Here is a list of all namespace members with links to the namespace documentation for each member:

- s -

• S : core::chemical::element
• S_p_sp3 : core::chemical::orbitals
• S_PEPTOID : core::chemical
• sa : core::scoring
• SA_EnergyCreator_registrator : core::init
• sa_faraggi_max() : protocols::frag_picker
• SACCHARIDE : core::enzymes
• safe_read() : core::chemical::gasteiger
• safe_secstruct() : protocols::jumping
• safe_set_conf() : protocols::environment
• safe_set_extended_torsions_and_idealize_loops() : protocols::loops
• safe_write() : core::chemical::gasteiger
• SaltBridgeFeaturesCOP : protocols::features
• SaltBridgeFeaturesOP : protocols::features
• same_link() : core::io
• same_polarization_group() : core::scoring
• same_pose() : protocols::denovo_design
• SameChiBinComboGrouperCOP : protocols::match::output
• SameChiBinComboGrouperOP : protocols::match::output
• SameRotamerComboGrouperCOP : protocols::match::output
• SameRotamerComboGrouperOP : protocols::match::output
• SameSequenceAndDSPositionGrouperCOP : protocols::match::output
• SameSequenceAndDSPositionGrouperOP : protocols::match::output
• SameSequenceGrouperCOP : protocols::match::output
• SameSequenceGrouperOP : protocols::match::output
• SameStrandCOP : protocols::jumping
• SameStrandOP : protocols::jumping
• SAMPLE : core::pose::full_model_info
• sample_all_rotations_at_jump() : protocols::toolbox::sample_around
• SAMPLE_APPLIER : protocols::stepwise::screener
• SAMPLE_APPLIER_WITH_RESIDUE_LIST : protocols::stepwise::screener
• sample_cis_peptide_bond : protocols::generalized_kinematic_closure::perturber
• sample_layer_lines_from_bins() : core::scoring::fiber_diffraction
• SampleApplierCOP : protocols::stepwise::screener
• SampleApplierOP : protocols::stepwise::screener
• SAMPLED_ROSETTA : protocols::cluster::calibur
• sampleEnum : protocols::hybridization
• SampleFarnesylMoverCOP : protocols::farnesyl
• SampleFarnesylMoverOP : protocols::farnesyl
• SampleGridCOP : protocols::magnesium
• SampleGridOP : protocols::magnesium
• SampleRotamersFromPDB_RotamerSetOperationCOP : protocols::splice
• SampleRotamersFromPDB_RotamerSetOperationOP : protocols::splice
• SampleRotamersFromPDBCOP : protocols::splice
• SampleRotamersFromPDBOP : protocols::splice
• SamplerPlusPlusOP : protocols::toolbox
• SamplerPlusPlusType : protocols::toolbox
• SampleTiltAnglesCOP : protocols::membrane::benchmark
• SampleTiltAnglesOP : protocols::membrane::benchmark
• SandwichFeaturesCOP : protocols::features::strand_assembly
• SandwichFeaturesOP : protocols::features::strand_assembly
• SaneDockingProtocolOP : protocols::docking::stateless
• SaneMinMoverCOP : protocols::minimization_packing
• SaneMinMoverOP : protocols::minimization_packing
• sap_atom_sasa() : core::pack::guidance_scoreterms::sap
• SAP_BLOCK_STORE_SCALE : core::pack::guidance_scoreterms::sap
• sap_constraint : core::scoring
• SAP_PROBE_SIZE : core::pack::guidance_scoreterms::sap
• SapConstraintCOP : core::pack::guidance_scoreterms::sap
• SapConstraintEnergyCreator_registrator : core::init
• SapConstraintEnergyOP : core::pack::guidance_scoreterms::sap
• SapConstraintHelperCOP : core::pack::guidance_scoreterms::sap
• SapConstraintHelperOP : core::pack::guidance_scoreterms::sap
• SapConstraintOP : core::pack::guidance_scoreterms::sap
• SapConstraintOptionsCOP : core::pack::guidance_scoreterms::sap
• SapConstraintOptionsOP : core::pack::guidance_scoreterms::sap
• SapDatabaseCOP : core::pack::guidance_scoreterms::sap
• SapDatabaseOP : core::pack::guidance_scoreterms::sap
• SapMathConstraintCOP : core::pack::guidance_scoreterms::sap
• SapMathConstraintOP : core::pack::guidance_scoreterms::sap
• SapScoreMetricCOP : core::pack::guidance_scoreterms::sap
• SapScoreMetricOP : core::pack::guidance_scoreterms::sap
• sasa_lr : core::scoring::methods
• SasaCalcCOP : core::scoring::sasa
• SasaCalcOP : core::scoring::sasa
• SASAEnergyCreator_registrator : core::init
• SasaMethodCOP : core::scoring::sasa
• SasaMethodEnum : core::scoring::sasa
• SasaMethodHPMode : core::scoring::sasa
• SasaMethodOP : core::scoring::sasa
• SasaMethodType_total : core::scoring::sasa
• SasaMetricCOP : core::simple_metrics::metrics
• SasaMetricOP : core::simple_metrics::metrics
• SasaOptionsOP : core::scoring::packstat
• SASAPotentialCOP : core::scoring
• SASAPotentialOP : core::scoring
• SasaRadii : core::scoring::sasa
• SasaRadii_total : core::scoring::sasa
• SasaResultOP : core::scoring::packstat
• SASAShouldItCount() : core::scoring
• satisfies_restriction() : core::fragment::rna
• save_schema() : protocols::rosetta_scripts
• SaveAndRetrieveSidechainsCOP : protocols::protein_interface_design::movers
• SaveAndRetrieveSidechainsOP : protocols::protein_interface_design::movers
• saved_native_pose() : core::pose
• saved_reference_pose() : core::pose , protocols::rosetta_scripts
• SavePDBInfoMoverCOP : protocols::fold_from_loops::movers
• SavePDBInfoMoverOP : protocols::fold_from_loops::movers
• SavePoseMoverCOP : protocols::rosetta_scripts
• SavePoseMoverOP : protocols::rosetta_scripts
• SaveResfileToDiskFilterCOP : protocols::simple_filters
• SaveResfileToDiskFilterOP : protocols::simple_filters
• SaveSequenceToCommentsMoverCOP : protocols::movers
• SaveSequenceToCommentsMoverOP : protocols::movers
• saxs_cen_score : core::scoring
• saxs_fa_score : core::scoring
• saxs_score : core::scoring
• SAXSEnergyCreator_registrator : core::init
• SAXSEnergyCreatorCEN_registrator : core::init
• SAXSEnergyCreatorFA_registrator : core::init
• SAXSScoreFilterCOP : protocols::simple_filters
• SAXSScoreFilterOP : protocols::simple_filters
• Sb : core::chemical::element
• Sc : core::chemical::element
• SC_BB : core::scoring::motif
• SC_BRANCH_POINT : core::chemical
• SC_FRAGMENT : core::chemical
• SC_ORBITALS : core::chemical
• SC_PH : core::scoring::motif
• SC_PO : core::scoring::motif
• SC_RMSD_CUTOFF : protocols::hbnet
• sc_sc : core::pack::interaction_graph
• SC_SC : core::scoring::motif
• sc_whole : core::pack::interaction_graph
• ScaffoldBuildPointCOP : protocols::match::upstream
• ScaffoldBuildPointOP : protocols::match::upstream
• scalar_weighted() : protocols::constraint_generator
• ScalarWeightedFuncCOP : core::scoring::func
• ScalarWeightedFuncOP : core::scoring::func
• SCALE1 : core::io::pdb
• SCALE2 : core::io::pdb
• SCALE3 : core::io::pdb
• SCdisplayState : protocols::viewer::graphics_states_param
• SchemePlaceMotifsMoverCOP : protocols::matdes
• SchemePlaceMotifsMoverOP : protocols::matdes
• SCMinMinimizerMapCOP : core::pack::scmin
• SCMinMinimizerMapOP : core::pack::scmin
• SCMinMultifuncCOP : core::pack::scmin
• SCMinMultifuncOP : core::pack::scmin
• Score : core::scoring
• score : protocols::hybridization
• SCORE12_PATCH : core::scoring
• SCORE13 : core::scoring
• SCORE4_SMOOTH_CART : core::scoring
• score_atom_centrally() : core::scoring::mm
• score_cst() : protocols::abinitio::abscript
• score_d8 : protocols::hybridization
• SCORE_FRAG_STORE : protocols::loops::loop_closure::ccd
• score_function_subtag_complex_type_namer() : protocols::parser
• score_function_subtag_group() : protocols::parser
• score_function_tag_group() : protocols::parser
• score_mapping() : core::io::pose_from_sfr
• score_sort_criterion() : protocols::stepwise::modeler::rna
• score_type_filter_tracer() : protocols::score_filters
• score_type_for_orb_params() : core::scoring::orbitals
• score_type_from_name() : core::scoring
• ScoreCacheCOP : core::energy_methods
• ScoreCacheOP : core::energy_methods
• ScoreCutoffFilterCOP : protocols::score_filters
• ScoreCutoffFilterOP : protocols::score_filters
• ScoredCandidate : protocols::frag_picker
• ScoredCandidatesVector1 : protocols::frag_picker
• ScoreFileOutputSpecificationCOP : protocols::jd3::pose_outputters
• ScoreFileOutputSpecificationOP : protocols::jd3::pose_outputters
• ScoreFileOutputterCOP : protocols::jd3::pose_outputters
• ScoreFileOutputterOP : protocols::jd3::pose_outputters
• ScoreFileSilentStructCreator_registrator : core::init
• ScoreFunctionCOP : core::scoring
• ScoreFunctionFeaturesCOP : protocols::features
• ScoreFunctionFeaturesOP : protocols::features
• ScoreFunctionInfoCOP : core::scoring
• ScoreFunctionInfoOP : core::scoring
• ScoreFunctionOP : core::scoring
• scorefxn_is_symmetric() : core::pose::symmetry
• scorefxn_update_from_options() : protocols::enzdes::enzutil
• ScoreJumpFileSilentStructCreator_registrator : core::init
• ScoreJumpFileSilentStructOP : core::io::silent
• ScoreList : protocols::nonlocal , protocols::simple_moves
• ScoreMap : protocols::qsar::scoring_grid
• ScoreMoverCOP : protocols::simple_moves
• ScoreMoverOP : protocols::simple_moves
• ScoreNormalizationCOP : protocols::qsar::scoring_grid
• ScoreNormalizationOP : protocols::qsar::scoring_grid
• ScorePair : core::import_pose::atom_tree_diffs
• ScorePoseSegmentFromResidueSelectorFilterCOP : protocols::fold_from_loops::filters
• ScorePoseSegmentFromResidueSelectorFilterOP : protocols::fold_from_loops::filters
• SCORER : protocols::stepwise::screener
• ScorerCOP : protocols::stepwise::screener
• ScoreResult : protocols::legacy_sewing
• ScoreResults : protocols::legacy_sewing
• ScoreRmsPointCOP : protocols::toolbox
• ScoreRmsPointOP : protocols::toolbox
• ScoreRmsPointsCOP : protocols::toolbox
• ScoreRmsPointsOP : protocols::toolbox
• ScorerOP : protocols::stepwise::screener
• Scores : core::import_pose::atom_tree_diffs , protocols::sic_dock , protocols::sic_dock::scores
• scores_to_alignments() : protocols::legacy_sewing
• ScoresPair : core::import_pose::atom_tree_diffs
• ScoresPairList : core::import_pose::atom_tree_diffs
• ScoreStructOP : core::io::raw_data
• ScoreTermValueBasedSelectorCOP : core::select::residue_selector
• ScoreTermValueBasedSelectorOP : core::select::residue_selector
• ScoreType : core::scoring
• ScoreTypeFeaturesCOP : protocols::features
• ScoreTypeFeaturesOP : protocols::features
• ScoreTypeFilterCOP : protocols::score_filters
• ScoreTypeFilterOP : protocols::score_filters
• ScoreTypes : core::scoring
• ScoringGridLoaderCOP : protocols::qsar::scoring_grid
• ScoringGridLoaderOP : protocols::qsar::scoring_grid
• ScoringSchemeOP : core::sequence
• ScoringSecMatchRPECOP : protocols::match::downstream
• ScoringSecMatchRPEOP : protocols::match::downstream
• SCPA_cterm_isopeptide_lariat : protocols::cyclic_peptide_predict
• SCPA_cyclization_type : protocols::cyclic_peptide_predict
• SCPA_invalid_type : protocols::cyclic_peptide_predict
• SCPA_n_to_c_amide_bond : protocols::cyclic_peptide_predict
• SCPA_nterm_isopeptide_lariat : protocols::cyclic_peptide_predict
• SCPA_number_of_types : protocols::cyclic_peptide_predict
• SCPA_sidechain_isopeptide : protocols::cyclic_peptide_predict
• SCPA_terminal_disulfide : protocols::cyclic_peptide_predict
• SCREENING_FILE : protocols::jd2::JobInputterInputSource
• ScreeningFeaturesCOP : protocols::features
• ScreeningFeaturesOP : protocols::features
• ScreeningJobInputterOP : protocols::jd2
• ScriptCMCOP : protocols::environment
• ScriptCMOP : protocols::environment
• SCS_Antibody_Database_ResultCOP : protocols::antibody::grafting
• SCS_Antibody_Database_ResultOP : protocols::antibody::grafting
• SCS_BaseCOP : protocols::antibody::grafting
• SCS_BaseOP : protocols::antibody::grafting
• SCS_BlastPlusCOP : protocols::antibody::grafting
• SCS_BlastPlusOP : protocols::antibody::grafting
• SCS_BlastResultCOP : protocols::antibody::grafting
• SCS_BlastResultOP : protocols::antibody::grafting
• SCS_FunctorCOP : protocols::antibody::grafting
• SCS_FunctorOP : protocols::antibody::grafting
• SCS_LoopOverSCsCOP : protocols::antibody::grafting
• SCS_LoopOverSCsOP : protocols::antibody::grafting
• SCS_ResultCOP : protocols::antibody::grafting
• SCS_ResultOP : protocols::antibody::grafting
• SCS_ResultsCOP : protocols::antibody::grafting
• SCS_ResultSetCOP : protocols::antibody::grafting
• SCS_ResultSetOP : protocols::antibody::grafting
• SCS_ResultsOP : protocols::antibody::grafting
• SCS_SubstitutionMatrixResultCOP : protocols::antibody::grafting
• SCS_SubstitutionMatrixResultOP : protocols::antibody::grafting
• Se : core::chemical::element
• sealed_symmetric_fold_tree() : core::pose::symmetry
• SealFoldTreeMoverCOP : protocols::denovo_design::movers
• SealFoldTreeMoverOP : protocols::denovo_design::movers
• search_x() : core::scoring::packstat
• SearchPatternCOP : protocols::hotspot_hashing
• SearchPatternOP : protocols::hotspot_hashing
• SearchPatternRotSetOpCOP : protocols::hotspot_hashing
• SearchPatternRotSetOpOP : protocols::hotspot_hashing
• SearchReal : protocols::indexed_structure_store::search
• secant() : core::scoring::fiber_diffraction
• SecMatchResiduePairEvaluatorCOP : protocols::match::downstream
• SecMatchResiduePairEvaluatorOP : protocols::match::downstream
• SecondaryMatcherToDownstreamResidueCOP : protocols::match::downstream
• SecondaryMatcherToDownstreamResidueOP : protocols::match::downstream
• SecondaryMatcherToUpstreamResidueCOP : protocols::match::downstream
• SecondaryMatcherToUpstreamResidueOP : protocols::match::downstream
• SecondaryMatchProtocolCAP : protocols::enzdes
• SecondaryMatchProtocolCOP : protocols::enzdes
• SecondaryMatchProtocolOP : protocols::enzdes
• SecondaryMatchUpstreamResProcessorCOP : protocols::match::downstream
• SecondaryMatchUpstreamResProcessorOP : protocols::match::downstream
• SecondaryOutputterMap : protocols::jd3::standard
• SecondaryPoseOutputterCOP : protocols::jd3::pose_outputters
• SecondaryPoseOutputterCreatorCOP : protocols::jd3::pose_outputters
• SecondaryPoseOutputterCreatorOP : protocols::jd3::pose_outputters
• SecondaryPoseOutputterOP : protocols::jd3::pose_outputters
• SecondaryRepresentativeOutputterMap : protocols::jd3::standard
• SecondarySimilarityCOP : protocols::frag_picker::scores
• SecondarySimilarityOP : protocols::frag_picker::scores
• SecondaryStructureCOP : core::fragment
• SecondaryStructureCountFilterCOP : protocols::fldsgn::filters
• SecondaryStructureCountFilterOP : protocols::fldsgn::filters
• SecondaryStructureEnergyCreator_registrator : core::init
• SecondaryStructureFilterCOP : protocols::fldsgn::filters
• SecondaryStructureFilterOP : protocols::fldsgn::filters
• SecondaryStructureHasResidueFilterCOP : protocols::fldsgn::filters
• SecondaryStructureHasResidueFilterOP : protocols::fldsgn::filters
• SecondaryStructureMetricCOP : core::simple_metrics::metrics
• SecondaryStructureMetricOP : core::simple_metrics::metrics
• SecondaryStructureOP : core::fragment
• SecondaryStructurePoolCOP : protocols::frag_picker::quota
• SecondaryStructurePoolOP : protocols::frag_picker::quota
• SecondaryStructurePotentialCOP : core::scoring
• SecondaryStructurePotentialOP : core::scoring
• SecondaryStructureSegmentFeaturesCOP : protocols::features
• SecondaryStructureSegmentFeaturesOP : protocols::features
• SecondaryStructureSelectorCOP : core::select::residue_selector
• SecondaryStructureSelectorOP : core::select::residue_selector
• SecondaryStructureType : protocols::loops::loop_closure::ccd
• SecretionPredictionFilterCOP : protocols::simple_filters
• SecretionPredictionFilterOP : protocols::simple_filters
• SecStructFinderCOP : protocols::ncbb
• SecStructFinderCreatorCOP : protocols::ncbb
• SecStructFinderCreatorOP : protocols::ncbb
• SecStructFinderOP : protocols::ncbb
• SecStructGenAP : core::fragment::picking_old::vall::gen
• SecStructGenCAP : core::fragment::picking_old::vall::gen
• SecStructGenCOP : core::fragment::picking_old::vall::gen
• SecStructGenOP : core::fragment::picking_old::vall::gen
• SecStructMinimizeMoverCOP : protocols::ncbb
• SecStructMinimizeMoverCreatorCOP : protocols::ncbb
• SecStructMinimizeMoverCreatorOP : protocols::ncbb
• SecStructMinimizeMoverOP : protocols::ncbb
• section() : protocols::sparta
• secx : protocols::hybridization
• secy : protocols::hybridization
• see_edge_or_core_or_loop_or_short_edge() : protocols::features::strand_assembly
• see_whether_model_is_H_bonded_by_terminal_strands() : protocols::legacy_sewing
• see_whether_sheet_is_antiparallel() : protocols::features::strand_assembly
• see_whether_sheets_can_be_combined() : protocols::features::strand_assembly
• see_whether_this_sw_has_SS_bond() : protocols::features::strand_assembly
• SeedFoldTreeCOP : protocols::seeded_abinitio
• SeedFoldTreeOP : protocols::seeded_abinitio
• SegmentAP : protocols::denovo_design::components
• SegmentCAP : protocols::denovo_design::components
• SegmentContactOrderScorerCOP : protocols::sewing::scoring
• SegmentContactOrderScorerCreatorCOP : protocols::sewing::scoring
• SegmentContactOrderScorerCreatorOP : protocols::sewing::scoring
• SegmentContactOrderScorerOP : protocols::sewing::scoring
• SegmentCOP : protocols::denovo_design::components
• SegmentCOPs : protocols::denovo_design::components
• SegmentedAtomPairConstraintGeneratorCOP : protocols::fold_from_loops::constraint_generator
• SegmentedAtomPairConstraintGeneratorOP : protocols::fold_from_loops::constraint_generator
• SegmentGraph : protocols::features
• SegmentInsert : protocols::protein_interface_design::movers
• SegmentInsertAP : protocols::forge::build
• SegmentInsertCAP : protocols::forge::build
• SegmentInsertCOP : protocols::forge::build
• SegmentInsertOP : protocols::forge::build
• SegmentMap : protocols::denovo_design::components
• SegmentName : protocols::denovo_design
• SegmentNameList : protocols::denovo_design
• SegmentNames : protocols::denovo_design
• SegmentNameSet : protocols::denovo_design
• SegmentOP : protocols::denovo_design::components
• SegmentOPs : protocols::denovo_design::components
• SegmentPair : protocols::denovo_design::components , protocols::legacy_sewing
• SegmentPairingCOP : protocols::denovo_design::components
• SegmentPairingCOPs : protocols::denovo_design::components
• SegmentPairingOP : protocols::denovo_design::components
• SegmentPairingOPs : protocols::denovo_design::components
• SegmentRebuild : protocols::protein_interface_design::movers
• SegmentRebuildAP : protocols::forge::build
• SegmentRebuildCAP : protocols::forge::build
• SegmentRebuildCOP : protocols::forge::build
• SegmentRebuildOP : protocols::forge::build
• SegmentResid : protocols::denovo_design::architects , protocols::denovo_design::components
• SegmentSequenceProfileMoverCOP : protocols::indexed_structure_store::movers
• SegmentSequenceProfileMoverOP : protocols::indexed_structure_store::movers
• SegmentSwap : protocols::protein_interface_design::movers
• SegmentSwapAP : protocols::forge::build
• SegmentSwapCAP : protocols::forge::build
• SegmentSwapCOP : protocols::forge::build
• SegmentSwapOP : protocols::forge::build
• SegmentVectorCOP : protocols::sewing::hashing
• SegmentVectorOP : protocols::sewing::hashing
• SegmentVertex : protocols::features
• select_best_poses() : protocols::ligand_docking
• select_cav_balls() : core::scoring::packstat
• select_coord_for_residue() : core::select::util
• select_epitope_residues() : protocols::antibody
• select_interface_residues() : protocols::interface
• select_loop_frags() : protocols::loops
• select_loop_residues() : protocols::loops
• select_RBsegments() : protocols::rbsegment_relax
• SelectByDeltaScoreOperationOP : protocols::task_operations
• SelectByDensityFitOperationCOP : protocols::task_operations
• SelectByDensityFitOperationOP : protocols::task_operations
• SelectBySASAOperationCOP : protocols::task_operations
• SelectBySASAOperationOP : protocols::task_operations
• SelectedResidueCountMetricCOP : core::simple_metrics::metrics
• SelectedResidueCountMetricOP : core::simple_metrics::metrics
• SelectedResiduesMetricCOP : core::simple_metrics::metrics
• SelectedResiduesMetricOP : core::simple_metrics::metrics
• SelectedResiduesPyMOLMetricCOP : core::simple_metrics::metrics
• SelectedResiduesPyMOLMetricOP : core::simple_metrics::metrics
• selection_positions() : core::select::residue_selector
• selector_type : protocols::generalized_kinematic_closure::selector
• SelectorLogicParserCOP : core::select::residue_selector
• SelectorLogicParserOP : core::select::residue_selector
• SelectRDC_EvaluatorCOP : protocols::simple_filters
• SelectRDC_EvaluatorOP : protocols::simple_filters
• SelectResiduesByLayerCOP : core::select::util
• SelectResiduesByLayerOP : core::select::util
• SelectResiduesWithinChainOperationCOP : protocols::task_operations
• SelectResiduesWithinChainOperationOP : protocols::task_operations
• separate_definitions_from_comments() : update_ResidueType_enum_files
• SeparateDnaFromNonDnaCOP : protocols::dna
• SeparateDnaFromNonDnaOP : protocols::dna
• SEPTANOSE : core::chemical
• seq_design_basic : protocols::antibody::design
• seq_design_conservative : protocols::antibody::design
• seq_design_none : protocols::antibody::design
• seq_design_profile_sets : protocols::antibody::design
• seq_design_profile_sets_combined : protocols::antibody::design
• seq_design_profiles : protocols::antibody::design
• seq_design_strategy_to_enum() : protocols::antibody::design
• seq_design_strategy_to_string() : protocols::antibody::design
• seq_num_sort_criterion() : protocols::stepwise::modeler::rna
• seq_pdb_str() : protocols::dna
• seq_sep_M2 : core::scoring::hbonds
• seq_sep_M3 : core::scoring::hbonds
• seq_sep_M4 : core::scoring::hbonds
• seq_sep_MAX : core::scoring::hbonds
• seq_sep_other : core::scoring::hbonds
• seq_sep_P2 : core::scoring::hbonds
• seq_sep_P3 : core::scoring::hbonds
• seq_sep_P4 : core::scoring::hbonds
• seq_sep_PM1 : core::scoring::hbonds
• seq_to_str() : protocols::dna
• SEQADV : core::io::pdb
• seqdep_ref : core::scoring
• SeqDesignStrategyEnum : protocols::antibody::design
• SeqDesignStrategyEnum_total : protocols::antibody::design
• seqpos_is_base_step_anchor() : core::scoring::dna
• SeqprofConsensusOperationOP : protocols::task_operations
• SEQRES : core::io::pdb
• seqs_from_cmd_lines() : core::sequence
• sequence_map_from_pdbinfo() : core::pose
• sequencealign() : protocols::frag_picker::scores
• SequenceAlignmentCOP : core::sequence
• SequenceAlignmentOP : core::sequence
• SequenceAnnotationCOP : core::environment
• SequenceAnnotationOP : core::environment
• SequenceClaimAP : protocols::topology_broker::claims
• SequenceClaimCAP : protocols::topology_broker::claims
• SequenceClaimCOP : protocols::topology_broker::claims
• SequenceClaimerAP : protocols::topology_broker
• SequenceClaimerCAP : protocols::topology_broker
• SequenceClaimerCOP : protocols::topology_broker
• SequenceClaimerOP : protocols::topology_broker
• SequenceClaimOP : protocols::topology_broker::claims
• SequenceClaims : protocols::topology_broker::claims
• SequenceConstraintCOP : core::scoring::aa_composition_energy
• SequenceConstraintOP : core::scoring::aa_composition_energy
• SequenceCOP : core::sequence
• SequenceCoupling1BDConstraintCOP : protocols::constraints_additional
• SequenceCoupling1BDConstraintOP : protocols::constraints_additional
• SequenceCouplingConstraintCOP : protocols::constraints_additional
• SequenceCouplingConstraintOP : protocols::constraints_additional
• SequenceCouplingCOP : core::sequence
• SequenceCouplingCreator_registrator : core::init
• SequenceCouplingOP : core::sequence
• SequenceCreatorCOP : core::sequence
• SequenceCreatorOP : core::sequence
• SequenceDependentRefEnergyCOP : core::energy_methods
• SequenceDependentRefEnergyOP : core::energy_methods
• SequenceFactoryOP : core::io::silent
• SequenceMapping : protocols::stepwise::monte_carlo::submotif
• SequenceMappingCOP : core::id
• SequenceMappingOP : core::id
• SequenceMetricCOP : core::simple_metrics::metrics , protocols::multistage_rosetta_scripts::cluster::metrics
• SequenceMetricMode : core::simple_metrics::metrics
• SequenceMetricOP : core::simple_metrics::metrics , protocols::multistage_rosetta_scripts::cluster::metrics
• SequenceMotifTaskOperationCOP : protocols::task_operations
• SequenceMotifTaskOperationOP : protocols::task_operations
• SequenceMoverCOP : protocols::moves
• SequenceMoverOP : protocols::moves
• SequenceNumberResolverAP : protocols::topology_broker
• SequenceNumberResolverCAP : protocols::topology_broker
• SequenceNumberResolverCOP : protocols::topology_broker
• SequenceNumberResolverOP : protocols::topology_broker
• SequenceOP : core::sequence
• SequenceProfileConstraintCOP : core::scoring::constraints
• SequenceProfileConstraintCreator_registrator : core::init
• SequenceProfileConstraintOP : core::scoring::constraints
• SequenceProfileCOP : core::sequence
• SequenceProfileCreator_registrator : core::init
• SequenceProfileMoverCOP : protocols::simple_moves
• SequenceProfileMoverOP : protocols::simple_moves
• SequenceProfileOP : core::sequence
• SequenceRecoveryFilterCOP : protocols::protein_interface_design::filters
• SequenceRecoveryFilterOP : protocols::protein_interface_design::filters
• SequenceRecoveryMetricCOP : protocols::analysis::simple_metrics
• SequenceRecoveryMetricOP : protocols::analysis::simple_metrics
• SequenceScores : protocols::dna
• SequenceSecStructPair : protocols::rna::denovo::coarse
• SequenceSimilarityMetricCOP : core::simple_metrics::metrics
• SequenceSimilarityMetricOP : core::simple_metrics::metrics
• SequenceSymmetricAnnealerOP : core::pack::annealer
• SEQUENTIAL : core::conformation::symmetry
• SequentialSymmetrySliderCOP : protocols::symmetry
• SequentialSymmetrySliderOP : protocols::symmetry
• seqx : protocols::hybridization
• seqy : protocols::hybridization
• serialize_graph_json() : protocols::legacy_sewing
• serialize_ids() : protocols::features
• serialize_residue_xyz_coords() : protocols::features
• serialized_loops_from_string() : protocols::loops
• SERIALIZED_POSE_FILE : protocols::jd2::JobInputterInputSource
• SerializedLoopList : protocols::loops
• SerializedPoseJobInputterOP : protocols::jd2
• SerializedPoseJobOutputterOP : protocols::jd2
• SeriesJacobiansCOP : core::kinematics::jacobian
• SeriesJacobiansOP : core::kinematics::jacobian
• SeriesJacobianTypeEnum : core::kinematics::jacobian
• set : protocols::generalized_kinematic_closure::perturber
• set_asymm_unit_fold_tree() : core::conformation::symmetry , core::pose::symmetry
• set_backbone_bin : protocols::generalized_kinematic_closure::perturber
• set_base_partner() : core::scoring::dna
• set_base_segment_chainbreak_constraints() : protocols::dna
• set_bb_movemap() : protocols::hydrate
• set_bb_torsion() : core::pose
• set_bfactors_from_atom_id_map() : core::pose
• set_bondangle : protocols::generalized_kinematic_closure::perturber
• set_bondlength : protocols::generalized_kinematic_closure::perturber
• set_CCD_torsions_to_zero() : protocols::stepwise::modeler::rna
• set_chi_according_to_coordinates() : core::conformation
• set_constraints() : protocols::rbsegment_relax
• set_dew_waters_not_to_be_included() : protocols::hydrate
• set_difference() : protocols::denovo_design , protocols::stepwise::modeler::rna
• set_dihedral : protocols::generalized_kinematic_closure::perturber
• set_dihedrals() : protocols::denovo_design::components
• set_dihedrals_from_linkage_conformer_data() : core::pose::carbohydrates
• set_extended_torsions() : protocols::loops
• set_extended_torsions_and_idealize_loops() : protocols::loops
• set_externally_generated_packer_solution() : core::pack::interaction_graph
• set_fold_tree_from_symm_data() : core::conformation::symmetry
• set_full_model_info() : core::pose::full_model_info
• set_gaussian_stdevs() : protocols::recces::scratch
• set_gaussian_stdevs_recces_turner() : protocols::recces
• set_gaussian_stdevs_recces_turner_from_secstruct() : protocols::recces
• set_gaussian_stdevs_recces_turner_legacy() : protocols::recces
• set_gaussian_stdevs_thermal_sampler() : protocols::recces
• set_glycan_iupac_bb_torsions() : core::pose::carbohydrates
• set_glycan_iupac_chi_torsions() : core::pose::carbohydrates
• set_glycosidic_torsion() : core::conformation::carbohydrates , core::pose::carbohydrates
• set_jumps() : protocols::ligand_docking
• set_ligpose_rotamer() : protocols::match
• set_local_movemap() : protocols::vip
• set_loop_cutpoint_in_pose_fold_tree() : protocols::loops
• set_loop_pose() : protocols::generalized_kinematic_closure
• set_map_data() : protocols::denovo_design::components
• set_mmtf_default_options() : core::io::mmtf
• set_model_index_if_not_empty() : core::io::mmtf
• set_move_map_for_centroid_loop() : protocols::loops
• set_native_cdr_sequence() : protocols::antibody::design
• set_native_in_mover() : protocols::jd2
• set_nucleotide_to_A_form() : protocols::stepwise::legacy::modeler::rna
• set_output_res_and_chain() : core::pose
• set_pose_and_scorefxn_for_edens_scoring() : protocols::electron_density
• set_pose_secstruct() : core::select::residue_selector
• set_protocol_and_batch_id() : protocols::features
• set_r_array() : core::scoring::fiber_diffraction
• set_r_inv_array() : core::scoring::fiber_diffraction
• set_rb_constraints() : protocols::rbsegment_relax
• set_reasonable_fold_tree() : core::pose
• set_repulsive_bb_cores() : protocols::ligand_docking
• set_residue_pair_xform() : core::scoring::motif
• set_rna_secstruct_legacy() : core::pose::rna::secstruct_legacy
• set_rotamer_sampling_data_for_RLT() : core::pack::task::operation
• set_sampler_gaussian_stdev() : protocols::recces
• set_scorefxn_from_tag() : protocols::loop_modeling::utilities
• set_secstruct_from_dssp() : protocols::loops
• set_secstruct_from_psipred_ss2() : protocols::loops
• set_single_loop_fold_tree() : protocols::forge::methods , protocols::loops
• set_sphere() : protocols::ligand_docking
• set_ss_from_phipsi() : core::pose
• set_task_and_movemap() : protocols::hydrate
• set_task_factory_from_tag() : protocols::loop_modeling::utilities
• set_task_with_de_novo_water_using_resfile() : protocols::hydrate
• set_to_origin() : protocols::toolbox::rigid_body
• set_union() : protocols::stepwise::modeler::rna
• set_up_mapfile_reassignments_from_commandline() : core::chemical
• set_up_packer_palette() : core::pack::task
• set_up_params_for_move() : protocols::stepwise::monte_carlo::mover
• set_vdw_cached_rep_screen_info() : protocols::scoring
• set_vdw_cached_rep_screen_info_from_pose() : protocols::scoring
• set_water_info_and_add_de_novo_water() : protocols::hydrate
• set_water_numbers_to_zero() : protocols::magnesium
• set_xyz_coord() : protocols::fibril
• SetAACompositionPotential_AP : protocols::fldsgn
• SetAACompositionPotential_CAP : protocols::fldsgn
• SetAACompositionPotential_COP : protocols::fldsgn
• SetAACompositionPotential_OP : protocols::fldsgn
• SetCatalyticResPackBehaviorCOP : protocols::enzdes
• SetCatalyticResPackBehaviorOP : protocols::enzdes
• SetChiMoverCOP : protocols::simple_moves::sidechain_moves
• SetChiMoverOP : protocols::simple_moves::sidechain_moves
• SetCrystWeightMover_subelement_ct_name() : protocols::cryst
• SetIGTypeOperationCOP : protocols::task_operations
• SetIGTypeOperationOP : protocols::task_operations
• SetMembraneCenterMoverCOP : protocols::membrane
• SetMembraneCenterMoverOP : protocols::membrane
• SetMembraneNormalMoverCOP : protocols::membrane
• SetMembraneNormalMoverOP : protocols::membrane
• SetMembranePositionMoverCOP : protocols::membrane
• SetMembranePositionMoverOP : protocols::membrane
• setPoseExtraScore() : core::pose
• SetResidueAliasMoverCOP : protocols::denovo_design::movers
• SetResidueAliasMoverOP : protocols::denovo_design::movers
• SetReturningPackRotamersMoverCOP : protocols::minimization_packing
• SetReturningPackRotamersMoverOP : protocols::minimization_packing
• SetRotamerCouplingsCreator_registrator : core::init
• SetRotamerCouplingsOP : core::pack::task::operation
• SetRotamerLinksCreator_registrator : core::init
• SetRotamerLinksOP : core::pack::task::operation
• SetSecStructEnergies_AP : protocols::fldsgn::potentials
• SetSecStructEnergies_CAP : protocols::fldsgn::potentials
• SetSecStructEnergies_COP : protocols::fldsgn::potentials
• SetSecStructEnergies_OP : protocols::fldsgn::potentials
• SetTemperatureFactorCOP : protocols::protein_interface_design::movers
• SetTemperatureFactorOP : protocols::protein_interface_design::movers
• SetTorsionCOP : protocols::simple_moves
• SetTorsionOP : protocols::simple_moves
• setup_A_LH_foldtree() : protocols::antibody
• setup_aa2name() : core::chemical
• setup_aa2oneletter() : core::chemical
• setup_atom_id_map() : core::pose::copydofs
• setup_atom_id_map_match_atom_names() : core::pose::copydofs
• setup_atom_links() : core::conformation
• setup_atom_pair_constraints() : protocols::medal
• setup_atom_type_reassignments_from_commandline() : core::chemical
• setup_atomic_charge_reassignments_from_commandline() : core::chemical
• setup_base_pair_constraints() : core::pose::rna
• setup_bgres_cops() : core::pack
• setup_bulge_jump_point() : protocols::stepwise::legacy::modeler::rna
• setup_cdr_template() : protocols::tcr
• setup_cdr_template_from_db() : protocols::tcr
• setup_cdr_template_from_pdbid() : protocols::tcr
• setup_centroid_constraints() : protocols::hybridization
• setup_centroid_scatter() : core::scoring::fiber_diffraction
• setup_chain_break_jump_point() : protocols::stepwise::legacy::modeler::rna
• setup_chain_break_variants() : protocols::stepwise::modeler::rna
• setup_coarse_chainbreak_constraints() : protocols::rna::denovo
• setup_conformer_map() : protocols::motifs
• setup_constraints() : protocols::hybridization , protocols::medal , protocols::star
• setup_convergence_checks_from_cmdline() : protocols::canonical_sampling::mc_convergence_checks
• setup_coordinate_constraints() : protocols::medal
• setup_copy_DOF_input() : protocols::stepwise::legacy::modeler::rna
• setup_corresponding_atoms() : core::conformation
• setup_cylindrical_coords() : core::scoring::fiber_diffraction
• setup_disconnected() : protocols::rbsegment_relax
• setup_dme_point_graph() : protocols::simple_moves
• setup_dock_jump() : protocols::docking
• setup_dof_mask_from_move_map() : core::pose
• setup_dof_to_torsion_map() : core::pose
• setup_edges_for_partner() : protocols::docking
• setup_element2name() : core::chemical::element
• setup_existing_glycans() : core::pose::carbohydrates
• setup_faraggi_map() : protocols::frag_picker
• setup_filter_stats() : protocols::ncbb
• setup_fold_trees() : core::import_pose
• setup_foldtree() : protocols::docking
• setup_foldtree_from_anchors() : protocols::membrane
• setup_foldtree_pose_com() : protocols::membrane
• setup_for_density_scoring() : core::import_pose
• setup_for_dna() : protocols::relax
• setup_form_factors() : core::scoring::fiber_diffraction
• setup_fullatom_constraints() : protocols::hybridization
• setup_fw_template() : protocols::tcr
• setup_fw_template_from_db() : protocols::tcr
• setup_fw_template_from_pdbid() : protocols::tcr
• setup_geometric_attribute_list() : protocols::toolbox::match_enzdes_util
• setup_glycosylation_foldtree() : protocols::glycopeptide_docking
• setup_icoor_reassignments_from_commandline() : core::chemical
• setup_jumps() : core::import_pose
• setup_LH_A_foldtree() : protocols::antibody
• setup_links() : core::conformation
• setup_links_simple() : core::conformation
• setup_matching_atoms_with_given_names() : core::scoring
• setup_matching_CA_atoms() : core::scoring
• setup_matching_heavy_atoms() : core::scoring
• setup_matching_protein_backbone_heavy_atoms() : core::scoring
• setup_membrane_topology() : protocols::relax
• setup_name2aa() : core::chemical
• setup_name2element() : core::chemical::element
• setup_name2type() : protocols::frag_picker
• setup_oneletter2aa() : core::chemical
• setup_orientation_template() : protocols::tcr
• setup_packer() : protocols::mpi_refinement
• setup_packer_task() : protocols::antibody
• setup_patch_atomic_charge_reassignments_from_commandline() : core::chemical
• setup_pert_foldtree() : protocols::ncbb
• setup_pose_from_rbsegs() : protocols::rbsegment_relax
• setup_pose_input_stream() : protocols::stepwise::modeler::protein
• setup_pose_rbsegs_keep_loops() : protocols::rbsegment_relax
• setup_pose_setup_class() : protocols::stepwise::legacy::modeler::rna
• setup_pose_with_moving_residue_alternative_list() : protocols::stepwise::modeler::rna::rigid_body
• setup_protein_backbone_atom_id_map() : protocols::stepwise::modeler::protein
• setup_rmsd_atom_names() : core::scoring
• setup_rna_working_parameters() : protocols::stepwise::legacy::modeler::rna
• setup_sampler() : protocols::stepwise::sampler::rna
• setup_score() : protocols::abinitio::abscript , protocols::star
• setup_simple_fold_tree() : protocols::stepwise::legacy::modeler::rna
• setup_simple_full_length_rna_working_parameters() : protocols::stepwise::legacy::modeler::rna
• setup_single_loop_double_arm_remodeling_foldtree() : protocols::grafting
• setup_single_loop_single_arm_remodeling_foldtree() : protocols::grafting
• setup_star_topology() : protocols::rbsegment_relax
• setup_suite_atom_id_map() : protocols::stepwise::modeler::rna
• setup_symmetric_conformation() : core::conformation::symmetry
• setup_template_from_pdbfile() : protocols::tcr
• setup_three_prime_phosphate_based_on_next_residue() : core::pose::rna
• setup_type2name() : protocols::frag_picker
• setup_unified_stepwise_modeler() : protocols::stepwise::monte_carlo::mover
• setup_user_coordinate_constraints() : protocols::hybridization
• setup_user_defined_jumps() : core::import_pose
• setup_vall_cheating_fragments() : protocols::frags
• setup_vall_fragments() : protocols::frags
• setup_vary_polar_hydrogen_geometry() : protocols::simple_moves
• setup_vary_rna_bond_geometry() : protocols::simple_moves
• setup_water_bank_for_magnesiums() : core::import_pose
• setup_water_builders_for_residue_type() : core::scoring::lkball
• setup_working_parameters_explicit() : protocols::stepwise::modeler::working_parameters
• setup_working_parameters_for_swa() : protocols::stepwise::modeler::working_parameters
• SetupForDensityScoringMoverOP : protocols::electron_density
• SetupForFibrilMoverCOP : protocols::fibril
• SetupForFibrilMoverOP : protocols::fibril
• SetupForSequenceSymmetryMoverCOP : protocols::symmetry
• SetupForSequenceSymmetryMoverOP : protocols::symmetry
• SetupForSymmetryMoverCOP : protocols::symmetry
• SetupForSymmetryMoverOP : protocols::symmetry
• SetupHotspotConstraintsLoopsMoverCOP : protocols::protein_interface_design::movers
• SetupHotspotConstraintsLoopsMoverOP : protocols::protein_interface_design::movers
• SetupHotspotConstraintsMoverCOP : protocols::protein_interface_design::movers
• SetupHotspotConstraintsMoverOP : protocols::protein_interface_design::movers
• SetupMetalsMoverCOP : protocols::simple_moves
• SetupMetalsMoverOP : protocols::simple_moves
• SetupNCSMoverCOP : protocols::symmetry
• SetupNCSMoverOP : protocols::symmetry
• SetupPB : protocols::pb_potential
• SetupPBCreator : protocols::pb_potential
• SetupPoissonBoltzmannPotentialAP : core::scoring
• SetupPoissonBoltzmannPotentialCAP : core::scoring
• SetupPoissonBoltzmannPotentialCOP : core::scoring
• SetupPoissonBoltzmannPotentialOP : core::scoring
• SewGraphCOP : protocols::legacy_sewing
• SewGraphOP : protocols::legacy_sewing
• SewSegmentCOP : protocols::legacy_sewing
• SewSegmentOP : protocols::legacy_sewing
• SF_ReplicaCOP : protocols::toolbox
• SF_ReplicaOP : protocols::toolbox
• SFHEADER_SCORE_LINE : core::io::silent
• SFHEADER_SCORE_TYPE_LINE : core::io::silent
• SFHEADER_SEQUENCE_LINE : core::io::silent
• sfr_to_sd() : core::io::mmtf
• sfrs_to_sd() : core::io::mmtf
• Sg : core::chemical::element
• SG_CONNECT : core::chemical
• SG_Dist_FuncOP : core::scoring::disulfides
• sgn() : core::io::pose_from_sfr
• SGSG_Dihedral_FuncOP : core::scoring::disulfides
• ShakeStructureMoverCOP : protocols::simple_moves
• ShakeStructureMoverOP : protocols::simple_moves
• SHAPE_1M7 : core::pose::rna
• ShapeComplementarityCalculatorCOP : core::scoring::sc
• ShapeComplementarityCalculatorOP : core::scoring::sc
• ShapeComplementarityFilterCOP : protocols::simple_filters
• ShapeComplementarityFilterOP : protocols::simple_filters
• ShapeSimilarityCalculatorCOP : core::scoring::sc
• ShapeSimilarityCalculatorOP : core::scoring::sc
• ShapeSimilarityMetricCOP : core::simple_metrics::metrics
• ShapeSimilarityMetricOP : core::simple_metrics::metrics
• share_axis_atoms() : core::scoring::power_diagram
• SharedSilentDataOP : core::io::silent
• SharedSilentDataType : core::io::silent
• ShearFreePeptideMoverCOP : protocols::backbone_moves::local_backbone_mover::free_peptide_movers
• ShearFreePeptideMoverOP : protocols::backbone_moves::local_backbone_mover::free_peptide_movers
• ShearMinCCDTrialCOP : protocols::loops::loop_mover::refine
• ShearMinCCDTrialOP : protocols::loops::loop_mover::refine
• ShearMoverCOP : protocols::simple_moves
• ShearMoverOP : protocols::simple_moves
• SHEET : core::io::pdb
• sheet : core::scoring
• SheetConstraintGeneratorCOP : protocols::fldsgn
• SheetConstraintGeneratorOP : protocols::fldsgn
• SheetCOP : protocols::fldsgn::topology
• SheetDBAP : protocols::denovo_design::components
• SheetDBCAP : protocols::denovo_design::components
• SheetDBCOP : protocols::denovo_design::components
• SheetDBOP : protocols::denovo_design::components
• SheetFoldType : protocols::fldsgn::topology
• SheetList : protocols::denovo_design::components
• SheetOP : protocols::fldsgn::topology
• SheetRemodelConstraintGeneratorCOP : protocols::fldsgn
• SheetRemodelConstraintGeneratorOP : protocols::fldsgn
• Sheets : protocols::fldsgn::topology
• SheetSamplerCOP : protocols::loop_grower
• SheetSamplerOP : protocols::loop_grower
• SheetSetCOP : protocols::fldsgn::topology
• SheetSetOP : protocols::fldsgn::topology
• SheetTopologyFilterCOP : protocols::fldsgn::filters
• SheetTopologyFilterOP : protocols::fldsgn::filters
• SheetTranslateCOP : protocols::nonlocal
• SheetTranslateOP : protocols::nonlocal
• shift_jump_numbers_in_dofs() : core::conformation::symmetry
• shift_jumps() : protocols::forge::methods
• SHOBuriedUnsatisfiedPolarsCalculatorCOP : protocols::pose_metric_calculators
• SHOBuriedUnsatisfiedPolarsCalculatorOP : protocols::pose_metric_calculators
• short_ss_loop_filter() : protocols::evolution::AlignmentCleanerTools
• ShortBackrubMoverCOP : protocols::simple_moves
• ShortBackrubMoverOP : protocols::simple_moves
• shortest_path() : core::chemical
• ShortestPathInFoldTreeAP : core::kinematics
• ShortestPathInFoldTreeCOP : core::kinematics
• ShortestPathInFoldTreeOP : core::kinematics
• ShortLoopClosureCOP : protocols::loops::loop_closure::ccd
• ShortLoopClosureOP : protocols::loops::loop_closure::ccd
• ShortRangeTwoBodyEnergyCOP : core::scoring::methods
• ShortRangeTwoBodyEnergyOP : core::scoring::methods
• ShortSize : core
• ShortToRealAngle() : protocols::loophash
• ShouldItCount() : core::scoring
• SHOVE_BB : core::chemical
• show_accuracy_report() : protocols::rna::movers
• show_adjacent_nt_connections() : core::pose
• SHOW_ALL_TRIALS : protocols::viewer::graphics_states_param
• show_atom_tree() : core::conformation
• SHOW_BACKBONE : protocols::viewer::graphics_states_param
• show_base_pair_params() : core::scoring::dna
• show_base_pair_params_with_z_scores() : core::scoring::dna
• show_base_step_params() : core::scoring::dna
• SHOW_BBSPHERES : protocols::viewer::graphics_states_param
• SHOW_BEST : protocols::viewer::graphics_states_param
• SHOW_CARTOON : protocols::viewer::graphics_states_param
• show_detail() : core::scoring
• show_dna_geometry() : protocols::dna
• show_dna_geometry_extra_details() : protocols::dna
• show_foldtree() : core::conformation::symmetry
• SHOW_H : protocols::viewer::graphics_states_param
• SHOW_LOW : protocols::viewer::graphics_states_param
• SHOW_MC_TRIALS : protocols::viewer::graphics_states_param
• show_new_base_step_params() : core::scoring::dna
• SHOW_NO_H : protocols::viewer::graphics_states_param
• SHOW_NOBB : protocols::viewer::graphics_states_param
• SHOW_NOSC : protocols::viewer::graphics_states_param
• show_residue_connections() : core::io::pose_from_sfr
• show_scorefxn_weight_lines() : protocols::stepwise::modeler::rna
• SHOW_SCSPHERES : protocols::viewer::graphics_states_param
• SHOW_STICK : protocols::viewer::graphics_states_param
• show_water_hb_network() : protocols::hydrate
• SHOW_WIREFRAME : protocols::viewer::graphics_states_param
• ShowHState : protocols::viewer::graphics_states_param
• Si : core::chemical::element
• SIALIC_ACID : core::chemical
• SICFastCOP : protocols::sic_dock
• SICFastOP : protocols::sic_dock
• side1 : protocols::analysis
• side2 : protocols::analysis
• SIDECHAIN : protocols::noesy_assign
• SIDECHAIN_AMINE : core::chemical
• SIDECHAIN_CONJUGATION : core::chemical
• sidechain_neighbors : core::scoring
• sidechain_rmsd_filter_tracer() : protocols::simple_filters
• SIDECHAIN_THIOL : core::chemical
• SidechainContactDistCutoffCOP : protocols::frag_picker
• SidechainContactDistCutoffOP : protocols::frag_picker
• SideChainCopierCOP : protocols::stepwise::modeler::packer
• SideChainCopierOP : protocols::stepwise::modeler::packer
• SidechainMCMoverCOP : protocols::simple_moves::sidechain_moves
• SidechainMCMoverOP : protocols::simple_moves::sidechain_moves
• SidechainMinMoverCOP : protocols::docking
• SidechainMinMoverOP : protocols::docking
• SidechainMoverBaseCOP : protocols::simple_moves::sidechain_moves
• SidechainMoverBaseOP : protocols::simple_moves::sidechain_moves
• SidechainMoverCOP : protocols::simple_moves::sidechain_moves
• SidechainMoverOP : protocols::simple_moves::sidechain_moves
• SidechainNeighborCountMetricCOP : core::simple_metrics::per_residue_metrics
• SidechainNeighborCountMetricOP : core::simple_metrics::per_residue_metrics
• SidechainStateAssignmentCOP : core::pack::scmin
• SidechainStateAssignmentOP : core::pack::scmin
• SIGMA : core::scoring::nmr
• SIGMA_ATOM : core::chemical
• sigmoid() : core::scoring::epr_deer , protocols::noesy_assign
• SigmoidCOP : protocols::calc_taskop_filters
• SigmoidFuncCOP : core::scoring::func
• SigmoidFuncOP : core::scoring::func
• sigmoidish_neighbor() : core::scoring::packing
• sigmoidish_neighbor_deriv() : core::scoring::packing
• SigmoidOP : protocols::calc_taskop_filters
• SigmoidWeightedCenListRealOP : core::scoring
• SigmoidWeightedCenListVectorOP : core::scoring
• SILENT_FILE : protocols::cluster::calibur , protocols::jd2::JobInputterInputSource
• SilentEnergy_sort_by_name() : core::io::silent
• SilentFileDataOP : core::io::silent
• SilentFileFullModelInputterCOP : protocols::jd3::full_model_inputters
• SilentFileFullModelInputterOP : protocols::jd3::full_model_inputters
• SilentFileHeaderLine : core::io::silent
• SilentFileJobInputterOP : protocols::jd2
• SilentFileJobOutputterOP : protocols::jd2
• SilentFileOptionsCOP : core::io::silent
• SilentFileOptionsOP : core::io::silent
• SilentFilePoseInputStreamOP : core::import_pose::pose_stream
• SilentFilePoseInputterCOP : protocols::jd3::pose_inputters
• SilentFilePoseInputterOP : protocols::jd3::pose_inputters
• SilentFilePoseOutputSpecificationCOP : protocols::jd3::pose_outputters
• SilentFilePoseOutputSpecificationOP : protocols::jd3::pose_outputters
• SilentFilePoseOutputterCOP : protocols::jd3::pose_outputters
• SilentFilePoseOutputterOP : protocols::jd3::pose_outputters
• SilentObserverOP : protocols::viewer
• SilentStructCOP : core::io::silent
• SilentStructCreatorCOP : core::io::silent
• SilentStructCreatorOP : core::io::silent
• SilentStructFactoryOP : core::io::silent
• SilentStructOP : core::io::silent
• SilentStructOPs : core::io::silent
• SilentStructStoreCOP : protocols::wum
• SilentStructStoreOP : protocols::wum
• SilentTrajectoryRecorderOP : protocols::canonical_sampling
• SimAnnealerBaseOP : core::pack::annealer
• SimPDBOP : protocols::cluster::calibur
• simple_fold_tree() : protocols::antibody , protocols::antibody_legacy , protocols::star
• simple_mapping_from_file() : core::sequence
• simple_metric_composite_real_data : core::io::mmtf
• simple_metric_composite_string_data : core::io::mmtf
• simple_metric_per_residue_real_data : core::io::mmtf
• simple_metric_per_residue_real_output : core::io::mmtf
• simple_metric_per_residue_string_data : core::io::mmtf
• simple_metric_per_residue_string_output : core::io::mmtf
• simple_metric_real_data : core::io::mmtf
• simple_metric_string_data : core::io::mmtf
• simple_numeric_deriv_check() : core::optimization
• simple_one_loop_fold_tree() : protocols::antibody , protocols::antibody_legacy
• SIMPLE_POSE_SELECTION : protocols::stepwise::screener
• SIMPLE_RMSD : protocols::stepwise::screener
• simple_visualize_fold_tree() : core::kinematics
• simple_visualize_fold_tree_and_movemap() : core::kinematics
• simple_visualize_fold_tree_and_movemap_bb_chi() : core::kinematics
• SimpleCycpepPredictApplicationCOP : protocols::cyclic_peptide_predict
• SimpleCycpepPredictApplicationCOPs : protocols::cyclic_peptide_predict
• SimpleCycpepPredictApplicationOP : protocols::cyclic_peptide_predict
• SimpleCycpepPredictApplicationOPs : protocols::cyclic_peptide_predict
• SimpleDerivCheckResultCOP : core::optimization
• SimpleDerivCheckResultOP : core::optimization
• SimpleGlycosylateMoverCOP : protocols::carbohydrates
• SimpleGlycosylateMoverOP : protocols::carbohydrates
• SimpleHbondsToAtomFilterCOP : protocols::simple_filters
• SimpleHbondsToAtomFilterOP : protocols::simple_filters
• SimpleInteractionGraphCOP : core::pack::interaction_graph
• SimpleInteractionGraphOP : core::pack::interaction_graph
• SimpleMetricCOP : core::simple_metrics
• SimpleMetricCreatorCOP : core::simple_metrics
• SimpleMetricCreatorOP : core::simple_metrics
• SimpleMetricDataAP : core::simple_metrics
• SimpleMetricDataCAP : core::simple_metrics
• SimpleMetricDataCOP : core::simple_metrics
• SimpleMetricDataOP : core::simple_metrics
• SimpleMetricFeaturesCOP : protocols::features
• SimpleMetricFeaturesOP : protocols::features
• SimpleMetricFilterCOP : protocols::simple_filters
• SimpleMetricFilterOP : protocols::simple_filters
• SimpleMetricOP : core::simple_metrics
• SimpleMetricSelectorCOP : core::select::residue_selector
• SimpleMetricSelectorOP : core::select::residue_selector
• SimpleNodeManagerCOP : protocols::jd3::dag_node_managers
• SimpleNodeManagerOP : protocols::jd3::dag_node_managers
• SimplePoseSelectionCOP : protocols::stepwise::legacy::screener
• SimplePoseSelectionOP : protocols::stepwise::legacy::screener
• SimpleRMSD_ScreenerCOP : protocols::stepwise::legacy::screener
• SimpleRMSD_ScreenerOP : protocols::stepwise::legacy::screener
• SimpleSequenceCreator_registrator : core::init
• simplesequencedata : core::io::silent
• SimpleSequenceDataOP : core::io::silent
• SimpleThreadingMoverCOP : protocols::simple_moves
• SimpleThreadingMoverOP : protocols::simple_moves
• SimpleTreeBuilderCOP : protocols::nonlocal
• SimpleTreeBuilderOP : protocols::nonlocal
• simplifyWhiteSpace() : protocols::sparta
• Simulated4PDEERTraceCOP : core::scoring::epr_deer
• Simulated4PDEERTraceFactoryCOP : core::scoring::epr_deer
• Simulated4PDEERTraceFactoryOP : core::scoring::epr_deer
• Simulated4PDEERTraceOP : core::scoring::epr_deer
• SimulatedTemperingCOP : protocols::canonical_sampling
• SimulatedTemperingOP : protocols::canonical_sampling , protocols::moves
• Single : protocols::canonical_sampling
• single : protocols::pdbinfo_manipulations
• SINGLE_GLYCAN : protocols::viewer::graphics_states_param
• single_ligand_motif_from_stream() : protocols::motifs
• single_motif_from_filename() : protocols::motifs
• single_motif_from_stream() : protocols::motifs
• SINGLE_NMR_VALUE_WEIGHTING : core::scoring::nmr
• single_residue_from_stream() : protocols::motifs
• SingleBasicRotamerLibraryCOP : core::pack::rotamers
• SingleBasicRotamerLibraryCreator_registrator : core::init
• SingleBasicRotamerLibraryCreatorCOP : core::pack::rotamers
• SingleBasicRotamerLibraryCreatorOP : core::pack::rotamers
• SingleBasicRotamerLibraryOP : core::pack::rotamers
• SingleBond : core::chemical
• SingleBondOrder : core::chemical
• SingleCenrotRotamerLibraryCreator_registrator : core::init
• SingleDownstreamResidueWriterCOP : protocols::match::output
• SingleDownstreamResidueWriterOP : protocols::match::output
• SingleFileBufferCOP : protocols::jd2
• SingleFileBufferOP : protocols::jd2
• SingleFragmentMoverCOP : protocols::nonlocal
• SingleFragmentMoverOP : protocols::nonlocal
• SingleGridCOP : protocols::qsar::scoring_grid
• SingleGridOP : protocols::qsar::scoring_grid
• SingleJobOutputPair : protocols::jd3
• SingleLigandRotamerLibraryAP : core::pack::rotamers
• SingleLigandRotamerLibraryCAP : core::pack::rotamers
• SingleLigandRotamerLibraryCOP : core::pack::rotamers
• SingleLigandRotamerLibraryCreator_registrator : core::init
• SingleLigandRotamerLibraryCreatorCOP : core::pack::rotamers
• SingleLigandRotamerLibraryCreatorOP : core::pack::rotamers
• SingleLigandRotamerLibraryOP : core::pack::rotamers
• SingleLoopMoverCOP : protocols::loops::loop_mover
• SingleLoopMoverOP : protocols::loops::loop_mover
• SingleMotifCOP : protocols::motifs
• SingleMotifCOPs : protocols::motifs
• SingleMotifOP : protocols::motifs
• SingleMotifOPs : protocols::motifs
• SingleNCAARotamerLibraryCreator_registrator : core::init
• SingleNCAARotamerLibraryCreatorCOP : core::pack::rotamers
• SingleNCAARotamerLibraryCreatorOP : core::pack::rotamers
• SingleResidueCenrotLibraryAP : core::pack::dunbrack::cenrot
• SingleResidueCenrotLibraryCAP : core::pack::dunbrack::cenrot
• SingleResidueCenrotLibraryCOP : core::pack::dunbrack::cenrot
• SingleResidueCenrotLibraryCreatorCOP : core::pack::dunbrack::cenrot
• SingleResidueCenrotLibraryCreatorOP : core::pack::dunbrack::cenrot
• SingleResidueCenrotLibraryOP : core::pack::dunbrack::cenrot
• SingleResidueDunbrackLibraryAP : core::pack::dunbrack
• SingleResidueDunbrackLibraryCAP : core::pack::dunbrack
• SingleResidueDunbrackLibraryCOP : core::pack::dunbrack
• SingleResidueDunbrackLibraryCreator_registrator : core::init
• SingleResidueDunbrackLibraryCreatorCOP : core::pack::dunbrack
• SingleResidueDunbrackLibraryCreatorOP : core::pack::dunbrack
• SingleResidueDunbrackLibraryOP : core::pack::dunbrack
• SingleResidueFragDataCOP : core::fragment
• SingleResidueFragDataOP : core::fragment
• SingleResidueInvrotTargetCOP : protocols::toolbox::match_enzdes_util
• SingleResidueInvrotTargetOP : protocols::toolbox::match_enzdes_util
• SingleResidueRotamerLibraryAP : core::pack::rotamers
• SingleResidueRotamerLibraryCAP : core::pack::rotamers
• SingleResidueRotamerLibraryCOP : core::pack::rotamers
• SingleResidueRotamerLibraryCreatorCOP : core::pack::rotamers
• SingleResidueRotamerLibraryCreatorOP : core::pack::rotamers
• SingleResidueRotamerLibraryOP : core::pack::rotamers
• SingleResidueTorsionFragmentLibraryOP : protocols::frags
• SingleStateCOP : protocols::multistate_design
• SingleStateCOPs : protocols::multistate_design
• SingleStateFitnessFunctionCOP : protocols::multistate_design
• SingleStateFitnessFunctionOP : protocols::multistate_design
• SingleStateOP : protocols::multistate_design
• SingleStateOPs : protocols::multistate_design
• SingleStructureDataCOP : protocols::optimize_weights
• SingleStructureDataOP : protocols::optimize_weights
• SingleStructureDataOPs : protocols::optimize_weights
• SITE : core::io::pdb
• site_constraint : core::scoring
• SiteConstraintCOP : core::scoring::constraints
• SiteConstraintCreator_registrator : core::init
• SiteConstraintOP : core::scoring::constraints
• SiteConstraintResiduesCOP : core::scoring::constraints
• SiteConstraintResiduesCreator_registrator : core::init
• SiteConstraintResiduesOP : core::scoring::constraints
• sixA_offset : core::energy_methods
• sixA_slope : core::energy_methods
• SixDTransRotPotentialCOP : core::scoring::loop_graph::evaluator
• SixDTransRotPotentialEvaluatorCOP : core::scoring::loop_graph::evaluator
• SixDTransRotPotentialEvaluatorOP : core::scoring::loop_graph::evaluator
• SixDTransRotPotentialOP : core::scoring::loop_graph::evaluator
• Size : core , protocols::fldsgn::potentials::sspot , protocols::flxbb
• Size3 : protocols::match
• Size4 : core::pack::dunbrack , protocols::match
• Size5 : core::pack::dunbrack
• SizeCR : core::pose::motif
• SIZED : protocols::toolbox
• SIZED_ANY : protocols::toolbox
• SIZED_COMB : protocols::toolbox
• SizeDIET : protocols::jd3::standard
• SizeInSegmentsRequirementCOP : protocols::sewing::requirements
• SizeInSegmentsRequirementCreatorCOP : protocols::sewing::requirements
• SizeInSegmentsRequirementCreatorOP : protocols::sewing::requirements
• SizeInSegmentsRequirementOP : protocols::sewing::requirements
• SizeList : protocols::abinitio , protocols::noesy_assign
• SizePair : protocols::denovo_design
• Sizes : core::scoring::motif , protocols::frags , protocols::kinmatch , protocols::sic_dock::scores , protocols::sic_dock
• SizeValuedParameterAP : core::conformation::parametric
• SizeValuedParameterCAP : core::conformation::parametric
• SizeValuedParameterCAPs : core::conformation::parametric
• SizeValuedParameterCOP : core::conformation::parametric
• SizeValuedParameterCOPs : core::conformation::parametric
• SizeValuedParameterOP : core::conformation::parametric
• SizeValuedParameterOPs : core::conformation::parametric
• SizeVectorValuedParameterAP : core::conformation::parametric
• SizeVectorValuedParameterCAP : core::conformation::parametric
• SizeVectorValuedParameterCAPs : core::conformation::parametric
• SizeVectorValuedParameterCOP : core::conformation::parametric
• SizeVectorValuedParameterCOPs : core::conformation::parametric
• SizeVectorValuedParameterOP : core::conformation::parametric
• SizeVectorValuedParameterOPs : core::conformation::parametric
• skip_rate : protocols::loops
• skip_redundant_constraints() : core::scoring::constraints
• slc : protocols::cluster::calibur
• sleep() : protocols::stepwise::modeler::rna
• slice() : protocols::stepwise::modeler
• slice_out_pose() : protocols::stepwise::modeler
• SliceIter : core::scoring::packstat
• SliceMode : core::select::residue_selector::slice_enums
• SliceResidueSelectorCOP : core::select::residue_selector
• SliceResidueSelectorOP : core::select::residue_selector
• Slices : core::scoring::packstat
• SliceToMiniProteinMoverCOP : protocols::pose_creation
• SliceToMiniProteinMoverOP : protocols::pose_creation
• slide_into_contact_and_score() : protocols::sic_dock
• slide_into_contact_and_score_DEPRICATED() : protocols::sic_dock
• slide_jump() : protocols::denovo_design
• slide_together_tracer() : protocols::ligand_docking
• SlideCriteriaType : core::conformation::symmetry
• SlideIntoContactCOP : protocols::docking
• SlideIntoContactOP : protocols::docking
• SlideType : core::conformation::symmetry
• SlidingWindowLoopClosureCOP : protocols::loops::loop_closure::ccd
• SlidingWindowLoopClosureOP : protocols::loops::loop_closure::ccd
• slope_12 : core::energy_methods
• slope_6 : core::energy_methods
• Sm : core::chemical::element
• SMALL_OVERLAP : core::scoring::motif
• SmallBBSamplerCOP : protocols::simple_moves::bb_sampler
• SmallBBSamplerOP : protocols::simple_moves::bb_sampler
• SmallFragWeightAP : protocols::topology_broker::weights
• SmallFragWeightCAP : protocols::topology_broker::weights
• SmallFragWeightCOP : protocols::topology_broker::weights
• SmallFragWeightOP : protocols::topology_broker::weights
• smallmer_from_largemer() : protocols::forge::methods
• SmallMinCCDTrialCOP : protocols::loops::loop_mover::refine
• SmallMinCCDTrialOP : protocols::loops::loop_mover::refine
• SmallMoveKinematicPerturberCOP : protocols::loops::loop_closure::kinematic_closure
• SmallMoveKinematicPerturberOP : protocols::loops::loop_closure::kinematic_closure
• SmallMoverCOP : protocols::simple_moves
• SmallMoverOP : protocols::simple_moves
• SmartAssemblyCOP : protocols::sewing::data_storage
• SmartAssemblyOP : protocols::sewing::data_storage
• SmartFixbbSimAnnealerOP : core::pack::annealer
• SmartSegmentCOP : protocols::sewing::data_storage
• SmartSegmentOP : protocols::sewing::data_storage
• SmartSewingResidueCOP : protocols::sewing::data_storage
• SmartSewingResidueOP : protocols::sewing::data_storage
• SMM_BASE_NAME : core::simple_metrics::metrics
• SMM_END_OF_LIST : core::simple_metrics::metrics
• SMM_FULL_NAME : core::simple_metrics::metrics
• SMM_INVALID_MODE : core::simple_metrics::metrics
• SMM_ONELETTER_CODE : core::simple_metrics::metrics
• SMM_THREELETTER_CODE : core::simple_metrics::metrics
• SmoothCenPairEnergyCreator_registrator : core::init
• SmoothEnvEnergyCreator_registrator : core::init
• SmoothEnvPairPotentialCOP : core::scoring
• SmoothEnvPairPotentialOP : core::scoring
• SmoothFragmentMoverCOP : protocols::simple_moves
• SmoothFragmentMoverOP : protocols::simple_moves
• SmoothFragWeightAP : protocols::topology_broker::weights
• SmoothFragWeightCAP : protocols::topology_broker::weights
• SmoothFragWeightCOP : protocols::topology_broker::weights
• SmoothFragWeightOP : protocols::topology_broker::weights
• SmoothStepFuncCOP : core::scoring::func
• SmoothStepFuncOP : core::scoring::func
• SmoothSymmetricFragmentMoverCOP : protocols::simple_moves
• SmoothSymmetricFragmentMoverOP : protocols::simple_moves
• Sn : core::chemical::element
• SnugDock : protocols::docking
• SnugDockCOP : protocols::antibody::snugdock
• SnugDockOP : protocols::antibody::snugdock
• SnugDockProtocolCOP : protocols::antibody::snugdock
• SnugDockProtocolOP : protocols::antibody::snugdock
• SoedingFuncOP : core::scoring::func
• SOFT_REP_DESIGN_WTS : core::scoring
• SOFT_REP_WTS : core::scoring
• softSanitize() : core::chemical::rdkit
• SOGFunc_ImplOP : core::scoring::func
• SOGFuncOP : core::scoring::func
• SOLID_STATE_NMR : core::io::rcsb
• SOLUTION_NMR : core::io::rcsb
• SOLUTION_SCATTERING : core::io::rcsb
• SOLUTION_SCATTERING_THEORETICAL_MODEL : core::io::rcsb
• SolutionList : protocols::kinematic_closure
• SolutionPickerCOP : protocols::kinematic_closure::solution_pickers
• SolutionPickerOP : protocols::kinematic_closure::solution_pickers
• SolvationGridCOP : protocols::qsar::scoring_grid
• SolvationGridOP : protocols::qsar::scoring_grid
• SOLVENT : core::chemical
• sort_by_binding() : protocols::ligand_docking
• SORT_BY_CIS_PEPTIDE_BONDS : protocols::cyclic_peptide_predict
• SORT_BY_ENERGIES : protocols::cyclic_peptide_predict
• SORT_BY_HBONDS : protocols::cyclic_peptide_predict
• sort_by_length() : protocols::fldsgn::topology
• SORT_BY_RMSD : protocols::cyclic_peptide_predict
• sort_by_second() : protocols::ligand_docking
• sort_copy_dofs() : protocols::stepwise::modeler::rna
• sort_function() : protocols::frag_picker
• sort_jobsummaries_list() : protocols::cyclic_peptide_predict
• sort_new_rotamers_into_rotset_vector() : core::pack::rotamer_set
• sort_numerically_ascending() : protocols::ddg
• sort_pair_list() : protocols::stepwise::legacy::modeler::rna
• sort_patchop_by_name() : core::chemical
• sort_pose_by_score() : core::pose
• sort_PoseWithScore() : protocols::abinitio
• sort_residue_type_pointers_by_name() : protocols::toolbox::match_enzdes_util
• sort_scores() : protocols::frag_picker::scores
• sort_seq_num_list() : protocols::stepwise::modeler::rna
• sort_xbond_func() : core::io::mmtf
• SOURCE : core::io::pdb
• SourcePositionsOP : protocols::rna::denovo::coarse
• SOUTH : core::chemical::rna
• SP2_HYBRID : core::chemical
• SP3_HYBRID : core::chemical
• SpacegroupSetting : protocols::cryst
• spacers : core::sequence
• span_ins : core::scoring
• SpanCOP : core::conformation::membrane
• spanfile_name() : core::conformation::membrane
• spanfile_names() : core::conformation::membrane
• SpanningTopologyCOP : core::conformation::membrane
• SpanningTopologyOP : core::conformation::membrane
• SpanOP : core::conformation::membrane
• SPARSE : core::select::residue_selector::slice_enums
• SPAtomCIter : core::scoring::packstat
• SPAtomIter : core::scoring::packstat
• SPAtoms : core::scoring::packstat
• spearman() : protocols::ligand_docking
• SPECIAL_ROT : core::chemical
• special_rot : core::scoring
• SPECIAL_SEGMENTS_OBSERVER : core::pose::datacache
• SpecialPackerPaletteBehaviour : core::pack::palette
• SpecialRotamerEnergyOP : protocols::scoring::methods
• SpecialRotamerRSOCOP : protocols::toolbox::rotamer_set_operations
• SpecialRotamerRSOOP : protocols::toolbox::rotamer_set_operations
• SpecialSegmentsObserverCOP : core::pose::datacache
• SpecialSegmentsObserverOP : core::pose::datacache
• SpecificResiduesNearInterfaceFilterCOP : protocols::protein_interface_design::filters
• SpecificResiduesNearInterfaceFilterOP : protocols::protein_interface_design::filters
• SPHERE_MODE_BB : protocols::viewer
• SPHERE_MODE_LIGAND : protocols::viewer
• SPHERE_MODE_SC : protocols::viewer
• SphereCIter : core::scoring::packstat
• SphereIter : core::scoring::packstat
• spheremode : protocols::viewer
• Spheres : core::scoring::packstat
• spherical() : protocols::fldsgn::potentials::sspot
• spin_down : protocols::pack_daemon
• SpinAroundPartnerMoverCOP : protocols::membrane
• SpinAroundPartnerMoverOP : protocols::membrane
• SPINLABEL : core::chemical
• SpinlabelDatabaseEntryCOP : core::io::nmr
• SpinlabelDatabaseEntryOP : core::io::nmr
• SpinlabelDatabaseHandlerCOP : core::io::nmr
• SpinlabelDatabaseHandlerOP : core::io::nmr
• SpliceCOP : protocols::splice
• SpliceIn_complex_type_name_for_subsubtag() : protocols::splice
• SpliceIn_complex_type_name_for_subtag() : protocols::splice
• SpliceInAntibody_complex_type_name_for_subsubtag() : protocols::splice
• SpliceInAntibody_complex_type_name_for_subtag() : protocols::splice
• SpliceInAntibodyCOP : protocols::splice
• SpliceInAntibodyOP : protocols::splice
• SpliceInCOP : protocols::splice
• SpliceInOP : protocols::splice
• SpliceInTail_complex_type_name_for_subsubtag() : protocols::splice
• SpliceInTail_complex_type_name_for_subtag() : protocols::splice
• SpliceInTailCOP : protocols::splice
• SpliceInTailOP : protocols::splice
• SpliceManagerCOP : protocols::splice
• SpliceManagerOP : protocols::splice
• SpliceOP : protocols::splice
• SpliceOut_complex_type_name_for_subsubtag() : protocols::splice
• SpliceOut_complex_type_name_for_subtag() : protocols::splice
• SpliceOutAntibody_complex_type_name_for_subsubtag() : protocols::splice
• SpliceOutAntibody_complex_type_name_for_subtag() : protocols::splice
• SpliceOutAntibodyCOP : protocols::splice
• SpliceOutAntibodyOP : protocols::splice
• SpliceOutCOP : protocols::splice
• SpliceOutOP : protocols::splice
• SpliceOutTail_complex_type_name_for_subsubtag() : protocols::splice
• SpliceOutTail_complex_type_name_for_subtag() : protocols::splice
• SpliceOutTailCOP : protocols::splice
• SpliceOutTailOP : protocols::splice
• SpliceSegmentCOP : protocols::splice
• SpliceSegmentOP : protocols::splice
• spline_coeffs() : core::scoring::electron_density
• SplineFuncCOP : core::scoring::func
• SplineFuncOP : core::scoring::func
• SPLIT : core::io::pdb
• split() : protocols::sparta
• split_by_ca_ca_dist() : protocols::loops
• split_by_resSeq() : protocols::loops
• split_mid_ranges() : protocols::fold_from_loops::utils
• split_pose() : protocols::stepwise::modeler
• split_segments_longer_than_6mers() : core::fragment::rna
• split_sequence_motif() : core::sequence
• split_string_based_on_inserts() : protocols::pdbinfo_manipulations
• split_topology_by_chain_noshift() : protocols::membrane
• split_topology_by_jump() : protocols::membrane
• split_topology_by_jump_noshift() : protocols::membrane
• SPLIT_UNFOLDED_BOLTZ : core::scoring
• SPLIT_UNFOLDED_ELE : core::scoring
• SPLIT_UNFOLDED_MEAN : core::scoring
• SPLIT_UNFOLDED_MEDIAN : core::scoring
• SPLIT_UNFOLDED_MM : core::scoring
• SPLIT_UNFOLDED_MODE() : core::scoring
• SPLIT_UNFOLDED_PDB() : core::scoring
• SPLIT_UNFOLDED_ROSETTA : core::scoring
• split_unfolded_two_body : core::scoring
• SPLIT_UNFOLDED_UNIQUE : core::scoring
• SPLIT_UNFOLDED_USER_DEFINED() : core::scoring
• split_up_remark_line() : protocols::toolbox::match_enzdes_util
• split_WhiteSpace() : protocols::sparta
• SplitAndMixPoseMoverCOP : protocols::fold_from_loops::movers
• SplitAndMixPoseMoverOP : protocols::fold_from_loops::movers
• SplitLine : core::scoring::epr_deer
• SplitLineMap : core::scoring::epr_deer
• SplitLines : core::scoring::epr_deer
• SplitUnfoldedTwoBodyEnergyCreator_registrator : core::init
• SplitUnfoldedTwoBodyEnergyOP : core::energy_methods
• SplitUnfoldedTwoBodyPotentialOP : core::scoring
• SPRSDE : core::io::pdb
• SQ() : core::energy_methods
• sqr() : core::energy_methods , core::scoring::motif , core::scoring::packing , core::scoring , protocols::cartesian , protocols::kinmatch , protocols::loophash , protocols::sic_dock
• square() : core::scoring::electron_density , core::scoring::electron_density_atomwise , core::scoring::fiber_diffraction , protocols::rbsegment_relax
• square_planar_metal : protocols::cyclic_peptide
• square_pyramidal_metal : protocols::cyclic_peptide
• SquarePlanarMetal_HelperCOP : protocols::cyclic_peptide::crosslinker
• SquarePlanarMetal_HelperOP : protocols::cyclic_peptide::crosslinker
• SquarePyramidalMetal_HelperCOP : protocols::cyclic_peptide::crosslinker
• SquarePyramidalMetal_HelperOP : protocols::cyclic_peptide::crosslinker
• SquareWell2FuncCOP : core::scoring::func
• SquareWell2FuncOP : core::scoring::func
• SquareWellFuncCOP : core::scoring::func
• SquareWellFuncOP : core::scoring::func
• Sr : core::chemical::element
• Srfp_complex_type_name_for_subsubtag() : protocols::splice
• Srfp_complex_type_name_for_subtag() : protocols::splice
• SRI : core::chemical
• SRLZ_file : core::import_pose
• SS_BaseCOP : protocols::fldsgn::topology
• SS_BaseOP : protocols::fldsgn::topology
• ss_contact_worst : core::scoring
• ss_index() : protocols::frag_picker::quota
• SS_Info2_COP : protocols::fldsgn::topology
• SS_Info2_OP : protocols::fldsgn::topology
• SS_InfoCOP : core::scoring
• SS_InfoOP : core::scoring
• SS_Killhairpins_InfoCOP : core::scoring
• SS_Killhairpins_InfoOP : core::scoring
• ss_length_check() : protocols::frags
• ss_pair : core::scoring
• SS_predictorAP : protocols::ss_prediction
• SS_predictorCAP : protocols::ss_prediction
• SS_predictorCOP : protocols::ss_prediction
• SS_predictorOP : protocols::ss_prediction
• SSBOND : core::io::pdb
• SSElementBisectddGFilterCOP : protocols::simple_ddg
• SSElementBisectddGFilterOP : protocols::simple_ddg
• SSElementLengthFilterCOP : protocols::simple_filters
• SSElementLengthFilterOP : protocols::simple_filters
• SSElementMotifContactEnergyCreator_registrator : core::init
• SSElementMotifContactFilterCOP : protocols::simple_filters
• SSElementMotifContactFilterOP : protocols::simple_filters
• SSElementSelectorCOP : core::select::residue_selector
• SSElementSelectorOP : core::select::residue_selector
• SSFeatureCOP : protocols::comparative_modeling::features
• SSFeatureOP : protocols::comparative_modeling::features
• SSize : core
• SSManagerCOP : core::sequence
• SSManagerOP : core::sequence
• SSMotifFinderCOP : protocols::simple_filters
• SSMotifFinderOP : protocols::simple_filters
• SSPairPotentialOP : protocols::fldsgn::potentials::sspot
• SSPredictionFilterCOP : protocols::denovo_design::filters
• SSPredictionFilterOP : protocols::denovo_design::filters
• SSShapeComplementarityFilterAP : protocols::denovo_design::filters
• SSShapeComplementarityFilterCAP : protocols::denovo_design::filters
• SSShapeComplementarityFilterCOP : protocols::denovo_design::filters
• SSShapeComplementarityFilterOP : protocols::denovo_design::filters
• SSType : protocols::comparative_modeling::features
• stack_elec : core::scoring
• stack_elec_base_base : core::scoring
• stack_elec_base_bb : core::scoring
• STACK_ELEC_NBLIST : core::scoring::EnergiesCacheableDataType
• StackElecEnergyCreator_registrator : core::init
• STAGE_1 : protocols::abinitio
• STAGE_2 : protocols::abinitio
• STAGE_3 : protocols::abinitio
• STAGE_3a : protocols::abinitio
• STAGE_3b : protocols::abinitio
• STAGE_4 : protocols::abinitio
• StageID : protocols::abinitio::abscript , protocols::abinitio
• StageIDs : protocols::abinitio::abscript
• StagePreparerCOP : protocols::abinitio::abscript
• StagePreparerOP : protocols::abinitio::abscript
• StandardInnerLarvalJobCOP : protocols::jd3::standard
• StandardInnerLarvalJobOP : protocols::jd3::standard
• StandardInnerLarvalJobs : protocols::jd3::standard
• StandardJobQueenCOP : protocols::jd3::standard
• StandardJobQueenOP : protocols::jd3::standard
• StandardNPDHBondInteractionGraph : core::pack::interaction_graph
• StandardNPDHBondInteractionGraphOP : core::pack::interaction_graph
• StandardPairingLibraryCOP : protocols::jumping
• StandardPairingLibraryOP : protocols::jumping
• StandardPivotsCOP : protocols::kinematic_closure::pivot_pickers
• StandardPivotsOP : protocols::kinematic_closure::pivot_pickers
• StandardPoseJobSummaryCOP : protocols::jd3::job_summaries
• StandardPoseJobSummaryOP : protocols::jd3::job_summaries
• StandardResultOutputterCOP : protocols::jd3::output
• StandardResultOutputterOP : protocols::jd3::output
• star_fold_tree() : protocols::protein_interface_design
• StarAbinitio_main() : protocols::star
• StarAbinitioCOP : protocols::star
• StarAbinitioOP : protocols::star
• start : protocols::loops
• START_BLOCK() : protocols::jd2
• start_cdr_loop : protocols::antibody
• start_sig : core::energy_methods
• start_sig2 : core::energy_methods
• StartFromOP : protocols::ligand_docking
• StartingNodeMotifScorerCOP : protocols::sewing::scoring
• StartingNodeMotifScorerCreatorCOP : protocols::sewing::scoring
• StartingNodeMotifScorerCreatorOP : protocols::sewing::scoring
• StartingNodeMotifScorerOP : protocols::sewing::scoring
• StarTreeBuilderCOP : protocols::nonlocal
• StarTreeBuilderOP : protocols::nonlocal
• StartStructClaimerAP : protocols::topology_broker
• StartStructClaimerCAP : protocols::topology_broker
• StartStructClaimerCOP : protocols::topology_broker
• StartStructClaimerOP : protocols::topology_broker
• StateAccumulatingMatchFilterCOP : protocols::match::output
• StateAccumulatingMatchFilterOP : protocols::match::output
• StatEntries : protocols::abinitio
• StatEntryList : protocols::abinitio
• static_batch_id_map_ : protocols::features
• static_protocol_id_ : protocols::features
• StatsType : protocols::moves
• steal_alignment() : core::sequence
• steal_constant_length_frag_set_from_pose() : core::fragment
• steal_frag_set_from_pose() : core::fragment
• steal_ligands() : protocols::comparative_modeling
• StealLigandMoverCOP : protocols::comparative_modeling
• StealLigandMoverOP : protocols::comparative_modeling
• StealSideChainsMoverCOP : protocols::comparative_modeling
• StealSideChainsMoverOP : protocols::comparative_modeling
• StemFinderCOP : protocols::simple_filters
• StemFinderOP : protocols::simple_filters
• stepwise_addable_pose_residue() : core::pose
• stepwise_addable_residue() : core::pose
• StepWiseBasicModelerOptionsCOP : protocols::stepwise::modeler::options
• StepWiseBasicModelerOptionsOP : protocols::stepwise::modeler::options
• StepWiseBasicOptionsCOP : protocols::stepwise::options
• StepWiseBasicOptionsOP : protocols::stepwise::options
• StepWiseBasicWorkingParametersCOP : protocols::stepwise::modeler::working_parameters
• StepWiseBasicWorkingParametersOP : protocols::stepwise::modeler::working_parameters
• StepWiseClustererCOP : protocols::stepwise::modeler::align
• StepWiseClustererOP : protocols::stepwise::modeler::align
• StepWiseConnectionSamplerCOP : protocols::stepwise::modeler
• StepWiseConnectionSamplerOP : protocols::stepwise::modeler
• StepWiseLegacyClustererCOP : protocols::stepwise::modeler::align
• StepWiseLegacyClustererOP : protocols::stepwise::modeler::align
• StepWiseLegacyClustererSilentBasedCOP : protocols::stepwise::modeler::align
• StepWiseLegacyClustererSilentBasedOP : protocols::stepwise::modeler::align
• StepWiseMasterMoverCOP : protocols::stepwise::monte_carlo::mover
• StepWiseMasterMoverOP : protocols::stepwise::monte_carlo::mover
• StepWiseMasterPackerCOP : protocols::stepwise::modeler::packer
• StepWiseMasterPackerOP : protocols::stepwise::modeler::packer
• StepWiseMinimizerCOP : protocols::stepwise::modeler
• StepWiseMinimizerOP : protocols::stepwise::modeler
• StepWiseModelerCOP : protocols::stepwise::modeler
• StepWiseModelerOP : protocols::stepwise::modeler
• StepWiseModelerOptionsCOP : protocols::stepwise::modeler::options
• StepWiseModelerOptionsOP : protocols::stepwise::modeler::options
• StepWiseMonteCarloCOP : protocols::stepwise::monte_carlo
• StepWiseMonteCarloOP : protocols::stepwise::monte_carlo
• StepWiseMonteCarloOptionsCOP : protocols::stepwise::monte_carlo::options
• StepWiseMonteCarloOptionsOP : protocols::stepwise::monte_carlo::options
• StepWiseMoveCOP : protocols::stepwise::monte_carlo::mover
• StepWiseMoveOP : protocols::stepwise::monte_carlo::mover
• StepWiseMoveSelectorCOP : protocols::stepwise::monte_carlo::mover
• StepWiseMoveSelectorOP : protocols::stepwise::monte_carlo::mover
• StepWiseMoveSelectorOptionsCOP : protocols::stepwise::monte_carlo::mover::options
• StepWiseMoveSelectorOptionsOP : protocols::stepwise::monte_carlo::mover::options
• StepWisePackerCOP : protocols::stepwise::modeler::packer
• StepWisePackerOP : protocols::stepwise::modeler::packer
• StepWisePoseAlignerCOP : protocols::stepwise::modeler::align
• StepWisePoseAlignerOP : protocols::stepwise::modeler::align
• StepWiseProteinCCD_CloserCOP : protocols::stepwise::modeler::protein::loop_close
• StepWiseProteinCCD_CloserOP : protocols::stepwise::modeler::protein::loop_close
• StepWiseProteinCCD_MultiPoseCloserCOP : protocols::stepwise::modeler::protein::loop_close
• StepWiseProteinCCD_MultiPoseCloserOP : protocols::stepwise::modeler::protein::loop_close
• StepWiseProteinMinimizerCOP : protocols::stepwise::legacy::modeler::protein
• StepWiseProteinMinimizerOP : protocols::stepwise::legacy::modeler::protein
• StepWiseProteinModelerOptionsCOP : protocols::stepwise::modeler::options
• StepWiseProteinModelerOptionsOP : protocols::stepwise::modeler::options
• StepWiseProteinPoseSetupCOP : protocols::stepwise::legacy::modeler::protein
• StepWiseProteinPoseSetupOP : protocols::stepwise::legacy::modeler::protein
• StepWiseResiduePairScreenerCOP : protocols::stepwise::screener
• StepWiseResiduePairScreenerOP : protocols::stepwise::screener
• StepWiseRNA_CombineLongLoopFiltererOP : protocols::stepwise::modeler::rna
• StepWiseRNA_CombineLongLoopFiltererpCOP : protocols::stepwise::modeler::rna
• StepWiseRNA_MinimizerCOP : protocols::stepwise::legacy::modeler::rna
• StepWiseRNA_MinimizerOP : protocols::stepwise::legacy::modeler::rna
• StepWiseRNA_ModelerOptionsCOP : protocols::stepwise::modeler::options
• StepWiseRNA_ModelerOptionsOP : protocols::stepwise::modeler::options
• StepWiseRNA_PoseSelectionCOP : protocols::stepwise::legacy::modeler::rna
• StepWiseRNA_PoseSelectionOP : protocols::stepwise::legacy::modeler::rna
• StepWiseRNA_PoseSetupCOP : protocols::stepwise::legacy::modeler::rna
• StepWiseRNA_PoseSetupOP : protocols::stepwise::legacy::modeler::rna
• StepWiseSampleAndScreenCOP : protocols::stepwise
• StepWiseSampleAndScreenOP : protocols::stepwise
• StepWiseSamplerCombOP : protocols::stepwise::sampler
• StepWiseSamplerCOP : protocols::stepwise::sampler
• StepWiseSamplerOneDOFOP : protocols::stepwise::sampler
• StepWiseSamplerOneTorsionOP : protocols::stepwise::sampler
• StepWiseSamplerOneValueCombOP : protocols::stepwise::sampler
• StepWiseSamplerOneValueOP : protocols::stepwise::sampler
• StepWiseSamplerOP : protocols::stepwise::sampler
• StepWiseSamplerRingConformerOP : protocols::stepwise::sampler
• StepWiseSamplerSizedAnyOP : protocols::stepwise::sampler
• StepWiseSamplerSizedCombOP : protocols::stepwise::sampler
• StepWiseSamplerSizedOP : protocols::stepwise::sampler
• StepWiseScreenerCOP : protocols::stepwise::screener
• StepWiseScreenerOP : protocols::stepwise::screener
• StepWiseScreenerType : protocols::stepwise::screener
• StepWiseWorkingParametersCOP : protocols::stepwise::modeler::working_parameters
• StepWiseWorkingParametersOP : protocols::stepwise::modeler::working_parameters
• STMStoredTaskCOP : protocols::task_operations
• STMStoredTaskOP : protocols::task_operations
• StochasticFilterCOP : protocols::filters
• StochasticFilterOP : protocols::filters
• stop : protocols::loops
• store_base_residue_type_name_in_sfr() : core::io::pdb
• store_chain_sequence_record_in_sfr() : core::io::pdb
• store_cis_peptide_record_in_sfr() : core::io::pdb
• store_connection_architect() : protocols::denovo_design::connection
• store_crystallographic_parameter_record_in_sfr() : core::io::pdb
• store_CSA_in_pose() : core::scoring
• store_DC_in_pose() : core::scoring
• store_denovo_architect() : protocols::denovo_design::architects
• store_distance_snapshot() : protocols::noesy_assign
• store_distmap_with_namedatoms() : protocols::noesy_assign
• store_formula_record_in_sfr() : core::io::pdb
• store_heterogen_name_record_in_sfr() : core::io::pdb
• store_heterogen_synonym_record_in_sfr() : core::io::pdb
• store_link_record_in_sfr() : core::io::pdb
• store_mod_res_record_in_sfr() : core::io::pdb
• store_RDC_in_pose() : core::scoring
• store_RDC_ROHL_in_pose() : core::scoring
• store_RDC_segments_in_pose() : protocols::scoring
• store_ssbond_record_in_sfr() : core::io::pdb
• store_unknown_records_in_sfr() : core::io::pdb
• StoreCombinedStoredTasksMoverCOP : protocols::task_operations
• StoreCombinedStoredTasksMoverOP : protocols::task_operations
• StoreCompoundTaskMoverCOP : protocols::task_operations
• StoreCompoundTaskMoverOP : protocols::task_operations
• StoredResidueSubsetSelectorCOP : protocols::residue_selectors
• StoredResidueSubsetSelectorOP : protocols::residue_selectors
• StoredRotamerLibraryCreator_registrator : core::init
• StoredRotamerLibrarySpecificationCOP : core::chemical::rotamers
• StoredRotamerLibrarySpecificationOP : core::chemical::rotamers
• StorePoseSnapshotCOP : protocols::simple_moves
• StorePoseSnapshotOP : protocols::simple_moves
• StoreResidueSubsetMoverCOP : protocols::residue_selectors
• StoreResidueSubsetMoverOP : protocols::residue_selectors
• StoreTaskMoverCOP : protocols::task_operations
• StoreTaskMoverOP : protocols::task_operations
• str() : protocols::kinmatch
• strand : protocols::loops::loop_closure::ccd
• strand_orientation_vector() : core::scoring::dna
• StrandArchitectCOP : protocols::denovo_design::architects
• StrandArchitectOP : protocols::denovo_design::architects
• StrandBulges : protocols::denovo_design::architects
• StrandBundleFeaturesCOP : protocols::features::strand_assembly
• StrandBundleFeaturesOP : protocols::features::strand_assembly
• StrandCOP : protocols::fldsgn::topology
• StrandCurvatureByLevelsCOP : protocols::fldsgn::filters
• StrandCurvatureByLevelsOP : protocols::fldsgn::filters
• StrandExtended : protocols::denovo_design::architects
• StrandExtensions : protocols::denovo_design::architects
• StrandHelixGeometryFilterCOP : protocols::fldsgn::filters
• StrandHelixGeometryFilterOP : protocols::fldsgn::filters
• StrandNameToNumberMap : protocols::denovo_design
• StrandOP : protocols::fldsgn::topology
• StrandOrientation : protocols::denovo_design::components
• StrandOrientations : protocols::denovo_design::components
• StrandPairingCOP : core::scoring::dssp , protocols::denovo_design::components , protocols::fldsgn::topology
• StrandPairingCOPs : protocols::denovo_design::components , protocols::fldsgn::topology
• StrandPairingOP : core::scoring::dssp , protocols::denovo_design::components , protocols::fldsgn::topology
• StrandPairingOPs : protocols::denovo_design::components
• StrandPairings : protocols::fldsgn::topology
• StrandPairingSetCOP : core::scoring::dssp , protocols::fldsgn::topology
• StrandPairingSetOP : core::scoring::dssp , protocols::fldsgn::topology
• Strands : protocols::fldsgn::topology
• Strategy : core::conformation
• streams_from_cmd_line() : core::import_pose::pose_stream
• STRICT_WC_STACKED_PAIR : core::scoring::rna
• string : core::import_pose::pose_stream
• String : core::import_pose , core::io::mmcif , core::io::pdb , core::io , protocols::flxbb
• string_from_type_set_mode() : core::chemical
• string_has_suffix() : protocols::relax
• string_join() : protocols::dna
• STRING_LIST() : core::chemical
• string_string_pair_msg : protocols::jd3::deallocation
• string_to_experimental_technique() : core::io::rcsb
• string_to_hb_eval_type() : core::scoring::hbonds
• string_to_icoord_type() : core::chemical
• string_to_int() : core::pose::rna , core::scoring::rna::chemical_shift , protocols::stepwise::modeler::rna
• string_to_real() : core::scoring::rna::chemical_shift , protocols::stepwise::modeler::rna
• string_to_size_vector() : protocols::rna::movers
• StringFilter_pair : protocols::filters
• StringList : protocols::sparta
• StringMap : protocols::denovo_design::components
• StringMetricCOP : core::simple_metrics
• StringMetricCreatorCOP : core::simple_metrics
• StringMetricCreatorOP : core::simple_metrics
• StringMetricOP : core::simple_metrics
• Strings : protocols::dna , protocols::optimize_weights
• StringUP : protocols::network
• StringVDMapping : core::chemical
• StringVec : protocols::cluster::calibur
• StringVecOP : protocols::cluster::calibur
• strip_brackets() : core::io::nmr
• strip_out_magnesiums() : protocols::magnesium
• strip_spacers() : core::sequence
• STRIP_VIRTUAL_SIDE_CHAIN : core::pack::palette
• strip_whitespace() : core::chemical::orbitals , core::scoring::packing
• STRIPEHASH : core::conformation
• StrStrMap : core::chemical::sdf
• struct_ids_from_tag() : protocols::features
• StructFileReaderOptionsCOP : core::io
• StructFileReaderOptionsOP : core::io
• StructFileRepCOP : core::io
• StructFileRepOP : core::io
• StructFileRepOptionsCOP : core::io
• StructFileRepOptionsOP : core::io
• StructFragmentMoverCOP : protocols::struct_fragment
• StructFragmentMoverOP : protocols::struct_fragment
• StructPerturberCMCOP : protocols::abinitio::abscript
• StructPerturberCMOP : protocols::abinitio::abscript
• StructProfileMoverCOP : protocols::simple_moves
• StructProfileMoverOP : protocols::simple_moves
• StructuralSimilarityEvaluatorCOP : protocols::simple_filters
• StructuralSimilarityEvaluatorOP : protocols::simple_filters
• Structure_Map : core::io::silent
• StructureArchitectCOP : protocols::denovo_design::architects
• StructureArchitectOP : protocols::denovo_design::architects
• STRUCTUREDATA_OBSERVER : core::pose::datacache
• StructureDataAP : protocols::denovo_design::components
• StructureDatabaseCOP : protocols::indexed_structure_store::search
• StructureDatabaseOP : protocols::indexed_structure_store::search
• StructureDataCAP : protocols::denovo_design::components
• StructureDataCOP : protocols::denovo_design::components
• StructureDataCOPs : protocols::denovo_design::components
• StructureDataFactoryCOP : protocols::denovo_design::components
• StructureDataFactoryOP : protocols::denovo_design::components
• StructureDataObserverAP : protocols::denovo_design::components
• StructureDataObserverCAP : protocols::denovo_design::components
• StructureDataObserverCOP : protocols::denovo_design::components
• StructureDataObserverOP : protocols::denovo_design::components
• StructureDataOP : protocols::denovo_design::components
• StructureDataOPs : protocols::denovo_design::components
• StructureDataPerturberCOP : protocols::denovo_design::components
• StructureDataPerturberCOPs : protocols::denovo_design::components
• StructureDataPerturberOP : protocols::denovo_design::components
• StructureDataPerturberOPs : protocols::denovo_design::components
• StructureDataPerturbers : protocols::denovo_design::components
• StructureFeaturesCOP : protocols::features
• StructureFeaturesOP : protocols::features
• StructureID : protocols::features
• StructureMap : core::io::raw_data
• StructureRestrictorCOP : protocols::moves
• StructureRestrictorOP : protocols::moves
• StructureScoresFeaturesCOP : protocols::features
• StructureScoresFeaturesOP : protocols::features
• StructureSlices : protocols::denovo_design::components
• StructureStoreAP : protocols::indexed_structure_store
• StructureStoreCOP : protocols::indexed_structure_store
• StructureStoreOP : protocols::indexed_structure_store
• StructureStoreProviderCOP : protocols::indexed_structure_store
• StructureStoreProviderOP : protocols::indexed_structure_store
• StruOP : protocols::cluster::calibur
• STUB_APPLIER : protocols::stepwise::screener
• STUB_DISTANCE : protocols::stepwise::screener
• stub_from_points() : protocols::hotspot_hashing
• stub_id_to_named_stub_id() : core::conformation , core::pose
• stub_tgt_angle() : protocols::hotspot_hashing
• stub_to_points() : protocols::hotspot_hashing
• StubApplierCOP : protocols::stepwise::screener
• StubApplierOP : protocols::stepwise::screener
• StubDistanceScreenerCOP : protocols::stepwise::screener
• StubDistanceScreenerOP : protocols::stepwise::screener
• StubScoreFilterCOP : protocols::protein_interface_design::filters
• StubScoreFilterOP : protocols::protein_interface_design::filters
• StubScoreLoopsFilterCOP : protocols::protein_interface_design::filters
• StubScoreLoopsFilterOP : protocols::protein_interface_design::filters
• StubStatus : protocols::hotspot_hashing
• StubStubType : core::pose::rna
• sub_to_full() : core::pose::full_model_info
• SUBMOTIF : protocols::stepwise::monte_carlo::mover
• SubMotifInfoCOP : core::pose::full_model_info
• SubMotifInfoOP : core::pose::full_model_info
• SubMotifLibraryCOP : protocols::stepwise::monte_carlo::submotif
• SubMotifLibraryOP : protocols::stepwise::monte_carlo::submotif
• SubMotifSequenceSet : protocols::stepwise::monte_carlo::submotif
• SubroutineMoverCOP : protocols::protein_interface_design::movers
• SubroutineMoverOP : protocols::protein_interface_design::movers
• SubsetPartnerMotifScorerCOP : protocols::sewing::scoring
• SubsetPartnerMotifScorerCreatorCOP : protocols::sewing::scoring
• SubsetPartnerMotifScorerCreatorOP : protocols::sewing::scoring
• SubsetPartnerMotifScorerOP : protocols::sewing::scoring
• substitute_residue() : protocols::dna
• subtag_for_backrubdd() : protocols::protein_interface_design::movers
• subtag_for_bbgrid() : protocols::helical_bundle
• subtag_for_bundgrid() : protocols::helical_bundle
• subtag_for_cyclize() : protocols::cyclic_peptide
• subtag_for_hotspothasher() : protocols::protein_interface_design::movers
• subtag_for_match_type() : protocols::fldsgn
• subtag_for_msd() : protocols::protein_interface_design::movers
• subtag_for_multiple_sigmoids() : protocols::calc_taskop_filters
• subtag_for_SetupHotspotConstraintsLoopsMover() : protocols::protein_interface_design::movers
• subtag_for_SetupHotspotConstraintsMover() : protocols::protein_interface_design::movers
• SUBTRACT : protocols::calc_taskop_filters
• subtract() : protocols::mean_field
• subtract_chi_angles() : core::pack::dunbrack
• Success : protocols::loops::loop_mover
• success_message : protocols::pack_daemon
• suck : core::scoring
• SuckerEnergyCreator_registrator : core::init
• suga : core::scoring::rna::chemical_shift
• SUGAR : core::chemical::rna
• sugar_atoms : core::chemical::rna
• sugar_bb : core::scoring
• SUGAR_INSTANTIATOR : protocols::stepwise::screener
• sugar_modifications_from_suffix() : core::io::carbohydrates
• sugar_torsion_atom_names() : core::scoring::dna
• SugarBackboneEnergyCOP : core::energy_methods
• SugarBackboneEnergyCreator_registrator : core::init
• SugarBackboneEnergyOP : core::energy_methods
• SugarBBSamplerCOP : protocols::simple_moves::bb_sampler
• SugarBBSamplerOP : protocols::simple_moves::bb_sampler
• SugarInstantiateMoverCOP : protocols::stepwise::modeler::rna::sugar
• SugarInstantiateMoverOP : protocols::stepwise::modeler::rna::sugar
• SugarInstantiatorCOP : protocols::stepwise::screener
• SugarInstantiatorOP : protocols::stepwise::screener
• SugarModelingCOP : protocols::stepwise::modeler::rna::sugar
• SugarModelingOP : protocols::stepwise::modeler::rna::sugar
• SugarModificationsNomenclatureTable : core::chemical::carbohydrates
• SugarVirtualizeMoverCOP : protocols::stepwise::modeler::rna::sugar
• SugarVirtualizeMoverOP : protocols::stepwise::modeler::rna::sugar
• suite_rmsd() : protocols::stepwise::modeler::rna
• suite_square_deviation() : protocols::stepwise::modeler::rna
• suiteness_bonus : core::scoring
• SULFATED_SUGAR : core::chemical
• SULFATION : core::chemical
• SULFOAMINO_SUGAR : core::chemical
• SULPH : protocols::match
• SUM : core::scoring::nmr
• sum : core::simple_metrics::metrics
• SUM : protocols::calc_taskop_filters
• sum_constraint_scoreterms() : protocols::enzdes::enzutil
• sum_IntraNOE() : protocols::noesy_assign
• sum_peak_volumes() : protocols::noesy_assign
• sum_total_residue_energy() : protocols::protein_interface_design
• sum_water_weights_iterator : core::energy_methods
• SumFuncOP : core::scoring::func
• summary_string_to_type() : core::simple_metrics::metrics
• summary_type : core::simple_metrics::metrics
• summary_type_total : core::simple_metrics::metrics
• superimpose() : protocols::toolbox
• superimpose_all() : protocols::mpi_refinement
• superimpose_overhangs_heavy() : protocols::grafting
• superimpose_pose() : core::scoring
• superimpose_pose_legacy() : protocols::stepwise::modeler::align
• superimpose_pose_on_subset_bb() : protocols::fibril
• superimpose_pose_on_subset_CA() : protocols::toolbox::pose_manipulation
• superimpose_with_stepwise_aligner() : protocols::stepwise::modeler::align
• SuperimposeMoverCOP : protocols::simple_moves
• SuperimposeMoverOP : protocols::simple_moves
• superposition_transform() : protocols::seeded_abinitio , protocols::toolbox
• surf_vol_available() : core::scoring::packing
• SURFACE : core::chemical
• surface : core::scoring
• SurfaceDockingProtocolOP : protocols::surface_docking
• SurfaceEnergiesCOP : core::scoring::solid_surface
• SurfaceEnergiesOP : core::scoring::solid_surface
• SurfaceEnergyCreator_registrator : core::init
• SurfaceOrientMoverOP : protocols::surface_docking
• SurfaceParametersCOP : protocols::surface_docking
• SurfaceParametersOP : protocols::surface_docking
• SurfaceVectorLoaderCOP : protocols::surface_docking
• SurfaceVectorLoaderOP : protocols::surface_docking
• SurfEnergyCreator_registrator : core::init
• SurfVolEnergyCreator_registrator : core::init
• surrogate_atom_for_orbital() : core::scoring::orbitals
• SurrogateVariableExpressionCOP : protocols::pack_daemon
• SurrogateVariableExpressionOP : protocols::pack_daemon
• SWAlignerCOP : core::sequence
• SWAlignerOP : core::sequence
• swap() : core::id
• swap4_aligned() : core::scoring::electron_density , core::scoring::electron_density_atomwise
• swap_bytes() : core::io::serialization
• swap_seqpos() : core::energy_methods
• swap_transform() : core::pose
• SWITCH_EDGE : protocols::legacy_sewing
• switch_focus_among_poses_randomly() : protocols::stepwise::modeler
• switch_focus_to_other_pose() : protocols::stepwise::modeler
• switch_to_centroid_rot_set() : core::util
• SWITCH_TO_FULLATOM : protocols::abinitio
• switch_to_residue_type_set() : core::util
• SwitchChainOrderMoverCOP : protocols::simple_moves
• SwitchChainOrderMoverOP : protocols::simple_moves
• SwitchMoverCOP : protocols::moves
• SwitchMoverOP : protocols::moves
• SwitchResidueTypeSetMoverCOP : protocols::simple_moves
• SwitchResidueTypeSetMoverOP : protocols::simple_moves
• sym_bonus_lr : core::scoring::methods
• sym_dof_jump_num() : core::pose::symmetry
• sym_dof_names() : core::pose::symmetry
• sym_lig : core::scoring
• sym_rmsd_with_super_subset() : core::scoring
• SymAtomTreeMinimizerCOP : core::optimization::symmetry
• SymAtomTreeMinimizerOP : core::optimization::symmetry
• SymDock_main() : protocols::symmetric_docking
• SymDockingHiResCOP : protocols::symmetric_docking
• SymDockingHiResOP : protocols::symmetric_docking
• SymDockingInitialPerturbationCOP : protocols::symmetry
• SymDockingInitialPerturbationOP : protocols::symmetry
• SymDockingLowResCOP : protocols::symmetric_docking
• SymDockingLowResOP : protocols::symmetric_docking
• SymDockProtocolCOP : protocols::symmetric_docking
• SymDockProtocolOP : protocols::symmetric_docking
• SymDofCOP : core::conformation::symmetry
• SymDofMoverCOP : protocols::matdes
• SymDofMoverOP : protocols::matdes
• SymDofOP : core::conformation::symmetry
• symE_bonus : core::scoring
• symECreator_registrator : core::init
• SymEnergyCutRotamerTrialsMoverCOP : protocols::minimization_packing::symmetry
• SymEnergyCutRotamerTrialsMoverOP : protocols::minimization_packing::symmetry
• SymFoldandDockMoveRbJumpMoverCOP : protocols::symmetric_docking
• SymFoldandDockMoveRbJumpMoverOP : protocols::symmetric_docking
• SymFoldandDockRbTrialMoverCOP : protocols::simple_moves::symmetry , protocols::symmetric_docking
• SymFoldandDockRbTrialMoverOP : protocols::simple_moves::symmetry , protocols::symmetric_docking
• SymFoldandDockSlideTrialMoverCOP : protocols::symmetric_docking
• SymFoldandDockSlideTrialMoverOP : protocols::symmetric_docking
• SymInterfaceSidechainMinMoverCOP : protocols::symmetric_docking
• SymInterfaceSidechainMinMoverOP : protocols::symmetric_docking
• SymmDataCOP : core::conformation::symmetry
• SymmDataLoaderCOP : core::conformation::symmetry
• SymmDataLoaderCreator_registrator : core::init
• SymmDataLoaderOP : core::conformation::symmetry
• SymmDataOP : core::conformation::symmetry
• SymmDataOptionsCOP : core::conformation::symmetry
• SymmDataOptionsOP : core::conformation::symmetry
• symmetric_components() : core::pose::symmetry
• symmetric_fold_tree() : protocols::denovo_design
• symmetric_repackable_residues() : core::pack
• symmetric_residue_subset() : protocols::denovo_design
• symmetric_rotamer_trials() : core::pack
• symmetric_secstruct() : protocols::denovo_design
• SymmetricAddMembraneMoverCOP : protocols::membrane::symmetry
• SymmetricAddMembraneMoverOP : protocols::membrane::symmetry
• SymmetricalResidueSelectorCOP : core::select::residue_selector
• SymmetricalResidueSelectorOP : core::select::residue_selector
• SymmetricConformation : core::pack
• SymmetricConformationCOP : core::conformation::symmetry
• SymmetricConformationOP : core::conformation::symmetry
• SymmetricCycpepAlignCOP : protocols::cyclic_peptide
• SymmetricCycpepAlignOP : protocols::cyclic_peptide
• SymmetricEnergiesCOP : core::scoring::symmetry
• SymmetricEnergiesOP : core::scoring::symmetry
• SymmetricFragmentMoverCOP : protocols::simple_moves
• SymmetricFragmentMoverOP : protocols::simple_moves
• SymmetricLigandEnergyCreator_registrator : core::init
• SymmetricRMSMoverCOP : protocols::symmetry
• SymmetricRMSMoverOP : protocols::symmetry
• SymmetricRotamerSet_COP : core::pack::rotamer_set::symmetry
• SymmetricRotamerSet_OP : core::pack::rotamer_set::symmetry
• SymmetricRotamerSetsCOP : core::pack::rotamer_set::symmetry
• SymmetricRotamerSetsOP : core::pack::rotamer_set::symmetry
• SymmetricScoreFunctionCOP : core::scoring::symmetry
• SymmetricScoreFunctionOP : core::scoring::symmetry
• symmetrize_fold_tree() : core::conformation::symmetry , core::pose::symmetry
• symmetrize_spans() : protocols::membrane::symmetry
• symmetrizeBfactors() : protocols::electron_density
• symmetry_info() : core::pose::symmetry
• SymmetryClaimAP : protocols::topology_broker::claims
• SymmetryClaimCAP : protocols::topology_broker::claims
• SymmetryClaimCOP : protocols::topology_broker::claims
• SymmetryClaimerAP : protocols::topology_broker
• SymmetryClaimerCAP : protocols::topology_broker
• SymmetryClaimerCOP : protocols::topology_broker
• SymmetryClaimerOP : protocols::topology_broker
• SymmetryClaimOP : protocols::topology_broker::claims
• SymmetryClaims : protocols::topology_broker::claims
• SymmetryInfo : core::pack
• SymmetryInfoCOP : core::conformation::symmetry
• SymmetryInfoOP : core::conformation::symmetry
• SymmetrySliderCOP : protocols::symmetry
• SymmetrySliderOP : protocols::symmetry
• SymmetryTransformCOP : core::conformation::symmetry
• SymmetryTransformOP : core::conformation::symmetry
• SymMinimizeInterface() : protocols::protein_interface_design
• SymMinimizerMapCOP : core::optimization::symmetry
• SymMinimizerMapOP : core::optimization::symmetry
• SymMinMoverCOP : protocols::minimization_packing::symmetry
• SymMinMoverOP : protocols::minimization_packing::symmetry
• SymmLinearMemoryInteractionGraphCOP : core::pack::interaction_graph
• SymmLinearMemoryInteractionGraphOP : core::pack::interaction_graph
• SymmMinimalistInteractionGraphCOP : core::pack::interaction_graph
• SymmMinimalistInteractionGraphOP : core::pack::interaction_graph
• SymmOnTheFlyInteractionGraphCOP : core::pack::interaction_graph
• SymmOnTheFlyInteractionGraphOP : core::pack::interaction_graph
• SymPackRotamersMoverCOP : protocols::minimization_packing::symmetry
• SymPackRotamersMoverOP : protocols::minimization_packing::symmetry
• SymRestrictTaskForDockingOP : protocols::symmetric_docking
• SymRotamerTrialsMoverCOP : protocols::minimization_packing::symmetry
• SymRotamerTrialsMoverOP : protocols::minimization_packing::symmetry
• SymShakeStructureMoverCOP : protocols::symmetry
• SymShakeStructureMoverOP : protocols::symmetry
• SymSidechainMinMoverCOP : protocols::symmetric_docking
• SymSidechainMinMoverOP : protocols::symmetric_docking
• SymSlideInfoCOP : core::conformation::symmetry
• SymSlideInfoOP : core::conformation::symmetry
• SymUnsatHbondFilterCOP : protocols::matdes
• SymUnsatHbondFilterOP : protocols::matdes
• SYN : core::chemical::rna , core::fragment::rna
• SYN_ANTI_RESTRICTION : core::fragment::rna