b8c4d2f2edba85a68ad46a3f Fixes for failing tests in main ---------------- Merge commit message: Fix rapidjson compilation issue with Clang 19.

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Test: ubuntu.clang.code_quality.clang_tidy

Failed sub-tests (click for more details):
src/core/scoring/etable/etrie/TrieCountPair1BC3.cc src/core/scoring/etable/etrie/TrieCountPair1BC4.cc src/protocols/drug_design/ReactionBasedAnalogSampler.cc src/protocols/drug_design/ReactionFragment.cc src/protocols/drug_design/ReactionGrow.cc src/protocols/drug_design/ReactionMultiTransform.cc src/protocols/drug_design/SubstituentReplace.cc src/protocols/drug_design/SubstructureReplace.cc src/protocols/ligand_evolution/FragmentLibrary.cc

Test: linux.clang.code_quality.submodule_regression

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

Failed sub-tests (click for more details):
replica_docking

Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):
ddG_of_mutation

Test: mac.clang.python39.integration

Failed sub-tests (click for more details):
revold

Test: ubuntu-20.04.gcc.cxx11thread.mpi.serialization.python36.scientific.peptide_pnear_vs_ic50

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Test: windows.cl.windows.build.debug

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branch: rosetta:commits 「№20769」
Commited by: Rocco Moretti
GitHub Pull Request link: 「№426」
Merge: 「e6f643b81」← 「1f90f96a7」 code diff
Scheduled at: 2025-05-29 16:22:37.685313

	linux.clang	linux.gcc	linux.srlz	mac.clang
debug
release
unit

Pull Request №426 RosettaCommons/rosetta/main ← roccomoretti/rosetta/test_fixes Merge: e6f643b818cda63c8e00156a266c408faac3c3dd←1f90f96a704024648b3faf4c9b3b81d7a2633ba4 Fixes for failing tests in main ---------------- Merge commit message: Attempt to make output parsing in peptide_pnear_vs_ic50 scientific test more robust.

Rosetta Benchmark 2 days
Tests for this revision was automatically canceled because newer set of tests for pull-request №426 was submitted!

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Test: linux.clang.code_quality.submodule_regression

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Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):
ddG_of_mutation

Test: mac.clang.python39.integration

Failed sub-tests (click for more details):
mp_f19_relax revold

branch: rosetta:commits 「№20768」
Commited by: Andrew Muenks
GitHub Pull Request link: 「№425」
Merge: 「e6f643b81」← 「74c81dea0」 code diff
Scheduled at: 2025-05-29 14:01:18.940167

	linux.clang	linux.gcc	linux.srlz	mac.clang
debug
release
unit

Pull Request №425 RosettaCommons/rosetta/main ← agmuenks/rosetta/ligand_density_id Merge: e6f643b818cda63c8e00156a266c408faac3c3dd←74c81dea014ce3f0afa9067af7917db691b35b6a Updates to cryoEM ligand identification in GALigandDock ---------------- Merge commit message: merged with updated rosetta/main

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Test: ubuntu.clang.cxx11thread.serialization.python38.PyRosetta.unit

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Test: ubuntu.gcc.code_quality.merge_size

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

Failed sub-tests (click for more details):
replica_docking

Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):
ddG_of_mutation

Test: mac.clang.python39.integration

Failed sub-tests (click for more details):
mp_f19_relax revold

branch: rosetta:commits 「№20767」
Commited by: Ari Benjamin Ginsparg
GitHub Pull Request link: 「№59」
Merge: 「1354d05da」← 「f3323403a」 code diff
Scheduled at: 2025-05-27 16:38:14.699173

	linux.clang	linux.gcc	linux.srlz	mac.clang
debug
release
unit

Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: 1354d05daa4c339d591afeecef3c94ca2d38680e←f3323403a22b3ea80e32370a95e789f1ec047c8d Updated Ligand Motifs Code ---------------- Merge commit message: beautifying changed proteingrid.cc

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Test: ubuntu.clang.cxx11thread.serialization.python38.PyRosetta.unit

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Test: ubuntu.gcc.code_quality.merge_size

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

Failed sub-tests (click for more details):
backbonegridsampler_nstruct_mode helical_bundle_predict helical_bundle_predict_psipred helical_bundle_predict_psipred_with_helix_globals helical_bundle_predict_sequence helical_bundle_predict_skipping_residues mpi_simple_cycpep_predict mpi_simple_cycpep_predict_4level mpi_simple_cycpep_predict_computing_pnear_to_all recon_design_mpi replica_docking simple_cycpep_predict_beta_thioether_lariat simple_cycpep_predict_bondangle_bondlength simple_cycpep_predict_cterm_isopeptide_lariat simple_cycpep_predict_cterm_isopeptide_lariat_tailless simple_cycpep_predict_design simple_cycpep_predict_lanthionine simple_cycpep_predict_nterm_isopeptide_lariat simple_cycpep_predict_nterm_isopeptide_lariat_tailless simple_cycpep_predict_sidechain_isopeptide simple_cycpep_predict_sidechain_isopeptide_reverse simple_cycpep_predict_terminal_disulfide_tails_2 simple_cycpep_predict_thioether_lariat threefold_symm_peptide_design

Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):
cmaes_minimizer features ligand_motif_discovery ligand_motif_identification real_motif_analysis remove_duplicate_motifs

Test: mac.clang.python39.integration

Failed sub-tests (click for more details):
ligand_motif_discovery ligand_motif_identification real_motif_analysis remove_duplicate_motifs revold

branch: rosetta:commits 「№20766」
Commited by: Ginsparg
GitHub Pull Request link: 「№59」
Merge: 「1354d05da」← 「d75bfce4a」 code diff
Scheduled at: 2025-05-27 16:25:29.205668

	linux.clang	linux.gcc	linux.srlz	mac.clang
debug
release
unit

Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: 1354d05daa4c339d591afeecef3c94ca2d38680e←d75bfce4a3051e4f7764df57653c485d95e3b8f8 Updated Ligand Motifs Code ---------------- Merge commit message: removing clone function, but keeping as a comment in case a clone function may be needed for the object in the future. The commented code can be a start

Summary
beautification

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Test: linux.gcc.code_quality.beautification

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branch: rosetta:commits 「№20765」
Commited by: Ginsparg
GitHub Pull Request link: 「№59」
Merge: 「1354d05da」← 「e83e7a1af」 code diff
Scheduled at: 2025-05-20 16:41:29.464373

	linux.clang	linux.gcc	linux.srlz	mac.clang
debug
release
unit

Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: 1354d05daa4c339d591afeecef3c94ca2d38680e←e83e7a1af964092c39db50927b126135fe8822fd Updated Ligand Motifs Code ---------------- Merge commit message: Merge branch 'main' into updated_ligand_discovery_search_code_ag_may_2024

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Test: ubuntu.clang.cxx11thread.serialization.python38.PyRosetta.unit

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Test: ubuntu.gcc.code_quality.merge_size

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

Failed sub-tests (click for more details):
backbonegridsampler_nstruct_mode helical_bundle_predict helical_bundle_predict_psipred helical_bundle_predict_psipred_with_helix_globals helical_bundle_predict_sequence helical_bundle_predict_skipping_residues mpi_simple_cycpep_predict mpi_simple_cycpep_predict_4level mpi_simple_cycpep_predict_computing_pnear_to_all replica_docking simple_cycpep_predict_beta_thioether_lariat simple_cycpep_predict_bondangle_bondlength simple_cycpep_predict_cterm_isopeptide_lariat simple_cycpep_predict_cterm_isopeptide_lariat_tailless simple_cycpep_predict_design simple_cycpep_predict_lanthionine simple_cycpep_predict_nterm_isopeptide_lariat simple_cycpep_predict_nterm_isopeptide_lariat_tailless simple_cycpep_predict_sidechain_isopeptide simple_cycpep_predict_sidechain_isopeptide_reverse simple_cycpep_predict_terminal_disulfide_tails_2 simple_cycpep_predict_thioether_lariat threefold_symm_peptide_design

Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):
cmaes_minimizer features ligand_motif_discovery ligand_motif_identification real_motif_analysis remove_duplicate_motifs

Test: mac.clang.python39.integration

Failed sub-tests (click for more details):
ligand_motif_discovery ligand_motif_identification mp_f19_relax real_motif_analysis remove_duplicate_motifs revold

Test: linux.clang.python312.scripts.pyrosetta

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branch: rosetta:commits 「№20764」
Commited by: Ginsparg
GitHub Pull Request link: 「№59」
Merge: 「74f819c4d」← 「c2adab8ca」 code diff
Scheduled at: 2025-05-20 13:34:42.812916

	linux.clang	linux.gcc	linux.srlz	mac.clang
debug
release
unit

Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: 74f819c4dd58142810833fb8e63211f2974ee342←c2adab8ca670811ec2a966e91719790c94116d0b Updated Ligand Motifs Code ---------------- Merge commit message: removing "other" variable from copy ctor and = overload when used for default so that it doesn't go unused

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Test: ubuntu.gcc.code_quality.merge_size

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

Failed sub-tests (click for more details):
backbonegridsampler_nstruct_mode helical_bundle_predict helical_bundle_predict_psipred helical_bundle_predict_psipred_with_helix_globals helical_bundle_predict_sequence helical_bundle_predict_skipping_residues mpi_simple_cycpep_predict mpi_simple_cycpep_predict_4level mpi_simple_cycpep_predict_computing_pnear_to_all recon_design_mpi replica_docking simple_cycpep_predict_beta_thioether_lariat simple_cycpep_predict_bondangle_bondlength simple_cycpep_predict_cterm_isopeptide_lariat simple_cycpep_predict_cterm_isopeptide_lariat_tailless simple_cycpep_predict_design simple_cycpep_predict_lanthionine simple_cycpep_predict_nterm_isopeptide_lariat simple_cycpep_predict_nterm_isopeptide_lariat_tailless simple_cycpep_predict_sidechain_isopeptide simple_cycpep_predict_sidechain_isopeptide_reverse simple_cycpep_predict_terminal_disulfide_tails_2 simple_cycpep_predict_thioether_lariat threefold_symm_peptide_design

Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):

Test: linux.clang.tensorflow.integration.tensorflow

Failed sub-tests (click for more details):

Test: linux.gcc.cxx11thread.integration.thread

Failed sub-tests (click for more details):

Test: torch.clang.torch.python39.integration.torch

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Test: mac.clang.python39.integration

Failed sub-tests (click for more details):

Test: linux.clang.performance

Failed sub-tests (click for more details):

Test: linux.clang.profile

Failed sub-tests (click for more details):

Test: linux.clang.score

Failed sub-tests (click for more details):

Test: linux.gcc.score

Failed sub-tests (click for more details):

Test: mac.clang.score

Failed sub-tests (click for more details):

branch: rosetta:commits 「№20763」
Commited by: Ari Benjamin Ginsparg
GitHub Pull Request link: 「№59」
Merge: 「74f819c4d」← 「be034f194」 code diff
Scheduled at: 2025-05-20 13:26:40.039709

	linux.clang	linux.gcc	linux.srlz	mac.clang
debug
release
unit

Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: 74f819c4dd58142810833fb8e63211f2974ee342←be034f1942d400f88b56e47ac5b6d3473741c951 Updated Ligand Motifs Code ---------------- Merge commit message: ran beautifier on these files

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Test: linux.gcc.build.debug

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Test: linux.clang.build.ninja_debug

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branch: rosetta:commits 「№20762」
Commited by: Ginsparg
GitHub Pull Request link: 「№59」
Merge: 「74f819c4d」← 「8f1743db5」 code diff
Scheduled at: 2025-05-20 13:19:00.374405

	linux.clang	linux.gcc	linux.srlz	mac.clang
debug
release
unit

Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: 74f819c4dd58142810833fb8e63211f2974ee342←8f1743db5c8ab3635f4a1ed2a3c33c7e05bba56e Updated Ligand Motifs Code ---------------- Merge commit message: removing default definitions from cc file and defining as default in hh

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Test: linux.gcc.cxx11thread.serialization.build.debug

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Test: linux.clang.build.ninja_debug

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Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):

branch: rosetta:commits 「№20761」
Commited by: Ginsparg
GitHub Pull Request link: 「№59」
Merge: 「74f819c4d」← 「f356c14b5」 code diff
Scheduled at: 2025-05-20 12:06:34.010817

	linux.clang	linux.gcc	linux.srlz	mac.clang
debug
release
unit

Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: 74f819c4dd58142810833fb8e63211f2974ee342←f356c14b5ae8d24d4a4aaa6b442592f101dd7ed0 Updated Ligand Motifs Code ---------------- Merge commit message: removing extraneous parentheses

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Test: ubuntu.clang.cxx11thread.serialization.python38.PyRosetta.unit

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Test: linux.clang.build.debug

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Test: linux.gcc.build.debug

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Test: linux.gcc.cxx11thread.serialization.build.debug

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Test: linux.gcc.mpi.build.debug

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Test: linux.gcc.mpi.serialization.build.debug

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Test: linux.clang.build.ninja_debug

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Test: linux.gcc.code_quality.beautification

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Test: ubuntu.gcc.code_quality.merge_size

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

Failed sub-tests (click for more details):
backbonegridsampler_nstruct_mode helical_bundle_predict helical_bundle_predict_psipred helical_bundle_predict_psipred_with_helix_globals helical_bundle_predict_sequence helical_bundle_predict_skipping_residues mpi_simple_cycpep_predict mpi_simple_cycpep_predict_4level mpi_simple_cycpep_predict_computing_pnear_to_all replica_docking simple_cycpep_predict_beta_thioether_lariat simple_cycpep_predict_bondangle_bondlength simple_cycpep_predict_cterm_isopeptide_lariat simple_cycpep_predict_cterm_isopeptide_lariat_tailless simple_cycpep_predict_design simple_cycpep_predict_lanthionine simple_cycpep_predict_nterm_isopeptide_lariat simple_cycpep_predict_nterm_isopeptide_lariat_tailless simple_cycpep_predict_sidechain_isopeptide simple_cycpep_predict_sidechain_isopeptide_reverse simple_cycpep_predict_terminal_disulfide_tails_2 simple_cycpep_predict_thioether_lariat threefold_symm_peptide_design

Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):

Test: linux.gcc.cxx11thread.integration.thread

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Test: torch.clang.torch.python39.integration.torch

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Test: mac.clang.python39.integration

Failed sub-tests (click for more details):

Test: linux.clang.performance

Failed sub-tests (click for more details):

Test: linux.clang.profile

Failed sub-tests (click for more details):

Test: linux.clang.score

Failed sub-tests (click for more details):

Test: linux.gcc.score

Failed sub-tests (click for more details):

Test: mac.clang.score

Failed sub-tests (click for more details):

Test: linux.clang.unit

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Test: linux.gcc.cxx11thread.serialization.unit

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Test: linux.gcc.unit

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branch: rosetta:commits 「№20760」
Commited by: Ginsparg
GitHub Pull Request link: 「№59」
Merge: 「74f819c4d」← 「c353b9848」 code diff
Scheduled at: 2025-05-20 11:55:26.304442

	linux.clang	linux.gcc	linux.srlz	mac.clang
debug
release
unit

Pull Request №59 RosettaCommons/rosetta/main ← RosettaCommons/rosetta/updated_ligand_discovery_search_code_ag_may_2024 Merge: 74f819c4dd58142810833fb8e63211f2974ee342←c353b98484b7c577040abc13d48084d6f2428da8 Updated Ligand Motifs Code ---------------- Merge commit message: adjusting the copy constructor and = overload to just be the default

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Test: linux.clang.build.debug

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Test: linux.gcc.cxx11thread.serialization.build.debug

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Test: linux.clang.build.ninja_debug

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Test: linux.clang.build.release

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Test: linux.clang.integration.release_debug_no_symbols

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Test: linux.clang.score

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Test: linux.clang.unit

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Test: linux.gcc.cxx11thread.serialization.unit

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queued	Queued Test
queued for comparison	Test finished running but not yet compared
running	Test is Running right now
comparing	Test results is now comparing with previous results
finished	Test is finished without errors
failed	Test failed
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script failed	Test results is unknow because test-script failed
canceled	Test was canceled