- p -

• p0() : protocols::features::helixAssembly::HelicalFragment
• p1() : protocols::features::helixAssembly::HelicalFragment
• p1_cosine_deriv() : core::scoring::constraints::DihedralConstraint
• p1_deriv() : core::scoring::constraints::AngleConstraint
• p1_theta_deriv() : core::scoring::constraints::AngleConstraint
• p2_cosine_deriv() : core::scoring::constraints::DihedralConstraint
• p2_deriv() : core::scoring::constraints::AngleConstraint
• P_AA() : core::scoring::P_AA
• P_AA_ABEGO3() : core::scoring::P_AA_ABEGO3
• P_AA_ABEGO3_energy() : core::scoring::P_AA_ABEGO3
• P_AA_Energy() : core::scoring::methods::P_AA_Energy
• P_AA_energy() : core::scoring::P_AA
• P_AA_initialize() : core::scoring::P_AA
• P_AA_pp_Energy() : core::scoring::methods::P_AA_pp_Energy
• P_AA_pp_energy() : core::scoring::P_AA
• P_AA_ss() : core::scoring::P_AA_ss
• P_AA_ss_Energy() : core::scoring::methods::P_AA_ss_Energy
• P_AA_ss_energy() : core::scoring::P_AA_ss
• p_atom_index() : core::chemical::rna::RNA_Info
• p_i_given_iplus1() : core::scoring::bin_transitions::BinTransitionCalculator
• p_iplus1_given_i() : core::scoring::bin_transitions::BinTransitionCalculator
• p_value() : protocols::frag_picker::scores::AdaptiveScoreHistogram
• pack() : protocols::splice::SpliceIn
• pack_all_side_chains() : protocols::stepwise::modeler::packer::StepWisePacker
• pack_and_minimize() : protocols::pose_creation::MergePDBMover
• pack_and_minimize_linker_and_sidechains() : protocols::cyclic_peptide::CrosslinkerMover
• pack_mg_water_hydrogens_in_pose() : protocols::magnesium::MgWaterHydrogenPacker
• pack_missing_sidechains() : core::import_pose::ImportPoseOptions , protocols::hybridization::MRMover
• pack_o2prime_hydrogens() : protocols::stepwise::modeler::packer::StepWisePacker
• pack_phosphate_penalty() : core::scoring::methods::FreeDOF_Options
• pack_protein_side_chains() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• pack_residue() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• pack_weights() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• packable() : protocols::protein_interface_design::filters::DesignableResiduesFilter , protocols::simple_filters::MutationsFilter , protocols::simple_filters::ResidueCountFilter
• packable_residues() : protocols::fold_from_loops::movers::NubInitioLoopClosureMover
• PackDaemon() : protocols::pack_daemon::PackDaemon
• packed_residues() : protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• packed_rotamer_2_regular_rotamer() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >
• packed_rotno() : core::pack::dunbrack::PackedDunbrackRotamer< S, N, P >
• packed_rotno_2_rotwell() : core::pack::dunbrack::SingleResidueDunbrackLibrary
• packed_rotno_2_sorted_rotno() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >
• PackedDunbrackRotamer() : core::pack::dunbrack::PackedDunbrackRotamer< S, N, P >
• packer() : protocols::stepwise::modeler::packer::StepWiseMasterPacker
• packer_loop() : protocols::ligand_docking::ga_ligand_dock::GridScorer
• packer_neighbor_graph() : core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >
• packer_palette() : core::pack::task::TaskFactory
• packer_palette_is_unpublished() : core::pack::palette::NCAADefaultPackerPalette , core::pack::palette::PackerPalette
• packer_palette_provides_citation_info() : core::pack::palette::CustomBaseTypePackerPalette , core::pack::palette::DefaultPackerPalette , core::pack::palette::PackerPalette
• packer_palette_xml_schema_group_name() : core::pack::palette::PackerPaletteFactory
• packer_task() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• PackerEnergyAdd() : core::pack::rotamer_set::symmetry::SymmetricRotamerSet_
• PackerEnergyMultiply() : core::pack::rotamer_set::symmetry::SymmetricRotamerSet_
• PackerEnergySubtract() : core::pack::rotamer_set::symmetry::SymmetricRotamerSet_
• PackerNeighborGraphFilter() : protocols::simple_filters::PackerNeighborGraphFilter
• PackerPalette() : core::pack::palette::PackerPalette
• packerpalette_loader_ct_namer() : protocols::parser::PackerPaletteLoaderCreator
• PackerPaletteFactory() : core::pack::palette::PackerPaletteFactory
• PackerPaletteLoader() : protocols::parser::PackerPaletteLoader
• PackerPaletteRegistrator() : core::pack::palette::PackerPaletteRegistrator< T >
• packertask() : protocols::flxbb::DesignTask
• PackerTask_() : core::pack::task::PackerTask_
• packing_angle_enum_to_string() : protocols::antibody::AntibodyEnumManager
• packing_angle_string_to_enum() : protocols::antibody::AntibodyEnumManager
• packing_interaction_cutoff() : core::scoring::methods::FACTSEnergy , core::scoring::methods::GenBornEnergy , core::scoring::methods::MultipoleElecEnergy , core::scoring::methods::SASAEnergy , core::scoring::methods::VdWTinkerEnergy
• packing_shell() : protocols::calc_taskop_filters::RelativePoseFilter
• packing_trials() : protocols::rna::denovo::movers::RNA_Minimizer
• PackingScore() : core::scoring::packstat::PackingScore
• PackingScoreResData() : core::scoring::packstat::PackingScoreResData
• PackingState() : protocols::multistate_design::PackingState
• PackRotamersMover() : protocols::minimization_packing::PackRotamersMover
• PackRotamersMoverLazy() : protocols::minimization_packing::PackRotamersMoverLazy
• PackRotamersMoverPartGreedy() : protocols::enzdes::PackRotamersMoverPartGreedy
• PackScreener() : protocols::stepwise::screener::PackScreener
• PackstatCalculator() : protocols::pose_metric_calculators::PackstatCalculator
• PackStatEnergy() : core::scoring::methods::PackStatEnergy
• PackStatFilter() : protocols::simple_filters::PackStatFilter
• PackStatMover() : protocols::analysis::PackStatMover
• pages() : core::fragment::picking_old::concepts::Book< Pages >
• pair_dp() : core::scoring::SecondaryStructurePotential , protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential
• pair_energy_H() : core::scoring::etable::AnalyticEtableEvaluator , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::etable::TableLookupEvaluator
• pair_energy_H_v() : core::scoring::etable::AnalyticEtableEvaluator , core::scoring::etable::EtableEvaluator , core::scoring::etable::TableLookupEvaluator
• pair_has_linkage_statistics() : core::chemical::carbohydrates::CarbohydrateInfoManager
• pair_list() : protocols::scoring::Interface
• pair_meets_starting_criteria() : protocols::hbnet::HBNet , protocols::hbnet::HBNetStapleInterface
• pair_overlap_tolerance() : protocols::match::BumpGrid
• pair_sets_with_positions() : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• pair_term_energy() : core::scoring::PairEPotential
• pair_term_energy_and_deriv() : core::scoring::PairEPotential
• pair_term_energy_exists() : core::scoring::PairEPotential
• pair_with_scaffold() : protocols::hotspot_hashing::HotspotStub , protocols::hotspot_hashing::HotspotStubSet
• paired() : core::scoring::dssp::Dssp , core::scoring::dssp::StrandPairing , core::scoring::dssp::StrandPairingSet , protocols::dna::DnaPosition
• PairedSheetResidueSelector() : protocols::denovo_design::residue_selectors::PairedSheetResidueSelector
• PairEnergy() : core::scoring::methods::PairEnergy
• PairEPotential() : core::scoring::PairEPotential
• PairFeatures() : protocols::features::PairFeatures
• PairFuncMap() : core::scoring::custom_pair_distance::PairFuncMap
• Pairing() : core::scoring::dssp::Pairing
• pairing() : protocols::abinitio::PairingStatEntry , protocols::denovo_design::components::StructureData
• pairing_group_namer() : protocols::denovo_design::architects::CompoundArchitect
• pairing_string() : protocols::denovo_design::components::HelixPairing , protocols::denovo_design::components::HelixSheetPairing , protocols::denovo_design::components::SegmentPairing , protocols::denovo_design::components::StrandPairing
• pairing_subelement_ct_namer() : protocols::denovo_design::architects::CompoundArchitect
• PairingLibrary() : protocols::jumping::PairingLibrary
• pairings() : protocols::abinitio::Templates
• pairings_begin() : protocols::denovo_design::components::StructureData
• pairings_end() : protocols::denovo_design::components::StructureData
• pairings_size() : protocols::jumping::MembraneJump
• PairingStatEntry() : protocols::abinitio::PairingStatEntry
• PairingStatistics() : protocols::abinitio::PairingStatistics
• PairingTemplate() : protocols::jumping::PairingTemplate
• PairQueryExecutor() : protocols::indexed_structure_store::search::PairQueryExecutor
• pairs() : core::sequence::PairScoringScheme
• PairScoringScheme() : core::sequence::PairScoringScheme
• PalesEvaluator() : protocols::simple_filters::PalesEvaluator
• PalesEvaluatorCreator() : protocols::simple_filters::PalesEvaluatorCreator
• ParaIon() : core::io::nmr::ParaIon
• parallel() : protocols::denovo_design::components::StrandPairing , protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator , protocols::splice::AlignEndsMover
• ParallelBetaPairingPreferenceFilter() : protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter
• ParallelTempering() : protocols::canonical_sampling::ParallelTempering
• param() : core::scoring::packing::HolesParamsRes
• param1() : protocols::branch_angle::BranchAngleOptimizer
• param2() : protocols::branch_angle::BranchAngleOptimizer
• param_cache() : protocols::toolbox::match_enzdes_util::EnzdesCstCache
• param_index() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• ParamagneticDatabaseHandler() : core::io::nmr::ParamagneticDatabaseHandler
• Parameter() : core::conformation::parametric::Parameter
• parameter() : core::conformation::parametric::ParametrizationCalculator
• parameter_cop() : core::conformation::parametric::Parameters , core::conformation::parametric::ParametrizationCalculator
• parameter_description() : core::conformation::parametric::Parameter
• parameter_description_from_enum() : protocols::helical_bundle::BundleParametrizationCalculator
• parameter_enum_from_name() : protocols::helical_bundle::BundleParametrizationCalculator
• parameter_name() : core::conformation::parametric::Parameter
• parameter_name_from_enum() : protocols::helical_bundle::BundleParametrizationCalculator
• parameter_op() : core::conformation::parametric::Parameters
• parameter_properties_from_enum() : protocols::helical_bundle::BundleParametrizationCalculator
• parameter_set4final() : protocols::hybridization::TMalign
• parameter_set4scale() : protocols::hybridization::TMalign
• parameter_set4search() : protocols::hybridization::TMalign
• parameter_type() : core::conformation::parametric::Parameter
• parameter_type_from_enum() : protocols::helical_bundle::BundleParametrizationCalculator
• parameter_units() : core::conformation::parametric::Parameter
• parameter_units_from_enum() : protocols::helical_bundle::BundleParametrizationCalculator
• parametercheck_filter() : protocols::loop_grower::LoopPartialSolutionStore
• ParameterizationCalculatorProperties() : core::conformation::parametric::ParameterizationCalculatorProperties
• Parameters() : core::conformation::parametric::Parameters
• parameters() : core::conformation::parametric::ParametersSet , protocols::helical_bundle_predict::HBPHelix
• parameters_cop() : core::conformation::parametric::ParametrizationCalculator
• parameters_for_restype() : core::scoring::methods::IdealParametersDatabase
• parameters_index() : protocols::helical_bundle::PerturbBundleHelix
• parameters_set() : core::conformation::Conformation
• parameters_set_index() : protocols::helical_bundle::PerturbBundleHelix
• ParametersSet() : core::conformation::parametric::ParametersSet
• ParametrizationCalculator() : core::conformation::parametric::ParametrizationCalculator
• params_database_tag() : core::scoring::hbonds::HBondOptions
• params_derivs_to_vars() : protocols::helical_bundle::FitSimpleHelixMultiFunc
• params_files_from_commandline() : core::chemical::GlobalResidueTypeSet
• ParaNMRScoreMover() : protocols::nmr::ParaNMRScoreMover
• paratope_residues_from_cdrs() : protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover , protocols::antibody::constraints::ParatopeSiteConstraintMover
• ParatopeEpitopeSiteConstraintMover() : protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover
• ParatopeMetric() : protocols::antibody::ParatopeMetric< T >
• ParatopeSiteConstraintMover() : protocols::antibody::constraints::ParatopeSiteConstraintMover
• parent() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_ , core::optimization::DOF_Node , protocols::jd3::JGResultNode , protocols::protein_interface_design::movers::CoordinateConstraintStack
• parent_full_model_parameters() : core::pose::full_model_info::FullModelParameters
• parent_id() : core::optimization::DOF_DataPoint
• parent_node() : protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase
• parents() : protocols::jd3::JGJobNode
• parin_favorite_output() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• parse() : core::chemical::mmCIF::mmCIFParser , core::chemical::sdf::CtabParserBase , core::chemical::sdf::CtabV2000Parser , core::chemical::sdf::CtabV3000Parser , core::chemical::sdf::SDFParser , core::scoring::BondOrderParser
• parse_a_penalty_definition() : core::scoring::aa_composition_energy::AACompositionEnergySetup , core::scoring::netcharge_energy::NetChargeEnergySetup
• parse_aa_line() : protocols::mean_field::AAMatrix
• parse_aa_matrix_line() : protocols::mean_field::AAMatrix
• parse_additional_residue_types() : core::pack::palette::CustomBaseTypePackerPalette
• parse_apply_to_pose_tag() : protocols::rosetta_scripts::RosettaScriptsParser
• parse_architect() : protocols::denovo_design::movers::BuildDeNovoBackboneMover
• parse_architect_tag() : protocols::denovo_design::architects::CompoundArchitect
• parse_architect_tags() : protocols::denovo_design::architects::CompoundArchitect
• parse_assembly_scorers() : protocols::sewing::movers::AssemblyMover
• parse_atom_line() : core::chemical::sdf::CtabV2000Parser , core::chemical::sdf::CtabV3000Parser
• parse_atom_pair_constraint() : core::scoring::constraints::ConstraintIO
• parse_attach_description() : protocols::pose_creation::MakeJunctionsMover
• parse_attributes_from_tag() : protocols::rotamer_recovery::RRComparer , protocols::rotamer_recovery::RRComparerChiDiff , protocols::rotamer_recovery::RRComparerRotBins , protocols::rotamer_recovery::RRProtocol , protocols::rotamer_recovery::RRProtocolReferenceStructure
• parse_base_tag() : core::simple_metrics::SimpleMetric
• parse_batch_description_tag_item() : protocols::features::ReportToDB
• parse_batch_id_tag_item() : protocols::features::ReportToDB
• parse_batch_name_tag_item() : protocols::features::ReportToDB
• parse_body_line() : core::pack::task::ResfileContents
• parse_bond_line() : core::chemical::sdf::CtabV2000Parser , core::chemical::sdf::CtabV3000Parser
• parse_cache_size_tag_item() : protocols::features::ReportToDB
• parse_cdr_design_option() : protocols::antibody::design::CDRSeqDesignOptionsParser
• parse_cdr_general_option() : protocols::antibody::design::CDRGraftDesignOptionsParser , protocols::antibody::design::CDRSeqDesignOptionsParser
• parse_cdr_graft_option() : protocols::antibody::design::CDRGraftDesignOptionsParser
• parse_cdr_option() : protocols::antibody::CDRSetOptionsParser , protocols::antibody::design::CDRGraftDesignOptionsParser , protocols::antibody::design::CDRSeqDesignOptionsParser
• parse_cdr_set_option() : protocols::antibody::CDRSetOptionsParser
• parse_chain_endings() : core::io::silent::BinarySilentStruct , core::io::silent::ProteinSilentStruct_Template< T >
• parse_chunks() : protocols::pose_creation::SliceToMiniProteinMover
• parse_command_line() : protocols::frag_picker::FragmentPicker
• parse_common_tag() : protocols::multistage_rosetta_scripts::MRSJobQueen
• parse_configuration_options() : protocols::loops::JSONFormattedLoopsFileReader
• parse_connection_tag() : protocols::denovo_design::architects::CompoundArchitect
• parse_connection_tags() : protocols::denovo_design::architects::CompoundArchitect
• parse_consensus_sequence() : core::enzymes::EnzymeManager
• parse_coordinate_constraint() : core::scoring::constraints::ConstraintIO
• parse_ctrl_str() : protocols::environment::claims::EnvClaim
• parse_default_and_user_options() : protocols::antibody::CDRSetOptionsParser , protocols::antibody::design::CDRGraftDesignOptionsParser , protocols::antibody::design::CDRSeqDesignOptionsParser
• parse_disulf_file() : core::io::raw_data::DisulfideFile
• parse_dna_geometry_log() : core::scoring::dna::DNA_DihedralPotential
• parse_dof_task_type() : protocols::minimization_packing::MinMover
• parse_dof_tasks() : protocols::minimization_packing::MinMover
• parse_elazar_polynom_table() : core::scoring::membrane::MPResidueLipophilicityEnergy
• parse_elazar_spline_table() : core::scoring::membrane::MPResidueLipophilicityEnergy , core::scoring::membrane::MPSpanInsertionEnergy
• parse_energies() : core::io::silent::SilentStruct
• parse_excluded_properites() : core::scoring::aa_composition_energy::AACompositionPropertiesSet
• parse_excluded_types() : core::scoring::aa_composition_energy::AACompositionPropertiesSet
• parse_extra_atom_list() : protocols::energy_based_clustering::EnergyBasedClusteringProtocol
• parse_file() : core::chemical::sdf::MolFileIOReader
• parse_files() : core::scoring::orbitals::OrbitalsLookup
• parse_filters() : protocols::denovo_design::movers::BuildDeNovoBackboneMover
• parse_folder() : protocols::denovo_design::movers::BuildDeNovoBackboneMover
• parse_global_requirements() : protocols::legacy_sewing::LegacyAssemblyMover
• parse_grid_sampling_options() : core::conformation::parametric::RealValuedParameter
• parse_gridset_tag() : protocols::qsar::scoring_grid::ScoringGridLoader
• parse_header_line() : core::pack::task::ResfileContents
• parse_ideal_contacts() : protocols::sewing::hashing::LigandBindingResPlacer
• parse_import_tag() : protocols::rosetta_scripts::RosettaScriptsParser
• parse_in_progress() : core::io::HeaderInformation
• parse_included_properites() : core::scoring::aa_composition_energy::AACompositionPropertiesSet
• parse_included_types() : core::scoring::aa_composition_energy::AACompositionPropertiesSet
• parse_input() : protocols::pose_length_moves::ConnectChainsMover
• parse_intra_segment_requirements() : protocols::legacy_sewing::LegacyAssemblyMover
• parse_job_definition_tags() : protocols::jd3::standard::StandardJobQueen , protocols::multistage_rosetta_scripts::MRSJobQueen
• parse_json_formatted_data() : protocols::loops::JSONFormattedLoopsFileReader
• parse_json_residue_info() : protocols::loops::JSONFormattedLoopsFileReader
• parse_jump_def() : protocols::abinitio::LoopJumpFoldCst
• parse_layer_secstruct_tag() : protocols::flxbb::LayerDesignOperation
• parse_layer_tag() : protocols::flxbb::LayerDesignOperation
• parse_ligand_conformers() : protocols::sewing::hashing::AlignmentFileGeneratorMover
• parse_ligand_files() : protocols::sewing::hashing::LigandBindingResPlacer
• parse_ligands_tag() : protocols::sewing::hashing::AlignmentFileGeneratorMover
• parse_line() : core::scoring::aa_repeat_energy::AARepeatEnergy
• parse_lines() : core::scoring::bin_transitions::BinTransitionCalculator
• parse_loop_tag() : protocols::loops::loops_definers::LoopsExplicitDefiner
• parse_lsm_spec() : protocols::hotspot_hashing::LSMSearchPattern
• parse_mainchain_torsions() : core::scoring::bin_transitions::BinTransitionCalculator
• parse_motif() : protocols::denovo_design::components::Segment
• parse_motif_string() : protocols::denovo_design::connection::ConnectionArchitect
• parse_movemap() : protocols::md::CartesianMD
• parse_movemap_factory() : protocols::minimization_packing::MinMover
• parse_movers() : protocols::denovo_design::movers::BuildDeNovoBackboneMover
• parse_multi() : core::chemical::sdf::MolFileIOMolecule
• parse_my_string_arguments_and_cast_to_globalPrivateSpaceVariables() : protocols::motif_grafting::movers::MotifGraftMover
• parse_my_tag() : core::import_pose::ImportPoseOptions , core::import_pose::options::RNA_BasicOptions , core::import_pose::options::RNA_DeNovoProtocolOptions , core::import_pose::options::RNA_FragmentMonteCarloOptions , core::import_pose::options::RNA_MinimizerOptions , core::io::StructFileReaderOptions , core::io::StructFileRepOptions , core::pack::palette::CustomBaseTypePackerPalette , core::pack::palette::DefaultPackerPalette , core::pack::palette::NCAADefaultPackerPalette , core::pack::palette::NoDesignPackerPalette , core::pack::palette::PackerPalette , core::pack::task::residue_selector::ClashBasedShellSelector , core::scoring::etable::EtableOptions , core::scoring::hbonds::HBondOptions , core::select::jump_selector::AndJumpSelector , core::select::jump_selector::InterchainJumpSelector , core::select::jump_selector::JumpIndexSelector , core::select::jump_selector::JumpSelector , core::select::jump_selector::NotJumpSelector , core::select::jump_selector::OrJumpSelector , core::select::movemap::MoveMapFactory , core::select::residue_selector::AndResidueSelector , core::select::residue_selector::AsymmetricUnitSelector , core::select::residue_selector::BinSelector , core::select::residue_selector::BondedResidueSelector , core::select::residue_selector::ChainSelector , core::select::residue_selector::CloseContactResidueSelector , core::select::residue_selector::DensityFitResidueSelector , core::select::residue_selector::FalseResidueSelector , core::select::residue_selector::GlycanLayerSelector , core::select::residue_selector::GlycanPositionSelector , core::select::residue_selector::GlycanResidueSelector , core::select::residue_selector::GlycanSequonsSelector , core::select::residue_selector::InterGroupInterfaceByVectorSelector , core::select::residue_selector::JumpDownstreamSelector , core::select::residue_selector::JumpUpstreamSelector , core::select::residue_selector::LayerSelector , core::select::residue_selector::NeighborhoodResidueSelector , core::select::residue_selector::NotResidueSelector , core::select::residue_selector::NumNeighborsSelector , core::select::residue_selector::OrResidueSelector , core::select::residue_selector::PhiSelector , core::select::residue_selector::PrimarySequenceNeighborhoodSelector , core::select::residue_selector::RandomGlycanFoliageSelector , core::select::residue_selector::RandomResidueSelector , core::select::residue_selector::ResidueIndexSelector , core::select::residue_selector::ResidueInMembraneSelector , core::select::residue_selector::ResidueInSequenceMotifSelector , core::select::residue_selector::ResidueNameSelector , core::select::residue_selector::ResiduePDBInfoHasLabelSelector , core::select::residue_selector::ResiduePropertySelector , core::select::residue_selector::ResidueSelector , core::select::residue_selector::ResidueSpanSelector , core::select::residue_selector::ReturnResidueSubsetSelector , core::select::residue_selector::ScoreTermValueBasedSelector , core::select::residue_selector::SecondaryStructureSelector , core::select::residue_selector::SliceResidueSelector , core::select::residue_selector::SSElementSelector , core::select::residue_selector::SymmetricalResidueSelector , core::select::residue_selector::TrueResidueSelector , core::simple_metrics::composite_metrics::CompositeEnergyMetric , core::simple_metrics::composite_metrics::ElectrostaticComplementarityMetric , core::simple_metrics::composite_metrics::ProtocolSettingsMetric , core::simple_metrics::CompositeRealMetric , core::simple_metrics::CompositeStringMetric , core::simple_metrics::metrics::CalculatorMetric , core::simple_metrics::metrics::DihedralDistanceMetric , core::simple_metrics::metrics::InteractionEnergyMetric , core::simple_metrics::metrics::ResidueSummaryMetric , core::simple_metrics::metrics::RMSDMetric , core::simple_metrics::metrics::SasaMetric , core::simple_metrics::metrics::SecondaryStructureMetric , core::simple_metrics::metrics::SelectedResidueCountMetric , core::simple_metrics::metrics::SelectedResiduesMetric , core::simple_metrics::metrics::SelectedResiduesPyMOLMetric , core::simple_metrics::metrics::SequenceMetric , core::simple_metrics::metrics::SequenceSimilarityMetric , core::simple_metrics::metrics::TimingProfileMetric , core::simple_metrics::metrics::TotalEnergyMetric , core::simple_metrics::per_residue_metrics::HbondMetric , core::simple_metrics::per_residue_metrics::PerResidueClashMetric , core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric , core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric , core::simple_metrics::per_residue_metrics::PerResidueGlycanLayerMetric , core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric , core::simple_metrics::per_residue_metrics::PerResidueSasaMetric , core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric , core::simple_metrics::PerResidueRealMetric , core::simple_metrics::PerResidueStringMetric , core::simple_metrics::RealMetric , core::simple_metrics::SimpleMetric , core::simple_metrics::StringMetric , core::simple_metrics::TestCompositeRealMetric , core::simple_metrics::TestCompositeStringMetric , core::simple_metrics::TestPerResidueRealMetric , core::simple_metrics::TestPerResidueStringMetric , core::simple_metrics::TestRealMetric , core::simple_metrics::TestStringMetric , protocols::aa_composition::AddCompositionConstraintMover , protocols::aa_composition::AddHelixSequenceConstraintsMover , protocols::aa_composition::AddMHCEpitopeConstraintMover , protocols::aa_composition::AddNetChargeConstraintMover , protocols::aa_composition::ClearCompositionConstraintsMover , protocols::abinitio::abscript::AbscriptLoopCloserCM , protocols::abinitio::abscript::AbscriptMover , protocols::abinitio::abscript::ConstraintPreparer , protocols::abinitio::abscript::FragmentCM , protocols::abinitio::abscript::FragmentJumpCM , protocols::abinitio::abscript::RigidChunkCM , protocols::abinitio::abscript::StructPerturberCM , protocols::abinitio::DomainAssembly , protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric , protocols::analysis::GlycanInfoMover , protocols::analysis::InterfaceAnalyzerMover , protocols::analysis::LoopAnalyzerMover , protocols::analysis::simple_metrics::RunSimpleMetricsMover , protocols::analysis::simple_metrics::SequenceRecoveryMetric , protocols::antibody::AntibodyCDRGrafter , protocols::antibody::AntibodyFeatures , protocols::antibody::AntibodyNumberingConverterMover , protocols::antibody::clusters::CDRClusterFeatures , protocols::antibody::constraints::CDRDihedralConstraintMover , protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover , protocols::antibody::constraints::ParatopeSiteConstraintMover , protocols::antibody::design::AntibodyDesignMover , protocols::antibody::design::MutateFrameworkForCluster , protocols::antibody::design::ResnumFromStringsWithRangesSelector , protocols::antibody::residue_selector::AntibodyRegionSelector , protocols::antibody::residue_selector::CDRResidueSelector , protocols::backbone_moves::local_backbone_mover::LocalBackboneMover , protocols::backbone_moves::RandomizeBBByRamaPrePro , protocols::backrub::BackrubMover , protocols::backrub::BackrubProtocol , protocols::backrub::BackrubSidechainMover , protocols::calc_taskop_filters::ConservedPosMutationFilter , protocols::calc_taskop_filters::MultipleSigmoids , protocols::calc_taskop_filters::Operator , protocols::calc_taskop_filters::RelativePoseFilter , protocols::calc_taskop_filters::RotamerBoltzmannWeight2 , protocols::calc_taskop_filters::RotamerBoltzmannWeight , protocols::calc_taskop_filters::Sigmoid , protocols::calc_taskop_movers::ConsensusDesignMover , protocols::calc_taskop_movers::CreateSequenceMotifMover , protocols::calc_taskop_movers::DesignRepackMover , protocols::calc_taskop_movers::ForceDisulfidesMover , protocols::canonical_sampling::BiasEnergy , protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::MetropolisHastingsMover , protocols::canonical_sampling::ParallelTempering , protocols::canonical_sampling::PDBTrajectoryRecorder , protocols::canonical_sampling::SidechainMetropolisHastingsMover , protocols::canonical_sampling::SilentTrajectoryRecorder , protocols::canonical_sampling::SimulatedTempering , protocols::canonical_sampling::TemperingBase , protocols::canonical_sampling::TrajectoryRecorder , protocols::canonical_sampling::TrialCounterObserver , protocols::carbohydrates::CreateGlycanSequonMover , protocols::carbohydrates::GlycanSampler , protocols::carbohydrates::GlycanTreeMinMover , protocols::carbohydrates::GlycanTreeModeler , protocols::carbohydrates::IdealizeAnomericHydrogens , protocols::carbohydrates::LinkageConformerMover , protocols::carbohydrates::RingPlaneFlipMover , protocols::carbohydrates::SimpleGlycosylateMover , protocols::carbohydrates::TautomerizeAnomerMover , protocols::chemically_conjugated_docking::UBQ_GTPaseMover , protocols::comparative_modeling::LoopRelaxMover , protocols::constraint_filters::ConstraintScoreCutoffFilter , protocols::constraint_filters::ConstraintScoreFilter , protocols::constraint_filters::SavePoseConstraintToFileFilter , protocols::constraint_filters::ShowConstraintsFilter , protocols::constraint_generator::AddConstraints , protocols::constraint_generator::ConstraintGenerator , protocols::constraint_generator::RemoveConstraints , protocols::constraint_movers::AddConstraintsToCurrentConformationMover , protocols::constraint_movers::ClearConstraintsMover , protocols::constraint_movers::ConstraintSetMover , protocols::constraint_movers::CstInfoMover , protocols::constraint_movers::ResidueTypeConstraintMover , protocols::contact_map::ContactMap , protocols::coupled_moves::CoupledMovesProtocol , protocols::cryst::CrystRMS , protocols::cryst::DockLatticeMover , protocols::cryst::FitBfactorsMover , protocols::cryst::LoadDensityMapMover , protocols::cryst::MakeLatticeMover , protocols::cryst::MakeLayerMover , protocols::cryst::RecomputeDensityMapMover , protocols::cryst::ReportGradientsMover , protocols::cryst::SetCrystWeightMover , protocols::cryst::SetRefinementOptionsMover , protocols::cryst::TagPoseWithRefinementStatsMover , protocols::cryst::UpdateCrystInfo , protocols::cryst::UpdateSolventMover , protocols::cutoutdomain::CutOutDomain , protocols::cyclic_peptide::CreateAngleConstraint , protocols::cyclic_peptide::CreateDistanceConstraint , protocols::cyclic_peptide::CreateTorsionConstraint , protocols::cyclic_peptide::CrosslinkerMover , protocols::cyclic_peptide::CycpepSymmetryFilter , protocols::cyclic_peptide::DeclareBond , protocols::cyclic_peptide::FlipChiralityMover , protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter , protocols::cyclic_peptide::PeptideCyclizeMover , protocols::cyclic_peptide::PeptideInternalHbondsFilter , protocols::cyclic_peptide::PeptideInternalHbondsMetric , protocols::cyclic_peptide::PeptideStubMover , protocols::cyclic_peptide::RamaMutationSelector , protocols::cyclic_peptide::SymmetricCycpepAlign , protocols::cyclic_peptide::TryDisulfPermutations , protocols::denovo_design::architects::StructureArchitect , protocols::denovo_design::components::CompoundPerturber , protocols::denovo_design::components::ConnectionPerturber , protocols::denovo_design::components::HelixPerturber , protocols::denovo_design::components::NullPerturber , protocols::denovo_design::components::PoseFolder , protocols::denovo_design::components::SegmentPairing , protocols::denovo_design::components::StructureDataPerturber , protocols::denovo_design::DisulfidizeMover , protocols::denovo_design::filters::CavityVolumeFilter , protocols::denovo_design::filters::ExposedHydrophobicsFilter , protocols::denovo_design::filters::PreProlineFilter , protocols::denovo_design::filters::SSPredictionFilter , protocols::denovo_design::filters::SSShapeComplementarityFilter , protocols::denovo_design::movers::AddSegmentDataMover , protocols::denovo_design::movers::AlignResiduesMover , protocols::denovo_design::movers::BridgeChainsMover , protocols::denovo_design::movers::BuildDeNovoBackboneMover , protocols::denovo_design::movers::DeclareStructureDataCovalentBondMover , protocols::denovo_design::movers::ExtendChainMover , protocols::denovo_design::movers::FastDesign , protocols::denovo_design::movers::FoldTreeFromFoldGraphMover , protocols::denovo_design::movers::MakeAsymmetricStructureDataMover , protocols::denovo_design::movers::RotateSegmentMover , protocols::denovo_design::movers::SealFoldTreeMover , protocols::denovo_design::movers::SetResidueAliasMover , protocols::denovo_design::residue_selectors::NamedSegmentSelector , protocols::denovo_design::residue_selectors::PairedSheetResidueSelector , protocols::design_opt::GreedyOptMutationMover , protocols::dna::DesignProteinBackboneAroundDNA , protocols::dna::DnaInterfaceMinMover , protocols::dna::DnaInterfaceMultiStateDesign , protocols::dna::DnaInterfacePacker , protocols::dna::SeparateDnaFromNonDna , protocols::dna_dock::DNAClashCheckFilter , protocols::dna_dock::PropagateClashCheckFilter , protocols::docking::DockingInitialPerturbation , protocols::docking::DockingProtocol , protocols::docking::DockingSlideIntoContact , protocols::docking::DockSetupMover , protocols::docking::membrane::MPDockingMover , protocols::docking::membrane::MPDockingSetupMover , protocols::docking::membrane::MPFindInterfaceMover , protocols::docking::membrane::QuickRelaxPartnersSeparately , protocols::docking::TemperedDocking , protocols::electron_density::BfactorFittingMover , protocols::electron_density::ReportFSC , protocols::electron_density::ScaleMapIntensities , protocols::electron_density::SetupForDensityScoringMover , protocols::electron_density::VoxelSpacingRefinementMover , protocols::environment::claims::EnvLabelSelector , protocols::environment::CoMTrackerCM , protocols::environment::EnvMover , protocols::environment::ScriptCM , protocols::enzdes::AddOrRemoveMatchCsts , protocols::enzdes::BackboneSampler , protocols::enzdes::DiffAtomSasaFilter , protocols::enzdes::EnzdesScorefileFilter , protocols::enzdes::EnzRepackMinimize , protocols::enzdes::EnzScoreFilter , protocols::enzdes::LigBurialFilter , protocols::enzdes::LigDSasaFilter , protocols::enzdes::LigInterfaceEnergyFilter , protocols::enzdes::PackRotamersMoverPartGreedy , protocols::enzdes::PredesignPerturbMover , protocols::enzdes::RemoveLigandFilter , protocols::enzdes::RepackWithoutLigandFilter , protocols::enzdes::ResidueConformerFilter , protocols::enzymatic_movers::EnzymaticMover , protocols::evolution::AASynthesisFitnessCost , protocols::evolution::AlignmentAAFinder , protocols::evolution::AlignmentGapInserter , protocols::evolution::EvolutionaryDynamicsMover , protocols::evolution::NucleotideMutation , protocols::farnesyl::InstallFarnesylMover , protocols::farnesyl::SampleFarnesylMover , protocols::features::AtomAtomPairFeatures , protocols::features::DdGFeatures , protocols::features::FeaturesReporter , protocols::features::HBondFeatures , protocols::features::HBondParameterFeatures , protocols::features::helixAssembly::HelixBundleFeatures , protocols::features::HelixCapFeatures , protocols::features::InterfaceDdGMover , protocols::features::InterfaceFeatures , protocols::features::LoopAnchorFeatures , protocols::features::ModelFeatures , protocols::features::ProteinRMSDFeatures , protocols::features::ProteinRMSDNoSuperpositionFeatures , protocols::features::ReportToDB , protocols::features::ResidueGridScoresFeatures , protocols::features::ResidueScoresFeatures , protocols::features::ResidueTotalScoresFeatures , protocols::features::RotamerBoltzmannWeightFeatures , protocols::features::RotamerRecoveryFeatures , protocols::features::ScoreFunctionFeatures , protocols::features::ScreeningFeatures , protocols::features::SecondaryStructureSegmentFeatures , protocols::features::SimpleMetricFeatures , protocols::features::SmotifFeatures , protocols::features::strand_assembly::SandwichFeatures , protocols::features::StructureScoresFeatures , protocols::features::TaskOperationFeatures , protocols::features::TotalScoreFeatures , protocols::features::TrajectoryReportToDB , protocols::features::UnrecognizedAtomFeatures , protocols::features::WaterFeatures , protocols::filters::CalculatorFilter , protocols::filters::CombinedFilter , protocols::filters::CompoundFilter , protocols::filters::ContingentFilter , protocols::filters::FalseFilter , protocols::filters::Filter , protocols::filters::FilterValueMetric , protocols::filters::IfThenFilter , protocols::filters::MoveBeforeFilter , protocols::filters::ReplicateFilter , protocols::filters::StochasticFilter , protocols::filters::TimeFilter , protocols::filters::TrueFilter , protocols::fldsgn::BluePrintBDR , protocols::fldsgn::CircularPermutation , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::filters::FragQualFilter , protocols::fldsgn::filters::HelixBendFilter , protocols::fldsgn::filters::HelixKinkFilter , protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::filters::HSSTripletFilter , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::fldsgn::filters::NcontactsFilter , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter , protocols::fldsgn::filters::SecondaryStructureCountFilter , protocols::fldsgn::filters::SecondaryStructureFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter , protocols::fldsgn::filters::SheetTopologyFilter , protocols::fldsgn::filters::StrandCurvatureByLevels , protocols::fldsgn::filters::StrandHelixGeometryFilter , protocols::fldsgn::MatchResidues , protocols::fldsgn::MatchResiduesMover , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::fldsgn::SheetRemodelConstraintGenerator , protocols::flexpep_docking::FlexPepDockingProtocol , protocols::flxbb::FlxbbDesign , protocols::flxbb::InterlockAroma , protocols::fold_from_loops::filters::ConstraintFulfilmentFilter , protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter , protocols::fold_from_loops::filters::ScorePoseSegmentFromResidueSelectorFilter , protocols::fold_from_loops::movers::AlignByResidueSelectorMover , protocols::fold_from_loops::movers::DisplayPoseLabelsMover , protocols::fold_from_loops::movers::LabelPoseFromResidueSelectorMover , protocols::fold_from_loops::movers::MoveMapFactoryToNamedMoveMapMover , protocols::fold_from_loops::movers::NubInitioLoopClosureMover , protocols::fold_from_loops::movers::ReleaseConstraintFromResidueMover , protocols::fold_from_loops::movers::ResidueLabelsToPymolSelectionMover , protocols::fold_from_loops::movers::SavePDBInfoMover , protocols::fold_from_loops::movers::SplitAndMixPoseMover , protocols::fold_from_loops::NubInitioMover , protocols::fold_from_loops::selectors::ConstraintResidueSelector , protocols::fold_from_loops::selectors::CutpointResidueSelector , protocols::fold_from_loops::selectors::ProteinResidueSelector , protocols::forge::constraints::InverseRotamersRCG , protocols::forge::constraints::InvrotTreeRCG , protocols::forge::constraints::NtoCConstraintGenerator , protocols::forge::constraints::RemoveRemodelCsts , protocols::forge::remodel::RemodelConstraintGenerator , protocols::forge::remodel::RemodelMover , protocols::forge::remodel::ResidueVicinityRCG , protocols::frag_picker::FragmentScoreFilter , protocols::generalized_kinematic_closure::GeneralizedKIC , protocols::grafting::AnchoredGraftMover , protocols::grafting::simple_movers::DeleteRegionMover , protocols::grafting::simple_movers::InsertPoseIntoPoseMover , protocols::grafting::simple_movers::KeepRegionMover , protocols::grafting::simple_movers::ReplaceRegionMover , protocols::hbnet::HBNet , protocols::hbnet::HBNetScore , protocols::hbnet::HBNetStapleInterface , protocols::hbnet::UnsatSelector , protocols::helical_bundle::BackboneGridSampler , protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::BundleReporterFilter , protocols::helical_bundle::FitSimpleHelix , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::PerturbBundle , protocols::hotspot_hashing::movers::PlaceSurfaceProbe , protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionSampler , protocols::hybridization::CartesianSampler , protocols::hybridization::HybridizeProtocol , protocols::idealize::IdealizeMover , protocols::indexed_structure_store::filters::FragmentLookupFilter , protocols::indexed_structure_store::movers::DirectSegmentLookupMover , protocols::indexed_structure_store::movers::SegmentSequenceProfileMover , protocols::legacy_sewing::LegacyAddStartnodeFragments , protocols::legacy_sewing::LegacyAppendAssemblyMover , protocols::legacy_sewing::LegacyAssemblyConstraintsMover , protocols::legacy_sewing::LegacyAssemblyMover , protocols::legacy_sewing::LegacyEnumerateAssemblyMover , protocols::legacy_sewing::LegacyGivenPathAssemblyMover , protocols::legacy_sewing::LegacyGreedyAssemblyMover , protocols::legacy_sewing::LegacyMonteCarloAssemblyMover , protocols::legacy_sewing::LegacyRepeatAssemblyMover , protocols::legacy_sewing::sampling::requirements::LegacyGlobalLengthRequirement , protocols::legacy_sewing::sampling::requirements::LegacyGlobalRequirement , protocols::legacy_sewing::sampling::requirements::LegacyIntraSegmentRequirement , protocols::legacy_sewing::sampling::requirements::LegacyResidueRetentionRequirement , protocols::legacy_sewing::sampling::requirements::LegacySegmentDsspRequirement , protocols::legacy_sewing::sampling::requirements::LegacySegmentLengthRequirement , protocols::ligand_docking::AddHydrogens , protocols::ligand_docking::AtomCountFilter , protocols::ligand_docking::ChainExistsFilter , protocols::ligand_docking::CompleteConnectionsFilter , protocols::ligand_docking::CompoundTranslate , protocols::ligand_docking::ComputeLigandRDF , protocols::ligand_docking::FinalMinimizer , protocols::ligand_docking::ga_ligand_dock::GALigandDock , protocols::ligand_docking::GrowLigand , protocols::ligand_docking::HBondAcceptorFilter , protocols::ligand_docking::HBondDonorFilter , protocols::ligand_docking::HeavyAtomFilter , protocols::ligand_docking::HighResDocker , protocols::ligand_docking::HighResEnsemble , protocols::ligand_docking::InterfaceBuilder , protocols::ligand_docking::InterfaceScoreCalculator , protocols::ligand_docking::LigandArea , protocols::ligand_docking::LigandDesign , protocols::ligand_docking::MinimizeBackbone , protocols::ligand_docking::MolarMassFilter , protocols::ligand_docking::MolecularMassFilter , protocols::ligand_docking::MoveMapBuilder , protocols::ligand_docking::ProtLigEnsemble , protocols::ligand_docking::RandomConformers , protocols::ligand_docking::rdf::RDFBase , protocols::ligand_docking::rdf::RDFBinaryHbondFunction , protocols::ligand_docking::rdf::RDFBinaryOrbitalFunction , protocols::ligand_docking::rdf::RDFChargeFunction , protocols::ligand_docking::rdf::RDFElecFunction , protocols::ligand_docking::rdf::RDFEtableFunction , protocols::ligand_docking::rdf::RDFHbondFunction , protocols::ligand_docking::rdf::RDFOrbitalFunction , protocols::ligand_docking::Rotate , protocols::ligand_docking::Rotates , protocols::ligand_docking::SlideTogether , protocols::ligand_docking::StartFrom , protocols::ligand_docking::Transform , protocols::ligand_docking::TransformEnsemble , protocols::ligand_docking::Translate , protocols::ligand_docking::WriteLigandMolFile , protocols::loop_build::LoopmodelWrapper , protocols::loop_grower::FragmentExtension , protocols::loop_modeler::LoopModeler , protocols::loop_modeling::LoopBuilder , protocols::loop_modeling::LoopMover , protocols::loop_modeling::LoopProtocol , protocols::loop_modeling::refiners::MinimizationRefiner , protocols::loop_modeling::refiners::RepackingRefiner , protocols::loop_modeling::refiners::RotamerTrialsRefiner , protocols::loop_modeling::utilities::PrepareForFullatom , protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashMoverWrapper , protocols::loops::filters::LoopAnalyzerFilter , protocols::loops::FoldTreeFromLoops , protocols::loops::loop_closure::ccd::CCDLoopClosureMover , protocols::loops::loop_closure::ccd::RamaCheckBase , protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover , protocols::loops::loop_mover::LoopCM , protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::loops::loops_definers::LoopsDatabaseDefiner , protocols::loops::loops_definers::LoopsDefiner , protocols::loops::loops_definers::LoopsExplicitDefiner , protocols::loops::loops_definers::LoopsFileDefiner , protocols::loops::loops_definers::LoopsStringDefiner , protocols::match::MatcherMover , protocols::matdes::ClashCheckFilter , protocols::matdes::ExtractSubposeMover , protocols::matdes::GetRBDOFValues , protocols::matdes::InterfacePackingFilter , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::OligomericAverageDegreeFilter , protocols::matdes::SchemePlaceMotifsMover , protocols::matdes::SymDofMover , protocols::matdes::SymUnsatHbondFilter , protocols::md::CartesianMD , protocols::mean_field::GenMeanFieldMover , protocols::membrane::AddMembraneMover , protocols::membrane::AddMembraneSpanConstraint , protocols::membrane::AddMembraneSpanTermZConstraint , protocols::membrane::AddMPLigandMover , protocols::membrane::AqueousPoreFinder , protocols::membrane::benchmark::MakeCanonicalHelix , protocols::membrane::benchmark::SampleTiltAngles , protocols::membrane::FlipMover , protocols::membrane::HelixFromSequence , protocols::membrane::MembranePositionFromTopologyMover , protocols::membrane::MPLipidAccessibility , protocols::membrane::MPMutateRelaxMover , protocols::membrane::MPQuickRelaxMover , protocols::membrane::OptimizeMembranePositionMover , protocols::membrane::OptimizeProteinEmbeddingMover , protocols::membrane::RotationMover , protocols::membrane::SetMembraneCenterMover , protocols::membrane::SetMembraneNormalMover , protocols::membrane::SetMembranePositionMover , protocols::membrane::SpinAroundPartnerMover , protocols::membrane::symmetry::SymmetricAddMembraneMover , protocols::membrane::TiltMover , protocols::membrane::TransformIntoMembraneMover , protocols::membrane::TranslationMover , protocols::membrane::TranslationRotationMover , protocols::membrane::visualize::VisualizeMembraneMover , protocols::membrane_benchmark::MembraneEnergyLandscapeSampler , protocols::membrane_benchmark::PeptideOrientationMover , protocols::minimization_packing::BoltzmannRotamerMover , protocols::minimization_packing::DisulfideOptimizationMover , protocols::minimization_packing::MinMover , protocols::minimization_packing::MinPackMover , protocols::minimization_packing::PackRotamersMover , protocols::minimization_packing::PackRotamersMoverLazy , protocols::minimization_packing::PertMinMover , protocols::minimization_packing::RepackSidechainsMover , protocols::minimization_packing::RotamerTrialsMinMover , protocols::minimization_packing::RotamerTrialsMover , protocols::minimization_packing::symmetry::TaskAwareSymMinMover , protocols::minimization_packing::TaskAwareMinMover , protocols::monte_carlo::GenericMonteCarloMover , protocols::monte_carlo::GenericSimulatedAnnealer , protocols::monte_carlo::MonteCarloRecover , protocols::monte_carlo::MonteCarloReset , protocols::monte_carlo::MonteCarloTest , protocols::monte_carlo::ResetBaselineMover , protocols::motif_grafting::movers::MotifGraftMover , protocols::moves::DsspMover , protocols::moves::FilterReportAsPoseExtraScoresMover , protocols::moves::IfMover , protocols::moves::IteratedConvergenceMover , protocols::moves::MonteCarloUtil , protocols::moves::Mover , protocols::moves::PyMOLMover , protocols::moves::RampingMover , protocols::moves::RandomMover , protocols::moves::StructureRestrictor , protocols::moves::SwitchMover , protocols::moves::TrialMover , protocols::multistage_rosetta_scripts::cluster::ClusterMetric , protocols::multistage_rosetta_scripts::cluster::metrics::JumpMetric , protocols::multistage_rosetta_scripts::cluster::metrics::SequenceMetric , protocols::multistage_rosetta_scripts::MRSJob , protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopCreatorMover , protocols::ncbb::oop::OopDockDesignProtocol , protocols::ncbb::ResidueReplacementRebuildMover , protocols::ncbb::SecStructFinder , protocols::ncbb::SecStructMinimizeMover , protocols::nmr::ParaNMRScoreMover , protocols::nmr::pcs::PCSLigandTransformMover , protocols::nmr::pre::PREMover , protocols::nonlocal::SingleFragmentMover , protocols::normalmode::NormalModeMinimizer , protocols::normalmode::NormalModeRelaxMover , protocols::pb_potential::SetupPoissonBoltzmannPotential , protocols::pdbinfo_manipulations::AlignPDBInfoToSequences , protocols::peptide_deriver::PeptideDeriverFilter , protocols::pose_creation::ExtendedPoseMover , protocols::pose_creation::MakeJunctionsMover , protocols::pose_creation::MakePolyXMover , protocols::pose_creation::MergePDBatOverlapMover , protocols::pose_creation::MergePDBMover , protocols::pose_creation::PoseFromSequenceMover , protocols::pose_creation::SliceToMiniProteinMover , protocols::pose_length_moves::AnalyzeLoopModeling , protocols::pose_length_moves::ConnectChainsMover , protocols::pose_length_moves::FixAllLoopsMover , protocols::pose_length_moves::InsertResMover , protocols::pose_length_moves::NearNativeLoopCloser , protocols::pose_metric_calculators::FragQualCalculator , protocols::pose_reporters::EnergyReporter , protocols::pose_reporters::FilterReporter , protocols::pose_reporters::RMSDReporter , protocols::pose_selectors::ClusterPoseSelector , protocols::pose_selectors::Filter , protocols::pose_selectors::LogicalSelector , protocols::pose_selectors::TopNByProperty , protocols::protein_interface_design::filters::AtomicContactCountFilter , protocols::protein_interface_design::filters::AverageDegreeFilter , protocols::protein_interface_design::filters::BindingStrainFilter , protocols::protein_interface_design::filters::BoltzmannFilter , protocols::protein_interface_design::filters::ClashWithTargetFilter , protocols::protein_interface_design::filters::DesignableResiduesFilter , protocols::protein_interface_design::filters::DisulfideFilter , protocols::protein_interface_design::filters::FilterScanFilter , protocols::protein_interface_design::filters::FNatFilter , protocols::protein_interface_design::filters::HbondsToAtomFilter , protocols::protein_interface_design::filters::HbondsToResidueFilter , protocols::protein_interface_design::filters::InterfaceHolesFilter , protocols::protein_interface_design::filters::IRmsdFilter , protocols::protein_interface_design::filters::LRmsdFilter , protocols::protein_interface_design::filters::RelativeSegmentFilter , protocols::protein_interface_design::filters::RmsdFilter , protocols::protein_interface_design::filters::RmsdSimpleFilter , protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter , protocols::protein_interface_design::filters::SSamountFilter , protocols::protein_interface_design::filters::StubScoreFilter , protocols::protein_interface_design::filters::StubScoreLoopsFilter , protocols::protein_interface_design::filters::Torsion , protocols::protein_interface_design::movers::AddChainBreak , protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots , protocols::protein_interface_design::movers::BackrubDDMover , protocols::protein_interface_design::movers::BestHotspotCstMover , protocols::protein_interface_design::movers::BuildAlaPose , protocols::protein_interface_design::movers::DesignMinimizeHbonds , protocols::protein_interface_design::movers::DisulfideMover , protocols::protein_interface_design::movers::DockAndRetrieveSidechains , protocols::protein_interface_design::movers::DockWithHotspotMover , protocols::protein_interface_design::movers::FavorNativeResiduePreCycle , protocols::protein_interface_design::movers::FavorNonNativeResiduePreCycle , protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover , protocols::protein_interface_design::movers::HotspotHasherMover , protocols::protein_interface_design::movers::InterfaceRecapitulationMover , protocols::protein_interface_design::movers::LoopFinder , protocols::protein_interface_design::movers::LoopLengthChange , protocols::protein_interface_design::movers::LoopMoverFromCommandLine , protocols::protein_interface_design::movers::LoopOver , protocols::protein_interface_design::movers::LoopRemodel , protocols::protein_interface_design::movers::MapHotspot , protocols::protein_interface_design::movers::PatchdockTransform , protocols::protein_interface_design::movers::PeptideStapleDesignMover , protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::protein_interface_design::movers::PlacementMinimizationMover , protocols::protein_interface_design::movers::PlaceOnLoop , protocols::protein_interface_design::movers::PlaceSimultaneouslyMover , protocols::protein_interface_design::movers::PlaceStubMover , protocols::protein_interface_design::movers::PrepackMover , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover , protocols::protein_interface_design::movers::RandomMutation , protocols::protein_interface_design::movers::RepackMinimize , protocols::protein_interface_design::movers::SaveAndRetrieveSidechains , protocols::protein_interface_design::movers::SetAtomTree , protocols::protein_interface_design::movers::SetTemperatureFactor , protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover , protocols::protein_interface_design::movers::SetupHotspotConstraintsMover , protocols::protein_interface_design::movers::ShoveResidueMover , protocols::protein_interface_design::movers::SpinMover , protocols::protein_interface_design::movers::SubroutineMover , protocols::protein_interface_design::movers::TaskAwareCsts , protocols::protein_interface_design::movers::TopologyBrokerMover , protocols::protein_interface_design::movers::TryRotamers , protocols::protein_interface_design::movers::VLB , protocols::qsar::qsarMover , protocols::qsar::RenderGridsToKinemage , protocols::qsar::scoring_grid::AtrGrid , protocols::qsar::scoring_grid::ChargeGrid , protocols::qsar::scoring_grid::ClassicGrid , protocols::qsar::scoring_grid::ConstantScoreBase , protocols::qsar::scoring_grid::GridBase , protocols::qsar::scoring_grid::HbaGrid , protocols::qsar::scoring_grid::HbdGrid , protocols::qsar::scoring_grid::LigandPropertyScore , protocols::qsar::scoring_grid::PCSMultiGrid , protocols::qsar::scoring_grid::PCSSingleGrid , protocols::qsar::scoring_grid::RepGrid , protocols::qsar::scoring_grid::ShapeGrid , protocols::qsar::scoring_grid::SingleGrid , protocols::qsar::scoring_grid::SiteGrid , protocols::qsar::scoring_grid::SolvationGrid , protocols::qsar::scoring_grid::SolvationMetaGrid , protocols::qsar::scoring_grid::VdwGrid , protocols::quantum_annealing::ExternalPackerResultLoader , protocols::quantum_annealing::InteractionGraphSummaryMetric , protocols::rbsegment_relax::IdealizeHelicesMover , protocols::rbsegment_relax::MakeStarTopologyMover , protocols::rbsegment_relax::OptimizeThreadingMover , protocols::recces::options::RECCES_Options , protocols::recces::scratch::ThermalMinimizer , protocols::recces::scratch::ThermalSamplingMover , protocols::recon_design::FindConsensusSequence , protocols::recon_design::FitnessFilter , protocols::recon_design::MSDMover , protocols::relax::AcceptToBestMover , protocols::relax::AtomCoordinateCstMover , protocols::relax::FastRelax , protocols::relax::LocalRelax , protocols::relax::membrane::MPFastRelaxMover , protocols::relax::membrane::MPRangeRelaxMover , protocols::relax::RepeatProteinRelax , protocols::residue_selectors::HBondSelector , protocols::residue_selectors::LigandMetalContactSelector , protocols::residue_selectors::NativeSelector , protocols::residue_selectors::StoredResidueSubsetSelector , protocols::residue_selectors::StoreResidueSubsetMover , protocols::residue_selectors::TaskSelector , protocols::rigid::RigidBodyPerturbNoCenterMover , protocols::rigid::RigidBodyTiltMover , protocols::rigid::RigidBodyTransMover , protocols::rigid::RollMover , protocols::rigid::UniformRigidBodyCM , protocols::rigid::UniformRigidBodyMover , protocols::rna::denovo::movers::RNA_DeNovoProtocolMover , protocols::rna::denovo::RNA_DeNovoProtocol , protocols::rna::movers::ERRASER2Protocol , protocols::rna::movers::ErraserMinimizerMover , protocols::rna::movers::RNAIdealizeMover , protocols::rna::movers::RNAThreadAndMinimizeMover , protocols::rosetta_scripts::AdditionalOutputWrapper , protocols::rosetta_scripts::MultipleOutputWrapper , protocols::rosetta_scripts::MultiplePoseMover , protocols::rosetta_scripts::ParsedProtocol , protocols::rosetta_scripts::PosePropertyReporter , protocols::rosetta_scripts::PoseSelector , protocols::rosetta_scripts::SavePoseMover , protocols::rotamer_recovery::RotamerRecoveryMover , protocols::score_filters::GeometryFilter , protocols::score_filters::ScoreCutoffFilter , protocols::score_filters::ScoreTypeFilter , protocols::seeded_abinitio::CAcstGenerator , protocols::seeded_abinitio::CloseFold , protocols::seeded_abinitio::CoordinateCst , protocols::seeded_abinitio::DefineMovableLoops , protocols::seeded_abinitio::GrowPeptides , protocols::seeded_abinitio::SeedFoldTree , protocols::seeded_abinitio::SeedSetupMover , protocols::seeded_abinitio::SegmentHybridizer , protocols::seeded_abinitio::SwapSegment , protocols::sewing::hashing::AlignmentFileGeneratorMover , protocols::sewing::movers::AppendAssemblyMover , protocols::sewing::movers::AssemblyMover , protocols::sewing::movers::LigandBindingAssemblyMover , protocols::simple_ddg::AlaScan , protocols::simple_ddg::ddG , protocols::simple_ddg::DdgFilter , protocols::simple_ddg::DdGScan , protocols::simple_ddg::InterfaceBindingEnergyDensityFilter , protocols::simple_ddg::SSElementBisectddGFilter , protocols::simple_filters::AngleToVector , protocols::simple_filters::AtomicContactFilter , protocols::simple_filters::AtomicDistanceFilter , protocols::simple_filters::AveragePathLengthFilter , protocols::simple_filters::BuriedSurfaceAreaFilter , protocols::simple_filters::BuriedUnsatHbondFilter , protocols::simple_filters::ChainBreak , protocols::simple_filters::ChainCountFilter , protocols::simple_filters::ContactMolecularSurfaceFilter , protocols::simple_filters::DeltaFilter , protocols::simple_filters::DisulfideEntropyFilter , protocols::simple_filters::DomainInterfaceFilter , protocols::simple_filters::EnergyPerResidueFilter , protocols::simple_filters::ExpiryFilter , protocols::simple_filters::FileExistFilter , protocols::simple_filters::FileRemoveFilter , protocols::simple_filters::HelixHelixAngleFilter , protocols::simple_filters::HolesFilter , protocols::simple_filters::InterfaceHbondsFilter , protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter , protocols::simple_filters::InterfaceSasaFilter , protocols::simple_filters::InterRepeatContactFilter , protocols::simple_filters::IntraRepeatContactFilter , protocols::simple_filters::LeastNativeLike9merFilter , protocols::simple_filters::LongestContinuousPolarSegmentFilter , protocols::simple_filters::MembAccesResidueLipophilicityFilter , protocols::simple_filters::MotifScoreFilter , protocols::simple_filters::MPSpanAngleFilter , protocols::simple_filters::MutationsFilter , protocols::simple_filters::NeighborTypeFilter , protocols::simple_filters::NetChargeFilter , protocols::simple_filters::NMerPSSMEnergyFilter , protocols::simple_filters::NMerSVMEnergyFilter , protocols::simple_filters::NonSequentialNeighborsFilter , protocols::simple_filters::PackStatFilter , protocols::simple_filters::PoseComment , protocols::simple_filters::PoseInfoFilter , protocols::simple_filters::RangeFilter , protocols::simple_filters::ReadPoseExtraScoreFilter , protocols::simple_filters::RepeatParameterFilter , protocols::simple_filters::ReportFilter , protocols::simple_filters::ResidueBurialFilter , protocols::simple_filters::ResidueChiralityFilter , protocols::simple_filters::ResidueCountFilter , protocols::simple_filters::ResidueDepthFilter , protocols::simple_filters::ResidueDistanceFilter , protocols::simple_filters::ResidueIEFilter , protocols::simple_filters::ResidueLipophilicityFilter , protocols::simple_filters::ResidueSelectionDistanceFilter , protocols::simple_filters::ResidueSetChainEnergyFilter , protocols::simple_filters::ResiduesInInterfaceFilter , protocols::simple_filters::SaveResfileToDiskFilter , protocols::simple_filters::SecretionPredictionFilter , protocols::simple_filters::SequenceDistance , protocols::simple_filters::ShapeComplementarityFilter , protocols::simple_filters::SidechainRmsdFilter , protocols::simple_filters::SimpleHbondsToAtomFilter , protocols::simple_filters::SimpleMetricFilter , protocols::simple_filters::SpanTopologyMatchPoseFilter , protocols::simple_filters::SSElementLengthFilter , protocols::simple_filters::SSElementMotifContactFilter , protocols::simple_filters::SSMotifFinder , protocols::simple_filters::StemFinder , protocols::simple_filters::SymmetricMotifFilter , protocols::simple_filters::TaskAwareSASAFilter , protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::simple_filters::TerminusDistanceFilter , protocols::simple_filters::TMsAACompFilter , protocols::simple_filters::TMsSpanMembraneFilter , protocols::simple_filters::TotalSasaFilter , protocols::simple_moves::AddChainMover , protocols::simple_moves::AddJobPairData , protocols::simple_moves::AddPDBInfoMover , protocols::simple_moves::AddResidueCouplingConstraint , protocols::simple_moves::AddResidueLabelMover , protocols::simple_moves::AlignChainMover , protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockMoveRbJumpMover , protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockRbTrialMover , protocols::simple_moves::BackboneMover , protocols::simple_moves::BBDihedralSamplerMover , protocols::simple_moves::BBGaussianMover , protocols::simple_moves::bin_transitions::InitializeByBins , protocols::simple_moves::bin_transitions::PerturbByBins , protocols::simple_moves::ConcatenatePosesMover , protocols::simple_moves::ContingentAcceptMover , protocols::simple_moves::ConvertRealToVirtualMover , protocols::simple_moves::ConvertVirtualToRealMover , protocols::simple_moves::CopyRotamerMover , protocols::simple_moves::CutChainMover , protocols::simple_moves::DeleteChainMover , protocols::simple_moves::DeleteChainsMover , protocols::simple_moves::DisulfideInsertionMover , protocols::simple_moves::DumpPdb , protocols::simple_moves::DumpSingleResidueRotamers , protocols::simple_moves::ExplicitWaterMover , protocols::simple_moves::FavorSequenceProfile , protocols::simple_moves::FavorSymmetricSequence , protocols::simple_moves::FoldTreeFromMotif , protocols::simple_moves::LoadPDBMover , protocols::simple_moves::LoadUnboundRotMover , protocols::simple_moves::MembraneTopology , protocols::simple_moves::ModifyVariantTypeMover , protocols::simple_moves::MutateResidue , protocols::simple_moves::PDBReloadMover , protocols::simple_moves::PeriodicBoxMover , protocols::simple_moves::PoseFromPoseResourceMover , protocols::simple_moves::PSSM2BfactorMover , protocols::simple_moves::RandomOmegaFlipMover , protocols::simple_moves::RandomTorsionMover , protocols::simple_moves::RepeatPropagationMover , protocols::simple_moves::ReportEffectivePKA , protocols::simple_moves::ReportXYZ , protocols::simple_moves::ResetFoldTree , protocols::simple_moves::ResetFullModelInfoMover , protocols::simple_moves::RingConformationMover , protocols::simple_moves::SaveSequenceToCommentsMover , protocols::simple_moves::ScoreMover , protocols::simple_moves::SequenceProfileMover , protocols::simple_moves::SetTorsion , protocols::simple_moves::SetupMetalsMover , protocols::simple_moves::ShortBackrubMover , protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover , protocols::simple_moves::sidechain_moves::PerturbChiSidechainMover , protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover , protocols::simple_moves::sidechain_moves::SetChiMover , protocols::simple_moves::sidechain_moves::SidechainMCMover , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase , protocols::simple_moves::SimpleThreadingMover , protocols::simple_moves::StorePoseSnapshot , protocols::simple_moves::StructProfileMover , protocols::simple_moves::SuperimposeMover , protocols::simple_moves::SwitchChainOrderMover , protocols::simple_moves::SwitchResidueTypeSetMover , protocols::simple_moves::Tumble , protocols::simple_moves::VirtualRootMover , protocols::simple_moves::WriteFiltersToPose , protocols::simple_moves::WriteSSEMover , protocols::splice::AlignEndsMover , protocols::splice::RBInMover , protocols::splice::RBOutMover , protocols::splice::RotLibOut , protocols::splice::Splice , protocols::splice::SpliceIn , protocols::splice::SpliceInAntibody , protocols::splice::SpliceInTail , protocols::splice::SpliceOut , protocols::splice::SpliceOutAntibody , protocols::splice::TailSegmentMover , protocols::stepwise::modeler::options::StepWiseBasicModelerOptions , protocols::stepwise::modeler::options::StepWiseModelerOptions , protocols::stepwise::modeler::options::StepWiseProteinModelerOptions , protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::monte_carlo::mover::AddMover , protocols::stepwise::monte_carlo::mover::DeleteMover , protocols::stepwise::monte_carlo::mover::FromScratchMover , protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions , protocols::stepwise::monte_carlo::mover::ResampleMover , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions , protocols::stepwise::options::StepWiseBasicOptions , protocols::struct_fragment::StructFragmentMover , protocols::switches::GraftSwitchMover , protocols::symmetric_docking::membrane::MPSymDockMover , protocols::symmetric_docking::SymDockProtocol , protocols::symmetric_docking::SymFoldandDockMoveRbJumpMover , protocols::symmetric_docking::SymFoldandDockRbTrialMover , protocols::symmetric_docking::SymFoldandDockSlideTrialMover , protocols::symmetry::DetectSymmetry , protocols::symmetry::ExtractAsymmetricPoseMover , protocols::symmetry::ExtractAsymmetricUnitMover , protocols::symmetry::SetupForSequenceSymmetryMover , protocols::symmetry::SetupForSymmetryMover , protocols::symmetry::SetupNCSMover , protocols::task_operations::StoreCombinedStoredTasksMover , protocols::task_operations::StoreCompoundTaskMover , protocols::task_operations::StoreTaskMover , protocols::vardist_solaccess::LoadVarSolDistSasaCalculatorMover
• parse_optional_data() : core::chemical::sdf::SDFParser
• parse_options() : core::simple_metrics::composite_metrics::ProtocolSettingsMetric , protocols::antibody::CDRSetOptionsParser , protocols::antibody::design::CDRGraftDesignOptionsParser , protocols::antibody::design::CDRSeqDesignOptionsParser , protocols::peptide_deriver::PeptideDeriverFilter
• parse_opts() : protocols::md::CartesianMD , protocols::minimization_packing::MinMover
• parse_or_properties() : core::scoring::aa_composition_energy::AACompositionPropertiesSet
• parse_output_mode() : protocols::hotspot_hashing::movers::PlaceProbeMover
• parse_pairing_tag() : protocols::denovo_design::architects::CompoundArchitect
• parse_pairing_tags() : protocols::denovo_design::architects::CompoundArchitect
• parse_pdb_code() : protocols::splice::Splice
• parse_pdb_file() : protocols::ligand_docking::StartFrom
• parse_pdbinfo_labels() : core::pose::PDBInfo
• parse_PDBnum_icode() : core::pack::task::ResfileContents
• parse_penalty_definitions() : core::scoring::aa_composition_energy::AACompositionEnergySetup
• parse_per_residue_tag() : core::simple_metrics::PerResidueRealMetric , core::simple_metrics::PerResidueStringMetric
• parse_perturbation_options() : core::conformation::parametric::RealValuedParameter
• parse_perturber() : protocols::denovo_design::movers::BuildDeNovoBackboneMover
• parse_place_probe_tag() : protocols::hotspot_hashing::movers::PlaceProbeMover
• parse_postfold_movers() : protocols::denovo_design::movers::BuildDeNovoBackboneMover
• parse_prefold_movers() : protocols::denovo_design::movers::BuildDeNovoBackboneMover
• parse_property() : core::scoring::aa_composition_energy::AACompositionPropertiesSet
• parse_property_line() : core::chemical::sdf::CtabV2000Parser
• parse_protocol_id_tag_item() : protocols::features::ReportToDB
• parse_protocol_tag() : protocols::rosetta_scripts::RosettaScriptsParser
• parse_psipred_horiz_output() : core::io::external::PsiPredInterface
• parse_psipred_output() : core::io::external::PsiPredInterface
• parse_psipred_output_probabilities() : core::io::external::PsiPredInterface
• parse_quota_command_line() : protocols::frag_picker::FragmentPicker
• parse_rama_map_file_shapovalov() : core::chemical::mainchain_potential::MainchainScoreTable
• parse_region_string() : protocols::contact_map::ContactMap
• parse_relevant_residues_mode_tag_item() : protocols::features::ReportToDB
• parse_remove_xray_virt_tag_item() : protocols::features::ReportToDB
• parse_report_format_string() : protocols::peptide_deriver::PeptideDeriverFilter
• parse_requirements() : protocols::legacy_sewing::LegacyAssemblyMover , protocols::sewing::movers::AssemblyMover
• parse_resfiles() : protocols::recon_design::FindConsensusSequence , protocols::recon_design::MSDMover
• parse_resid() : core::pack::task::ResfileContents
• parse_residue() : core::scoring::constraints::ConstraintIO
• parse_resources_tag() : protocols::rosetta_scripts::RosettaScriptsParser
• parse_schfile() : protocols::md::MDBase
• parse_score_function() : protocols::minimization_packing::MinPackMover , protocols::minimization_packing::PackRotamersMover , protocols::minimization_packing::RepackSidechainsMover , protocols::switches::GraftSwitchMover
• parse_segments() : protocols::splice::SpliceManager
• parse_setting() : core::conformation::parametric::BooleanValuedParameter , core::conformation::parametric::Parameter , core::conformation::parametric::RealValuedParameter , core::conformation::parametric::RealVectorValuedParameter , core::conformation::parametric::SizeValuedParameter , core::conformation::parametric::SizeVectorValuedParameter
• parse_setting_only() : core::conformation::parametric::RealValuedParameter , protocols::helical_bundle::parameters::OmegaBundleParameter
• parse_single_job_tag() : protocols::multistage_rosetta_scripts::MRSJobQueen
• parse_single_stage_tag() : protocols::multistage_rosetta_scripts::MRSJobQueen
• parse_SpliceOut_tags() : protocols::splice::SpliceOut
• parse_ss() : core::select::residue_selector::SSElementSelector , protocols::pose_creation::SliceToMiniProteinMover
• parse_stage_id() : protocols::abinitio::abscript::AbscriptMover
• parse_startfrom_file() : protocols::ligand_docking::StartFrom
• parse_stride_tag_item() : protocols::features::TrajectoryReportToDB
• parse_string_to_residue_selector() : core::select::residue_selector::SelectorLogicParser
• parse_sub_filters_tag() : core::pack::task::operation::ResFilterComposition
• parse_subtag() : protocols::denovo_design::components::StructureData , protocols::environment::EnvMover
• parse_subtags() : protocols::abinitio::abscript::AbscriptMover
• parse_tag() : core::pack::task::operation::AddBehaviorRLT , core::pack::task::operation::ChainIs , core::pack::task::operation::ClashBasedRepackShell , core::pack::task::operation::DesignRestrictions , core::pack::task::operation::DisallowIfNonnative , core::pack::task::operation::DisallowIfNonnativeRLT , core::pack::task::operation::EnableMultiCoolAnnealer , core::pack::task::operation::EnableSmartAnnealer , core::pack::task::operation::ExtraChiCutoff , core::pack::task::operation::ExtraChiCutoffRLT , core::pack::task::operation::ExtraRotamers , core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::operation::ExtraRotamersGenericRLT , core::pack::task::operation::FillAUTOTaskOperation , core::pack::task::operation::InitializeFromCommandline , core::pack::task::operation::InitializeFromOptionCollection , core::pack::task::operation::KeepSequenceSymmetry , core::pack::task::operation::OperateOnCertainResidues , core::pack::task::operation::OperateOnResidueSubset , core::pack::task::operation::PreventRepacking , core::pack::task::operation::ProhibitResidueProperties , core::pack::task::operation::ProhibitSpecifiedBaseResidueTypes , core::pack::task::operation::ReadResfile , core::pack::task::operation::ReadResfileAndObeyLengthEvents , core::pack::task::operation::ResFilter , core::pack::task::operation::ResFilterComposition , core::pack::task::operation::ResidueHasProperty , core::pack::task::operation::ResidueIndexIs , core::pack::task::operation::ResidueName3Is , core::pack::task::operation::ResiduePDBIndexIs , core::pack::task::operation::ResiduePDBInfoHasLabel , core::pack::task::operation::ResidueTypeFilter , core::pack::task::operation::ResLvlTaskOperation , core::pack::task::operation::RestrictAbsentCanonicalAAS , core::pack::task::operation::RestrictAbsentCanonicalAASExceptNativeRLT , core::pack::task::operation::RestrictAbsentCanonicalAASRLT , core::pack::task::operation::RestrictInteractionGraphThreadsOperation , core::pack::task::operation::RestrictResidueToRepacking , core::pack::task::operation::RestrictToRepacking , core::pack::task::operation::RestrictToResidueProperties , core::pack::task::operation::RestrictToSpecifiedBaseResidueTypes , core::pack::task::operation::RotamerExplosion , core::pack::task::operation::TaskOperation , core::pack::task::operation::UseMultiCoolAnnealer , protocols::antibody::task_operations::AddCDRProfileSetsOperation , protocols::antibody::task_operations::AddCDRProfilesOperation , protocols::antibody::task_operations::DisableAntibodyRegionOperation , protocols::antibody::task_operations::DisableCDRsOperation , protocols::antibody::task_operations::RestrictToCDRsAndNeighbors , protocols::constraint_generator::AtomPairConstraintGenerator , protocols::constraint_generator::ConstraintGenerator , protocols::constraint_generator::CoordinateConstraintGenerator , protocols::constraint_generator::DihedralConstraintGenerator , protocols::constraint_generator::DistanceConstraintGenerator , protocols::constraint_generator::HydrogenBondConstraintGenerator , protocols::constraint_generator::MembraneSpanConstraintGenerator , protocols::constraint_generator::MetalContactsConstraintGenerator , protocols::constraint_generator::ResidueTypeConstraintGenerator , protocols::constraint_generator::TerminiConstraintGenerator , protocols::denovo_design::architects::BetaSheetArchitect , protocols::denovo_design::architects::BlueprintArchitect , protocols::denovo_design::architects::CompoundArchitect , protocols::denovo_design::architects::DeNovoArchitect , protocols::denovo_design::architects::DeNovoMotifArchitect , protocols::denovo_design::architects::HelixArchitect , protocols::denovo_design::architects::PoseArchitect , protocols::denovo_design::architects::StrandArchitect , protocols::denovo_design::architects::StructureArchitect , protocols::denovo_design::components::HelixPairing , protocols::denovo_design::components::HelixSheetPairing , protocols::denovo_design::components::NullPoseFolder , protocols::denovo_design::components::PoseFolder , protocols::denovo_design::components::RandomTorsionPoseFolder , protocols::denovo_design::components::RemodelLoopMoverPoseFolder , protocols::denovo_design::components::Segment , protocols::denovo_design::components::SegmentPairing , protocols::denovo_design::components::StrandPairing , protocols::denovo_design::components::StructureData , protocols::denovo_design::connection::ConnectionArchitect , protocols::denovo_design::constraints::FileConstraintGenerator , protocols::denovo_design::task_operations::ConsensusLoopDesignOperation , protocols::dna::RestrictDesignToProteinDNAInterface , protocols::dna::WatsonCrickRotamerCouplings , protocols::enzdes::AddLigandMotifRotamers , protocols::enzdes::AddRigidBodyLigandConfs , protocols::enzdes::DetectProteinLigandInterface , protocols::enzdes::ProteinLigandInterfaceUpweighter , protocols::enzdes::SetCatalyticResPackBehavior , protocols::fldsgn::SheetConstraintGenerator , protocols::flxbb::LayerDesignOperation , protocols::fold_from_loops::constraint_generator::AutomaticSheetConstraintGenerator , protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator , protocols::fold_from_loops::utils::Nub , protocols::forge::remodel::RemodelRotamerLinks , protocols::hbnet::ConstrainHBondNetwork , protocols::hotspot_hashing::AddSearchPatternRotSetOp , protocols::legacy_sewing::LegacyReadNativeRotamersFile , protocols::matdes::BuildingBlockInterfaceOperation , protocols::pack_interface::ProteinProteinInterfaceUpweighter , protocols::parser::FragmentReader , protocols::simple_task_operations::RestrictToInterface , protocols::simple_task_operations::RestrictToLoops , protocols::simple_task_operations::RestrictToLoopsAndNeighbors , protocols::splice::DesignInterfacesOperation , protocols::splice::FindEndpointsOperation , protocols::splice::SampleRotamersFromPDB , protocols::task_operations::AlignedThreadOperation , protocols::task_operations::ConservativeDesignOperation , protocols::task_operations::CrystalContactsOperation , protocols::task_operations::DatabaseThread , protocols::task_operations::DesignAroundOperation , protocols::task_operations::DsspDesignOperation , protocols::task_operations::ImportUnboundRotamersOperation , protocols::task_operations::InteractingRotamerExplosion , protocols::task_operations::JointSequenceOperation , protocols::task_operations::LimitAromaChi2Operation , protocols::task_operations::LinkResidues , protocols::task_operations::ModifyAnnealer , protocols::task_operations::pHVariantTaskOperation , protocols::task_operations::PreventChainFromRepackingOperation , protocols::task_operations::PreventResiduesFromRepackingOperation , protocols::task_operations::ProteinCore , protocols::task_operations::ProteinInterfaceDesignOperation , protocols::task_operations::PruneBuriedUnsatsOperation , protocols::task_operations::ReadResfileFromDB , protocols::task_operations::ResfileCommandOperation , protocols::task_operations::ResidueProbDesignOperation , protocols::task_operations::RestrictChainToRepackingOperation , protocols::task_operations::RestrictConservedLowDdgOperation , protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation , protocols::task_operations::RestrictIdentitiesOperation , protocols::task_operations::RestrictNativeResiduesOperation , protocols::task_operations::RestrictNonSurfaceToRepackingOperation , protocols::task_operations::RestrictResiduesToRepackingOperation , protocols::task_operations::RestrictToAlignedSegmentsOperation , protocols::task_operations::RestrictToInterfaceVectorOperation , protocols::task_operations::RestrictToTerminiOperation , protocols::task_operations::RetrieveStoredTaskOperation , protocols::task_operations::SelectByDeltaScoreOperation , protocols::task_operations::SelectByDensityFitOperation , protocols::task_operations::SelectBySASAOperation , protocols::task_operations::SelectResiduesWithinChainOperation , protocols::task_operations::SeqprofConsensusOperation , protocols::task_operations::SequenceMotifTaskOperation , protocols::task_operations::SetIGTypeOperation , protocols::task_operations::ThreadSequenceOperation
• parse_tags() : protocols::splice::SpliceManager
• parse_target_tag() : protocols::pdbinfo_manipulations::AlignPDBInfoToSequences
• parse_task_operations() : protocols::constraint_movers::AddConstraintsToCurrentConformationMover , protocols::minimization_packing::MinPackMover , protocols::minimization_packing::PackRotamersMover , protocols::minimization_packing::TaskAwareMinMover , protocols::monte_carlo::GenericMonteCarloMover , protocols::switches::GraftSwitchMover
• parse_use_transactions_tag_item() : protocols::features::ReportToDB
• ParsedProtocol() : protocols::rosetta_scripts::ParsedProtocol
• ParsedTagCache() : protocols::multistage_rosetta_scripts::ParsedTagCache
• parser() : protocols::jd2::JobDistributor
• ParserJobInputter() : protocols::protein_interface_design::ParserJobInputter
• partial_assign_relaxed_state() : core::pack::interaction_graph::FASTERNode
• partial_assign_state() : core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode
• partial_assign_state_with_lowest_one_body_energy() : core::pack::interaction_graph::FASTERNode
• partial_charge() : core::chemical::sdf::MolFileIOAtom
• partial_state_assignment() : protocols::flexpack::interaction_graph::FlexbbNode
• partially_assign_state() : protocols::flexpack::interaction_graph::MinimalistFlexbbNode
• partially_solvated() : core::scoring::sc::ElectrostaticComplementarityCalculator , core::simple_metrics::composite_metrics::ElectrostaticComplementarityMetric
• partialrms() : protocols::loop_grower::LoopPartialSolution
• PartialSecondarySimilarity() : protocols::frag_picker::scores::PartialSecondarySimilarity
• PartialThreadingMover() : protocols::comparative_modeling::PartialThreadingMover
• Particle() : core::optimization::Particle
• ParticleSwarmMinimizer() : core::optimization::ParticleSwarmMinimizer
• partition() : protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator
• partition_by_jump() : core::kinematics::FoldTree
• partition_by_residue() : core::kinematics::FoldTree
• partition_coloring() : core::kinematics::FoldTree
• partition_definition() : protocols::rna::denovo::coarse::CoarseRNA_LoopCloser , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• partition_splits_an_input_domain() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• PartitionAggregateFunction() : protocols::multistate_design::PartitionAggregateFunction
• PartitionContactScreener() : protocols::stepwise::screener::PartitionContactScreener
• PartitionedSearchPattern() : protocols::hotspot_hashing::PartitionedSearchPattern
• partitions_split_a_submotif() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• partner() : protocols::docking::DockingEnsemble
• partner1() : protocols::contact_map::Contact
• partner2() : protocols::contact_map::Contact
• PartnerMotifScorer() : protocols::sewing::scoring::PartnerMotifScorer
• partners() : core::scoring::PDvertex , core::scoring::power_diagram::PDvertex , protocols::docking::DockingHighRes , protocols::docking::DockingProtocol , protocols::docking::DockSetupMover , protocols::docking::TemperedDocking , protocols::protein_interface_design::filters::HbondsToResidueFilter
• pass_1_merge_residues_as_necessary() : core::io::pose_from_sfr::PoseFromSFRBuilder
• pass_2_resolve_residue_types() : core::io::pose_from_sfr::PoseFromSFRBuilder
• pass_3_verify_sufficient_backbone_atoms() : core::io::pose_from_sfr::PoseFromSFRBuilder
• pass_4_redo_termini() : core::io::pose_from_sfr::PoseFromSFRBuilder
• pass_5_note_discarded_atoms() : core::io::pose_from_sfr::PoseFromSFRBuilder
• pass_all_filters() : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• pass_clash_check() : protocols::stepwise::modeler::rna::phosphate::PhosphateMover
• pass_count() : protocols::stepwise::screener::AlignRMSD_Screener
• pass_FARFAR_no_auto_bulge_filter() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• pass_metropolis() : core::pack::annealer::SimAnnealerBase , protocols::canonical_sampling::SidechainMetropolisHastingsMover , protocols::simple_moves::sidechain_moves::SidechainMCMover
• pass_metropolis_multiple_nodes_changing() : protocols::flexpack::annealer::FlexbbSimAnnealer
• pass_start_pose() : protocols::antibody::H3RefineCCD
• pass_the_loop() : protocols::antibody::H3PerturbCCD
• passed_automorphism() : protocols::motifs::MotifHit
• passes_com_vector_criterion() : protocols::match::NumNeighborsMPM
• passes_etable_filter() : protocols::match::output::UpstreamDownstreamCollisionFilter
• passes_fast_scan() : protocols::rna::movers::RNA_LoopCloser
• passes_filter() : protocols::match::output::LimitHitsPerRotamerFilter , protocols::match::output::MatchCollisionFilter , protocols::match::output::MatchFilter , protocols::match::output::StateAccumulatingMatchFilter , protocols::match::output::UpstreamCollisionFilter , protocols::match::output::UpstreamDownstreamCollisionFilter , protocols::topology_broker::TopologyClaimer
• passes_filters() : protocols::match::output::MatchProcessor
• passes_hardsphere_filter() : protocols::match::output::UpstreamCollisionFilter , protocols::match::output::UpstreamDownstreamCollisionFilter
• passport() : protocols::environment::ClientMover , protocols::environment::EXCN_Env_Security_Exception
• passport_updated() : protocols::abinitio::abscript::AbscriptLoopCloserCM , protocols::abinitio::abscript::FragmentCM , protocols::abinitio::abscript::RigidChunkCM , protocols::environment::ClientMover , protocols::environment::CoMTrackerCM , protocols::environment::ScriptCM , protocols::loops::loop_mover::LoopCM , protocols::rigid::UniformRigidBodyCM
• Patch() : core::chemical::Patch
• patch_map() : core::chemical::PoseResidueTypeSet , core::chemical::ResidueTypeSet
• patch_name_from_affix() : core::chemical::carbohydrates::CarbohydrateInfoManager
• patch_names() : core::chemical::ResidueTypeFinder
• patch_str() : core::sequence::AnnotatedSequence
• patchdock_entry_num() : protocols::protein_interface_design::PatchdockReader
• patchdock_fname() : protocols::protein_interface_design::PatchdockReader
• PatchdockReader() : protocols::protein_interface_design::PatchdockReader
• PatchdockTransform() : protocols::protein_interface_design::movers::PatchdockTransform
• patched_name() : core::chemical::Patch
• patches() : core::chemical::PoseResidueTypeSet , core::chemical::ResidueTypeSet
• patches_can_apply() : protocols::mainchain_potential::GenerateMainchainPotential
• PatchOperation() : protocols::canonical_sampling::PatchOperation
• path() : protocols::legacy_sewing::Assembly , protocols::motifs::Motif
• path_dist() : core::scoring::AtomNeighbor , core::scoring::SmallAtNb
• path_distance() : core::chemical::ResidueType , core::conformation::Residue , core::scoring::etable::count_pair::CountPairGeneric
• path_distance_OK() : core::scoring::carbon_hbonds::CarbonHBondEnergy
• path_distances() : core::chemical::ResidueType , core::conformation::Residue
• path_length() : protocols::loop_grower::DensSkeleton
• path_tightness() : protocols::simple_filters::AveragePathLengthFilter
• pb_bound_tag() : core::scoring::methods::EnergyMethodOptions
• pb_unbound_tag() : core::scoring::methods::EnergyMethodOptions
• pbest() : core::optimization::Particle
• PBLifetimeCache() : core::scoring::methods::PBLifetimeCache
• PBP_clustering_at_chain_closure() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• PcaEvaluator() : protocols::abinitio::PcaEvaluator
• PCluster() : protocols::pockets::PCluster
• PClusterSet() : protocols::pockets::PClusterSet
• pconf_creation() : protocols::environment::Environment
• pconf_destruction() : protocols::environment::Environment
• PCS_data() : protocols::scoring::methods::pcs::PCS_data
• PCS_data_from_pose() : protocols::scoring::methods::pcs::PCS_Energy , protocols::scoring::methods::pcsTs1::PCS_Energy_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_Ts4
• PCS_data_input() : protocols::scoring::methods::pcs::PCS_data_input
• PCS_data_input_manager() : protocols::scoring::methods::pcs::PCS_data_input_manager
• PCS_data_input_manager_Ts1() : protocols::scoring::methods::pcsTs1::PCS_data_input_manager_Ts1
• PCS_data_input_manager_Ts2() : protocols::scoring::methods::pcsTs2::PCS_data_input_manager_Ts2
• PCS_data_input_manager_Ts3() : protocols::scoring::methods::pcsTs3::PCS_data_input_manager_Ts3
• PCS_data_input_manager_Ts4() : protocols::scoring::methods::pcsTs4::PCS_data_input_manager_Ts4
• PCS_data_input_Ts1() : protocols::scoring::methods::pcsTs1::PCS_data_input_Ts1
• PCS_data_input_Ts2() : protocols::scoring::methods::pcsTs2::PCS_data_input_Ts2
• PCS_data_input_Ts3() : protocols::scoring::methods::pcsTs3::PCS_data_input_Ts3
• PCS_data_input_Ts4() : protocols::scoring::methods::pcsTs4::PCS_data_input_Ts4
• PCS_data_per_lanthanides() : protocols::scoring::methods::pcs::PCS_data_per_lanthanides
• PCS_data_per_lanthanides_Ts1() : protocols::scoring::methods::pcsTs1::PCS_data_per_lanthanides_Ts1
• PCS_data_per_lanthanides_Ts2() : protocols::scoring::methods::pcsTs2::PCS_data_per_lanthanides_Ts2
• PCS_data_per_lanthanides_Ts3() : protocols::scoring::methods::pcsTs3::PCS_data_per_lanthanides_Ts3
• PCS_data_per_lanthanides_Ts4() : protocols::scoring::methods::pcsTs4::PCS_data_per_lanthanides_Ts4
• PCS_data_Ts1() : protocols::scoring::methods::pcsTs1::PCS_data_Ts1
• PCS_data_Ts2() : protocols::scoring::methods::pcsTs2::PCS_data_Ts2
• PCS_data_Ts3() : protocols::scoring::methods::pcsTs3::PCS_data_Ts3
• PCS_data_Ts4() : protocols::scoring::methods::pcsTs4::PCS_data_Ts4
• PCS_Energy() : protocols::scoring::methods::pcs::PCS_Energy
• PCS_Energy_parameters_manager() : protocols::scoring::methods::pcs::PCS_Energy_parameters_manager
• PCS_Energy_parameters_manager_Ts1() : protocols::scoring::methods::pcsTs1::PCS_Energy_parameters_manager_Ts1
• PCS_Energy_parameters_manager_Ts2() : protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2
• PCS_Energy_parameters_manager_Ts3() : protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3
• PCS_Energy_parameters_manager_Ts4() : protocols::scoring::methods::pcsTs4::PCS_Energy_parameters_manager_Ts4
• PCS_Energy_Ts1() : protocols::scoring::methods::pcsTs1::PCS_Energy_Ts1
• PCS_Energy_Ts2() : protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2
• PCS_Energy_Ts3() : protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3
• PCS_Energy_Ts4() : protocols::scoring::methods::pcsTs4::PCS_Energy_Ts4
• PCS_experimental() : protocols::scoring::methods::pcs::PCS_line_data , protocols::scoring::methods::pcsTs1::PCS_line_data_Ts1 , protocols::scoring::methods::pcsTs2::PCS_line_data_Ts2 , protocols::scoring::methods::pcsTs3::PCS_line_data_Ts3 , protocols::scoring::methods::pcsTs4::PCS_line_data_Ts4
• PCS_file_data() : protocols::scoring::methods::pcs::PCS_file_data
• PCS_file_data_Ts1() : protocols::scoring::methods::pcsTs1::PCS_file_data_Ts1
• PCS_file_data_Ts2() : protocols::scoring::methods::pcsTs2::PCS_file_data_Ts2
• PCS_file_data_Ts3() : protocols::scoring::methods::pcsTs3::PCS_file_data_Ts3
• PCS_file_data_Ts4() : protocols::scoring::methods::pcsTs4::PCS_file_data_Ts4
• PCS_FragDistance() : protocols::frag_picker::scores::PCS_FragDistance
• PCS_line_data() : protocols::scoring::methods::pcs::PCS_line_data
• PCS_line_data_Ts1() : protocols::scoring::methods::pcsTs1::PCS_line_data_Ts1
• PCS_line_data_Ts2() : protocols::scoring::methods::pcsTs2::PCS_line_data_Ts2
• PCS_line_data_Ts3() : protocols::scoring::methods::pcsTs3::PCS_line_data_Ts3
• PCS_line_data_Ts4() : protocols::scoring::methods::pcsTs4::PCS_line_data_Ts4
• PCS_multi_data_from_noone() : protocols::scoring::methods::pcs2::PcsEnergy
• PCS_multi_data_from_pose() : protocols::scoring::methods::pcs2::PcsEnergy
• PCS_tensor() : protocols::scoring::methods::pcs::PCS_tensor
• PCS_tensor_Ts1() : protocols::scoring::methods::pcsTs1::PCS_tensor_Ts1
• PCS_tensor_Ts2() : protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2
• PCS_tensor_Ts3() : protocols::scoring::methods::pcsTs3::PCS_tensor_Ts3
• PCS_tensor_Ts4() : protocols::scoring::methods::pcsTs4::PCS_tensor_Ts4
• PCS_tolerance() : protocols::scoring::methods::pcs::PCS_line_data , protocols::scoring::methods::pcsTs1::PCS_line_data_Ts1 , protocols::scoring::methods::pcsTs2::PCS_line_data_Ts2 , protocols::scoring::methods::pcsTs3::PCS_line_data_Ts3 , protocols::scoring::methods::pcsTs4::PCS_line_data_Ts4
• PCSData() : core::scoring::nmr::pcs::PCSData
• PcsDataCenter() : protocols::scoring::methods::pcs2::PcsDataCenter
• PcsDataCenterManager() : protocols::scoring::methods::pcs2::PcsDataCenterManager
• PcsDataCenterManagerSingleton() : protocols::scoring::methods::pcs2::PcsDataCenterManagerSingleton
• PcsDataLanthanide() : protocols::scoring::methods::pcs2::PcsDataLanthanide
• PCSEnergy() : protocols::nmr::pcs::PCSEnergy
• PcsEnergy() : protocols::scoring::methods::pcs2::PcsEnergy
• PcsEnergyController() : protocols::topology_broker::PcsEnergyController
• PcsEnergyParameter() : protocols::scoring::methods::pcs2::PcsEnergyParameter
• PcsEnergyParameterManager() : protocols::scoring::methods::pcs2::PcsEnergyParameterManager
• PcsGridSearchParameter() : protocols::scoring::methods::pcs2::PcsGridSearchParameter
• PcsGridSearchParameterManager() : protocols::scoring::methods::pcs2::PcsGridSearchParameterManager
• PcsInputCenter() : protocols::scoring::methods::pcs2::PcsInputCenter
• PcsInputCenterManager() : protocols::scoring::methods::pcs2::PcsInputCenterManager
• PcsInputFile() : protocols::scoring::methods::pcs2::PcsInputFile
• PcsInputLine() : protocols::scoring::methods::pcs2::PcsInputLine
• PCSLigandTransformMover() : protocols::nmr::pcs::PCSLigandTransformMover
• PCSMultiGrid() : protocols::qsar::scoring_grid::PCSMultiGrid
• PCSMultiSet() : core::scoring::nmr::pcs::PCSMultiSet
• PCSSingle() : core::scoring::nmr::pcs::PCSSingle
• PCSSingleGrid() : protocols::qsar::scoring_grid::PCSSingleGrid
• PCSSingleSet() : core::scoring::nmr::pcs::PCSSingleSet
• PCSTensor() : core::scoring::nmr::pcs::PCSTensor
• PcsTensor() : protocols::scoring::methods::pcs2::PcsTensor
• PCSTensorOptimizer() : protocols::nmr::pcs::PCSTensorOptimizer
• pd_edge_table_all_zeros() : core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::PDEdge
• pd_reader() : protocols::protein_interface_design::movers::PatchdockTransform
• pdamp() : core::scoring::MultipoleParameter
• PDatom() : core::scoring::PDatom
• pdb() : core::scoring::motif::ResPairMotif
• PDB() : protocols::sparta::PDB
• pdb2pose() : core::pose::PDBInfo
• pdb_author() : core::io::StructFileRepOptions
• pdb_chain() : protocols::pmut_scan::MutationData
• pdb_code_from_rosetta_name() : core::io::NomenclatureManager
• pdb_comments() : core::io::StructFileRep , core::io::StructFileRepOptions
• pdb_components_directory() : core::chemical::GlobalResidueTypeSet
• pdb_components_overrides() : core::chemical::GlobalResidueTypeSet
• pdb_count() : protocols::fold_from_loops::movers::ResidueLabelsToPymolSelectionMover
• pdb_end() : protocols::antibody::clusters::CDRCluster
• pdb_info() : core::pose::Pose
• pdb_name() : protocols::calc_taskop_filters::RelativePoseFilter
• pdb_numb() : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• pdb_numbering() : protocols::hbnet::HBNet
• pdb_output() : protocols::helical_bundle::BackboneGridSampler , protocols::helical_bundle::BundleGridSampler
• pdb_parents() : core::io::StructFileRepOptions
• pdb_prefix() : protocols::helical_bundle::BackboneGridSampler , protocols::helical_bundle::BundleGridSampler
• pdb_profile() : protocols::splice::RotLibdb , protocols::splice::SpliceSegment
• pdb_rotamers_file() : core::chemical::rotamers::PDBRotamerLibrarySpecification
• pdb_segments() : protocols::sewing::data_storage::SmartAssembly , protocols::sewing::hashing::AlignmentGenerator , protocols::sewing::hashing::BasisMapGenerator , protocols::sewing::hashing::EdgeMapGenerator , protocols::sewing::hashing::Hasher , protocols::splice::SpliceManager
• pdb_start() : protocols::antibody::clusters::CDRCluster
• pdb_to_next_allowed_partners() : protocols::splice::BBMatching
• pdb_to_prev_allowed_partners() : protocols::splice::BBMatching
• pdb_to_profile_map() : protocols::splice::SpliceSegment
• PDBChunkLibraryInputter() : protocols::jd3::chunk_library_inputters::PDBChunkLibraryInputter
• PdbDataFeatures() : protocols::features::PdbDataFeatures
• PDBDumpMover() : protocols::moves::PDBDumpMover
• PDBFullModelInputter() : protocols::jd3::full_model_inputters::PDBFullModelInputter
• pdbid() : core::fragment::AnnotatedFragData , core::fragment::FragData
• PDBInfo() : core::pose::PDBInfo
• PDBJobInputter() : protocols::jd2::PDBJobInputter
• PDBJobOutputter() : protocols::jd2::PDBJobOutputter
• PDBLandmark() : protocols::antibody::PDBLandmark
• pdbname() : protocols::cryst::Spacegroup , protocols::cryst::WallpaperGroup , protocols::dna::DnaInterfacePacker , protocols::simple_filters::SSMotifFinder
• pdboutput() : protocols::dna::DnaInterfacePacker
• PDBOutput() : protocols::dna::PDBOutput
• pdbpos() : core::fragment::AnnotatedFragData , core::fragment::FragData
• PDBPoseInputStream() : core::import_pose::pose_stream::PDBPoseInputStream
• PDBPoseInputter() : protocols::jd3::pose_inputters::PDBPoseInputter
• PDBPoseMap() : core::pose::PDBPoseMap
• PDBPoseOutputSpecification() : protocols::jd3::pose_outputters::PDBPoseOutputSpecification
• PDBPoseOutputter() : protocols::jd3::pose_outputters::PDBPoseOutputter
• PDBReloadMover() : protocols::simple_moves::PDBReloadMover
• PDBRotamerLibrarySpecification() : core::chemical::rotamers::PDBRotamerLibrarySpecification
• PDBSilentStruct() : core::import_pose::PDBSilentStruct
• PDBSilentStructCreator() : core::import_pose::PDBSilentStructCreator
• PDBTrajectoryRecorder() : protocols::canonical_sampling::PDBTrajectoryRecorder
• PDBWriter() : protocols::match::output::PDBWriter
• PDDFEnergy() : protocols::scoring::methods::saxs::PDDFEnergy
• PDDFEnergyCreator() : protocols::scoring::methods::saxs::PDDFEnergyCreator
• PDDFScoreFilter() : protocols::simple_filters::PDDFScoreFilter
• PDEdge() : core::pack::interaction_graph::PDEdge
• PDinter() : core::scoring::PDinter , core::scoring::power_diagram::PDinter
• PDInteractionGraph() : core::pack::interaction_graph::PDInteractionGraph
• PDNode() : core::pack::interaction_graph::PDNode
• PDsphere() : core::scoring::power_diagram::PDsphere
• PDvertex() : core::scoring::PDvertex , core::scoring::power_diagram::PDvertex
• peak_id() : protocols::noesy_assign::CrossPeak
• peak_volume() : protocols::noesy_assign::PeakAssignment
• PeakAssignment() : protocols::noesy_assign::PeakAssignment
• PeakAssignmentParameters() : protocols::noesy_assign::PeakAssignmentParameters
• PeakAssignmentResidueMap() : protocols::noesy_assign::PeakAssignmentResidueMap
• PeakCalibrator() : protocols::noesy_assign::PeakCalibrator
• PeakCalibratorMap() : protocols::noesy_assign::PeakCalibratorMap
• PeakFileFormat() : protocols::noesy_assign::PeakFileFormat
• PeakFileFormat_Base() : protocols::noesy_assign::PeakFileFormat_Base
• PeakFileFormat_Sparky() : protocols::noesy_assign::PeakFileFormat_Sparky
• PeakFileFormat_xeasy() : protocols::noesy_assign::PeakFileFormat_xeasy
• PeakFileFormat_xpk() : protocols::noesy_assign::PeakFileFormat_xpk
• peaks() : protocols::noesy_assign::CrossPeakList , protocols::noesy_assign::PeakCalibrator
• peek_back() : protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering >
• peek_front() : protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering >
• penalties() : core::scoring::aa_repeat_energy::AARepeatEnergy
• penalty() : core::fragment::picking_old::vall::eval::ABEGOEval , core::scoring::MembraneEmbed , core::scoring::netcharge_energy::NetChargeEnergySetup
• penalty_from_score() : protocols::simple_filters::ResidueIEFilter
• peptide_chain() : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_entry() : protocols::peptide_deriver::PeptideDeriverBasicStreamOutputter , protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter , protocols::peptide_deriver::PeptideDeriverOutputter , protocols::peptide_deriver::PeptideDeriverOutputterContainer , protocols::peptide_deriver::PeptideDeriverPoseOutputter
• peptide_first_res() : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_last_res() : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_length() : protocols::peptide_deriver::PeptideDeriverBasicStreamOutputter , protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter , protocols::peptide_deriver::PeptideDeriverOutputter , protocols::peptide_deriver::PeptideDeriverOutputterContainer , protocols::peptide_deriver::PeptideDeriverPoseOutputter
• peptide_nres() : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_random_loop_model() : protocols::flexpep_docking::FlexPepDockingProtocol
• peptide_stub_mover_initialized() : protocols::helical_bundle::BackboneGridSampler
• PeptideBondEnergy() : core::scoring::methods::PeptideBondEnergy
• PeptideCyclizeMover() : protocols::cyclic_peptide::PeptideCyclizeMover
• PeptideDeriverBasicStreamOutputter() : protocols::peptide_deriver::PeptideDeriverBasicStreamOutputter
• PeptideDeriverFilter() : protocols::peptide_deriver::PeptideDeriverFilter
• PeptideDeriverMarkdownStreamOutputter() : protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter
• PeptideDeriverOutputter() : protocols::peptide_deriver::PeptideDeriverOutputter
• PeptideDeriverOutputterContainer() : protocols::peptide_deriver::PeptideDeriverOutputterContainer
• PeptideDeriverPoseOutputter() : protocols::peptide_deriver::PeptideDeriverPoseOutputter
• PeptideInternalHbondsFilter() : protocols::cyclic_peptide::PeptideInternalHbondsFilter
• PeptideInternalHbondsMetric() : protocols::cyclic_peptide::PeptideInternalHbondsMetric
• PeptideOrientationMover() : protocols::membrane_benchmark::PeptideOrientationMover
• PeptideStapleDesignMover() : protocols::protein_interface_design::movers::PeptideStapleDesignMover
• PeptideStapleMover() : protocols::simple_moves::PeptideStapleMover
• PeptideStubMover() : protocols::cyclic_peptide::PeptideStubMover
• per_atom_lipid_accessibility() : core::conformation::membrane::ImplicitLipidInfo
• per_chain_renumbering() : core::io::StructFileRepOptions
• per_constraint_build_points() : protocols::match::Matcher
• percent_native() : protocols::legacy_sewing::Assembly
• perform_all_reactions() : protocols::enzymatic_movers::EnzymaticMover
• perform_bump_check() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• perform_checks() : core::chemical::ResidueType
• perform_local_refinement() : protocols::hotspot_hashing::movers::PlaceProbeMover
• perform_major_reaction_only() : protocols::enzymatic_movers::EnzymaticMover
• perform_rama_check() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• perform_reaction() : protocols::enzymatic_movers::DNAMethyltransferaseMover , protocols::enzymatic_movers::EnzymaticMover , protocols::enzymatic_movers::GlycosyltransferaseMover , protocols::enzymatic_movers::KinaseMover , protocols::enzymatic_movers::NTerminalAcetyltransferaseMover
• perform_single_iteration() : protocols::cyclic_peptide::PeptideStubMover
• perform_structure_rmsd() : protocols::indexed_structure_store::search::PairQueryExecutor , protocols::indexed_structure_store::search::SingleQueryExecutor
• perform_validation_test() : core::pack::annealer::SmartFixbbSimAnnealer
• performing_pure_insertion() : protocols::forge::build::SegmentInsert
• performs_major_reaction_only() : protocols::enzymatic_movers::EnzymaticMover
• period() : core::scoring::methods::BBDepCartBondedParameters , core::scoring::methods::BBIndepCartBondedParameters , core::scoring::methods::CartBondedParameters
• periodic_range() : protocols::canonical_sampling::CanonicalSamplingMover
• PeriodicBoundFunc() : core::scoring::constraints::PeriodicBoundFunc
• PeriodicBoxMover() : protocols::simple_moves::PeriodicBoxMover
• PeriodicFunc() : core::scoring::func::PeriodicFunc
• periodicity() : core::scoring::dna::TorsionFourierComponent , protocols::toolbox::match_enzdes_util::GeomSampleInfo
• permitted_overlap() : protocols::match::MatcherTask
• permutate_n_vv_of_pairs() : protocols::motif_grafting::movers::MotifGraftMover
• permute_string() : protocols::energy_based_clustering::EnergyBasedClusteringProtocol
• PerNativeRRReporterHuman() : protocols::rotamer_recovery::PerNativeRRReporterHuman
• PerResidueClashMetric() : core::simple_metrics::per_residue_metrics::PerResidueClashMetric
• PerResidueDensityFitMetric() : core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric
• PerResidueEnergyMetric() : core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric
• PerResidueGlycanLayerMetric() : core::simple_metrics::per_residue_metrics::PerResidueGlycanLayerMetric
• PerResidueRealMetric() : core::simple_metrics::PerResidueRealMetric
• PerResidueRMSDMetric() : core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric
• PerResidueSasaMetric() : core::simple_metrics::per_residue_metrics::PerResidueSasaMetric
• PerResidueStringMetric() : core::simple_metrics::PerResidueStringMetric
• PerSphereAccumulator() : core::scoring::packstat::PerSphereAccumulator
• pert() : protocols::minimization_packing::PertMinMover
• pert_protein() : protocols::simple_filters::ResidueDepthCalculator
• pert_size() : protocols::minimization_packing::PertMinMover
• PertMinMover() : protocols::minimization_packing::PertMinMover
• perturb() : protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionSampler , protocols::kinematic_closure::perturbers::Perturber , protocols::ligand_docking::ga_ligand_dock::EntropyEstimator , protocols::mpi_refinement::Serial_Refine , protocols::protein_interface_design::movers::LoopMoverFromCommandLine , protocols::protein_interface_design::movers::LoopRemodel
• perturb_anchor() : protocols::anchored_design::AnchoredDesignMover
• perturb_angles() : protocols::kinematic_closure::ClosureProblem
• perturb_beta_residue() : protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber
• perturb_c_n() : protocols::kinematic_closure::ClosureProblem
• perturb_c_n_ca() : protocols::kinematic_closure::ClosureProblem
• perturb_ca_c() : protocols::kinematic_closure::ClosureProblem
• perturb_ca_c_n() : protocols::kinematic_closure::ClosureProblem
• perturb_chain() : protocols::loops::loop_closure::kinematic_closure::BaseTabooPerturber , protocols::loops::loop_closure::kinematic_closure::KinematicPerturber , protocols::loops::loop_closure::kinematic_closure::NeighborDependentTorsionSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::VicinitySamplingKinematicPerturber
• perturb_chi() : protocols::simple_moves::sidechain_moves::SidechainMCMover , protocols::simple_moves::sidechain_moves::SidechainMover
• perturb_chis() : protocols::cryst::DockLatticeMover
• perturb_dBR_and_relax() : core::pack::interaction_graph::FASTERInteractionGraph
• perturb_lattice() : protocols::cryst::DockLatticeMover
• perturb_lengths() : protocols::kinematic_closure::ClosureProblem
• perturb_lig() : protocols::ligand_docking::ga_ligand_dock::LigandAligner
• perturb_molecule_move() : protocols::simple_moves::PeriodicBoxMover
• perturb_n_ca() : protocols::kinematic_closure::ClosureProblem
• perturb_n_ca_c() : protocols::kinematic_closure::ClosureProblem
• perturb_omega() : protocols::kinematic_closure::ClosureProblem
• perturb_phi() : protocols::kinematic_closure::ClosureProblem
• perturb_pose() : protocols::rna::movers::RNAIdealizeMover
• perturb_psi() : protocols::kinematic_closure::ClosureProblem
• perturb_rb() : protocols::cryst::DockLatticeMover
• perturb_rot_within_well() : protocols::simple_moves::sidechain_moves::SidechainMover
• perturb_sBR_and_relax() : core::pack::interaction_graph::FASTERInteractionGraph
• perturb_sequence() : protocols::loop_modeler::perturbers::LoopHashPerturber
• perturb_subset() : protocols::kinematic_closure::perturbers::BondAnglePerturber , protocols::kinematic_closure::perturbers::FragmentPerturber , protocols::kinematic_closure::perturbers::IdealizeNonPhiPsi , protocols::kinematic_closure::perturbers::LogFilePerturber , protocols::kinematic_closure::perturbers::OmegaPerturber , protocols::kinematic_closure::perturbers::Perturber , protocols::kinematic_closure::perturbers::PerturberSet , protocols::kinematic_closure::perturbers::Rama2bPerturber , protocols::kinematic_closure::perturbers::RamaPerturber , protocols::kinematic_closure::perturbers::UniformPerturber , protocols::kinematic_closure::perturbers::VicinityPerturber , protocols::kinematic_closure::perturbers::WalkingBondAnglePerturber , protocols::kinematic_closure::perturbers::WalkingPerturber , protocols::loop_modeler::perturbers::LoopHashPerturber
• perturb_subset_with_balance() : protocols::kinematic_closure::perturbers::IdealizeNonPhiPsi , protocols::kinematic_closure::perturbers::Perturber , protocols::kinematic_closure::perturbers::PerturberSet , protocols::kinematic_closure::perturbers::RamaPerturber , protocols::kinematic_closure::perturbers::UniformPerturber , protocols::kinematic_closure::perturbers::VicinityPerturber , protocols::kinematic_closure::perturbers::WalkingBondAnglePerturber , protocols::kinematic_closure::perturbers::WalkingPerturber , protocols::loop_modeler::perturbers::LoopHashPerturber
• perturb_torsion() : core::import_pose::RNA_HelixAssembler
• perturb_torsions() : protocols::kinematic_closure::ClosureProblem
• perturb_values() : protocols::helical_bundle::PerturbBundle
• perturb_weights() : core::scoring::ScoreFunction
• perturb_with_balance() : protocols::kinematic_closure::perturbers::Perturber
• perturbation_magnitude() : core::conformation::parametric::RealValuedParameter , protocols::simple_moves::SetTorsion
• perturbation_set() : core::conformation::parametric::RealValuedParameter
• perturbation_type() : core::conformation::parametric::RealValuedParameter , protocols::simple_moves::SetTorsion
• perturbation_type_enum_from_string() : core::conformation::parametric::RealValuedParameter
• perturbation_type_string_from_enum() : core::conformation::parametric::RealValuedParameter
• PerturbBundle() : protocols::helical_bundle::PerturbBundle
• PerturbBundleHelix() : protocols::helical_bundle::PerturbBundleHelix
• PerturbByBins() : protocols::simple_moves::bin_transitions::PerturbByBins
• PerturbChiSidechainMover() : protocols::simple_moves::sidechain_moves::PerturbChiSidechainMover
• perturbed_sequence() : protocols::kinematic_closure::ClosureProblem
• perturber() : protocols::docking::DockingProtocol , protocols::loops::loop_closure::kinematic_closure::KinematicMover
• perturber_ct_namer() : protocols::denovo_design::movers::BuildDeNovoBackboneMover
• perturber_exhausted() : protocols::loops::loop_closure::kinematic_closure::KinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber
• perturber_group_name() : protocols::denovo_design::movers::BuildDeNovoBackboneMover
• perturber_type() : protocols::loops::loop_closure::kinematic_closure::KinematicPerturber , protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::NeighborDependentTorsionSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TabooSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::VicinitySamplingKinematicPerturber
• PerturberSet() : protocols::kinematic_closure::perturbers::PerturberSet
• PerturbRotamerSidechainMover() : protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover
• pH_mode() : core::pack::palette::PackerPalette
• Pharmacophore() : protocols::ligand_docking::ga_ligand_dock::Pharmacophore
• pharmacophores_defined() : protocols::ligand_docking::ga_ligand_dock::ConstraintInfo
• phase() : core::scoring::dna::TorsionFourierComponent
• pHEnergy() : core::scoring::methods::pHEnergy
• PhenixInterface() : core::scoring::cryst::PhenixInterface
• phi() : core::chemical::Adduct , core::chemical::AtomICoor , core::chemical::MutableICoorRecord , core::chemical::orbitals::ICoorOrbitalData , core::fragment::picking_old::vall::VallResidue , core::io::raw_data::DecoyStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::pose::Pose , core::scoring::motif::Xfres , core::scoring::power_diagram::SAnode , core::scoring::SAnode , protocols::backbone_moves::local_backbone_mover::FreePeptide , protocols::backbone_moves::local_backbone_mover::Residue , protocols::denovo_design::components::ResidueDihedrals , protocols::fldsgn::topology::DimerPairing , protocols::frag_picker::PhiPsiTalosIO
• Phi() : protocols::frag_picker::scores::Phi
• phi() : protocols::frag_picker::VallResidue , protocols::frags::RMSVallData , protocols::frags::VallData , protocols::kinematic_closure::ClosureProblem , protocols::loophash::BackboneSegment , protocols::match::upstream::ProteinBackboneBuildPoint , protocols::optimize_weights::PNatRotOptEPositionData , protocols::splice::BBDofs , protocols::stepwise::modeler::protein::MainChainTorsionSet
• phi_index() : core::scoring::OmegaTether
• phi_max() : core::sequence::ABEGO
• phi_min() : core::sequence::ABEGO
• phipsi_in_allowed_rama() : core::scoring::Ramachandran
• phipsi_in_forbidden_rama() : core::scoring::Ramachandran
• PhiPsiRmsd() : protocols::frag_picker::scores::PhiPsiRmsd
• PhiPsiSquareWell() : protocols::frag_picker::scores::PhiPsiSquareWell
• PhiPsiTalosIO() : protocols::frag_picker::PhiPsiTalosIO
• PhiSelector() : core::select::residue_selector::PhiSelector
• phore_overlaps_with_existing() : protocols::ligand_docking::ga_ligand_dock::ConstraintInfo
• phores() : protocols::ligand_docking::ga_ligand_dock::ConstraintInfo
• phosphate_move_list() : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• PhosphateMove() : protocols::stepwise::modeler::rna::phosphate::PhosphateMove
• PhosphateMover() : protocols::stepwise::modeler::rna::phosphate::PhosphateMover
• PhosphateScreener() : protocols::stepwise::screener::PhosphateScreener
• pHVariantTaskOperation() : protocols::task_operations::pHVariantTaskOperation
• physical() : protocols::environment::claims::JumpClaim
• pick() : protocols::backbone_moves::local_backbone_mover::gap_solution_pickers::GapSolutionPicker , protocols::backbone_moves::local_backbone_mover::gap_solution_pickers::RandomGapSolutionPicker , protocols::kinematic_closure::pivot_pickers::EndToEndPivots , protocols::kinematic_closure::pivot_pickers::FixedOffsetPivots , protocols::kinematic_closure::pivot_pickers::FixedOffsetsPivots , protocols::kinematic_closure::pivot_pickers::FixedPivots , protocols::kinematic_closure::pivot_pickers::LoopPivots , protocols::kinematic_closure::pivot_pickers::PivotPicker , protocols::kinematic_closure::pivot_pickers::StandardPivots
• pick_a_rotamer() : core::pack::annealer::RotamerAssigningAnnealer , protocols::flexpack::annealer::FlexbbSimAnnealer
• pick_a_rotamer_for_node() : core::pack::annealer::RotamerAssigningAnnealer
• pick_a_rotamer_for_sBR() : core::pack::annealer::FASTERAnnealer
• pick_all_fragments() : protocols::forge::components::VarLengthBuild
• pick_and_apply() : protocols::kinematic_closure::solution_pickers::FilteredSolutions , protocols::kinematic_closure::solution_pickers::RandomSolutions , protocols::kinematic_closure::solution_pickers::SolutionPicker
• pick_and_cache_fragments() : protocols::denovo_design::components::Picker
• pick_baserotamer_from_rotblock() : core::pack::rotamer_set::ContinuousRotamerSet
• pick_candidates() : protocols::frag_picker::FragmentPicker
• pick_chunk_candidates() : protocols::frag_picker::FragmentPicker
• pick_consensus_AA() : protocols::recon_design::FindConsensusSequence
• pick_consensus_AA_mpi() : protocols::recon_design::FindConsensusSequence
• pick_enrich_methods() : protocols::mpi_refinement::Scheduler
• pick_fragment_library() : core::fragment::rna::FullAtomRNA_Fragments
• pick_fragments() : protocols::forge::components::VarLengthBuild
• pick_fragments_for_resid() : protocols::denovo_design::components::Picker
• pick_fragments_public() : protocols::denovo_design::components::VLBProtected
• pick_frags() : protocols::abinitio::Templates
• pick_large_frags() : protocols::abinitio::Template , protocols::abinitio::Templates
• pick_loop_frags() : protocols::protein_interface_design::movers::LoopRemodel
• pick_new_cutpoint() : protocols::anchored_design::AnchorMoversData
• pick_new_cutpoints() : protocols::anchored_design::AnchorMoversData
• pick_objfunction() : protocols::mpi_refinement::Scheduler
• pick_pivots() : protocols::generalized_kinematic_closure::GeneralizedKIC
• pick_random_chunk() : protocols::hybridization::ChunkTrialMover
• pick_random_fragment() : core::fragment::rna::FullAtomRNA_Fragments , protocols::rna::denovo::coarse::CoarseRNA_Fragments
• pick_random_starting_segment() : protocols::sewing::data_storage::SmartAssembly
• pick_random_template() : protocols::hybridization::ChunkTrialMover
• pick_rotamer_for_node() : core::pack::annealer::FASTERAnnealer
• pick_sequence_from_database() : protocols::task_operations::DatabaseThread
• pick_solution() : protocols::kinematic_closure::BalancedKicMover
• pick_solutions() : protocols::backbone_moves::local_backbone_mover::GapCloser
• pick_starting_template() : protocols::hybridization::HybridizeProtocol
• pick_strategy() : protocols::mpi_refinement::Scheduler
• Picker() : protocols::denovo_design::components::Picker
• picking_rounds() : protocols::task_operations::ResidueProbDesignOperation
• piece() : protocols::grafting::GraftMoverBase
• pieces() : protocols::fold_from_loops::utils::Nub
• PIKAA() : core::pack::task::PIKAA
• PiPiCalculator() : protocols::pose_metric_calculators::PiPiCalculator
• pivot1() : protocols::backbone_moves::local_backbone_mover::FreePeptide
• pivot2() : protocols::backbone_moves::local_backbone_mover::FreePeptide
• pivot_atoms() : protocols::backrub::BackrubMover , protocols::kinematic_closure::ClosureProblem
• pivot_loop() : protocols::kinematic_closure::ClosureProblem
• pivot_range_randomly() : protocols::simple_moves::BBGaussianMover
• pivot_residues() : protocols::backrub::BackrubMover , protocols::kinematic_closure::ClosureProblem
• place() : core::conformation::Residue
• place_adducts() : core::chemical::GlobalResidueTypeSet
• place_atom() : protocols::motifs::Motif
• place_atom_() : protocols::motifs::Motif
• place_atoms() : protocols::motifs::Motif
• place_atoms_() : protocols::motifs::Motif
• place_c() : protocols::kinmatch::BruteFunGroupTK , protocols::kinmatch::FunGroupTK , protocols::kinmatch::KinFunGroupTK
• place_cut_site_in_segment() : protocols::splice::SpliceOut , protocols::splice::SpliceOutAntibody , protocols::splice::SpliceOutTail
• place_d() : protocols::kinmatch::BruteFunGroupTK , protocols::kinmatch::FunGroupTK , protocols::kinmatch::KinFunGroupTK
• place_h() : protocols::kinmatch::BruteFunGroupTK , protocols::kinmatch::FunGroupTK , protocols::kinmatch::KinFunGroupTK
• place_near_origin() : protocols::cryst::MakeLatticeMover , protocols::cryst::MakeLayerMover
• place_origin_point() : protocols::pockets::NonPlaidFingerprint
• place_peptide_on_binding_site() : protocols::flexpep_docking::FlexPepDockingProtocol
• place_residue() : protocols::motifs::Motif
• place_residue_() : protocols::motifs::Motif
• place_residue_helper() : protocols::motifs::Motif
• place_rots_on_pose() : protocols::hbnet::HBNet
• place_sidechain_in_pose() : core::scoring::motif::Xfres
• place_stub() : protocols::protein_interface_design::movers::PlaceStubMover
• place_stubs() : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• place_tma_asymmetric() : protocols::cyclic_peptide::crosslinker::TMA_Helper
• place_tma_symmetric() : protocols::cyclic_peptide::crosslinker::TMA_Helper
• place_VRT_at_residue_COM() : protocols::antibody::snugdock::SnugDockProtocol
• placeholder_clone() : core::chemical::MutableResidueType , core::chemical::ResidueType
• placeholder_info() : core::scoring::FACTSPoseInfo , core::scoring::GenBornPoseInfo , core::scoring::MultipoleElecPoseInfo , core::scoring::VdWTinkerPoseInfo
• placeholder_residue() : core::scoring::FACTSPoseInfo , core::scoring::GenBornPoseInfo , core::scoring::MultipoleElecPoseInfo , core::scoring::VdWTinkerPoseInfo
• PlacementAuctionMover() : protocols::protein_interface_design::movers::PlacementAuctionMover
• PlacementMinimizationMover() : protocols::protein_interface_design::movers::PlacementMinimizationMover
• PlaceOnLoop() : protocols::protein_interface_design::movers::PlaceOnLoop
• PlaceProbeMover() : protocols::hotspot_hashing::movers::PlaceProbeMover
• placeResidueAtTransform() : protocols::hotspot_hashing::StubGenerator
• placeResidueOnPose() : protocols::hotspot_hashing::StubGenerator
• PlaceSimultaneouslyMover() : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• PlaceStubMover() : protocols::protein_interface_design::movers::PlaceStubMover
• PlaceSurfaceProbe() : protocols::hotspot_hashing::movers::PlaceSurfaceProbe
• PlaidFingerprint() : protocols::pockets::PlaidFingerprint
• PlainPdbJobDistributor() : protocols::jobdist::PlainPdbJobDistributor
• PlainRawJobDistributor() : protocols::jobdist::PlainRawJobDistributor
• PlainSilentFileJobDistributor() : protocols::jobdist::PlainSilentFileJobDistributor
• Pleating() : core::scoring::dssp::Pairing
• pleats1() : protocols::fldsgn::topology::StrandPairing
• pleats2() : protocols::fldsgn::topology::StrandPairing
• pmatch() : protocols::noesy_assign::FloatingResonance , protocols::noesy_assign::Resonance
• PNatAAOptEPositionData() : protocols::optimize_weights::PNatAAOptEPositionData
• PNatAAOptERotamerData() : protocols::optimize_weights::PNatAAOptERotamerData
• PNatLigPoseOptEData() : protocols::optimize_weights::PNatLigPoseOptEData
• PNatRotOptEPositionData() : protocols::optimize_weights::PNatRotOptEPositionData
• PNatRotOptERotamerData() : protocols::optimize_weights::PNatRotOptERotamerData
• PNatStructureOptEData() : protocols::optimize_weights::PNatStructureOptEData
• pnear() : protocols::cyclic_peptide_predict::HierarchicalHybridJD_PNearToArbitraryStateSummary
• PNearCalculator() : protocols::cyclic_peptide_predict::PNearCalculator
• PocketConstraint() : protocols::pockets::PocketConstraint
• PocketConstraintCreator() : protocols::pockets::PocketConstraintCreator
• PocketExemplarMultifunc() : protocols::pockets::PocketExemplarMultifunc
• PocketGrid() : protocols::pockets::PocketGrid
• Point() : core::scoring::packstat::Point
• point_clash_energy() : protocols::ligand_docking::ga_ligand_dock::GridScorer
• point_energy() : protocols::ligand_docking::ga_ligand_dock::GridScorer
• point_for_nonchitip_atom() : protocols::match::upstream::UpstreamResTypeGeometry
• point_graph() : core::scoring::Energies
• point_inside() : protocols::splice::FindEndpointsOperation
• point_on_ellipsoid() : protocols::docking::EllipsoidalRandomizationMover
• point_orbitals_to_closest_ligands() : protocols::magnesium::MgOrbitalFrameFinder
• PointGraphEdgeData() : core::conformation::PointGraphEdgeData
• PointGraphVertexData() : core::conformation::PointGraphVertexData
• PointMutationCalculator() : protocols::design_opt::PointMutationCalculator
• PointMutScanDriver() : protocols::pmut_scan::PointMutScanDriver
• PointPair() : core::scoring::packstat::PointPair
• points_for_nonchitip_atoms() : protocols::match::upstream::UpstreamResTypeGeometry
• PointWaterEnergy() : core::scoring::methods::PointWaterEnergy
• PointWaterPotential() : core::scoring::PointWaterPotential
• PoissonBoltzmannEnergy() : core::scoring::methods::PoissonBoltzmannEnergy
• PoissonBoltzmannPotential() : core::scoring::PoissonBoltzmannPotential
• polar_sasa() : protocols::cyclic_peptide_predict::HierarchicalHybridJD_SASASummary
• polar_sc_atoms_not_satisfied_by_background() : core::scoring::hbonds::graph::HBondNode
• polar_scale() : protocols::ligand_docking::ga_ligand_dock::ConstraintInfo
• PolarGroupBurialPyMolStringMetric() : protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric
• polarH() : protocols::ligand_docking::ga_ligand_dock::AtomProperties
• PolarHydrogenFilter() : core::chemical::PolarHydrogenFilter
• PolarHydrogenPacker() : protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker
• polarity() : core::scoring::MultipoleParameter
• Policy() : protocols::nonlocal::Policy
• poly_ala() : protocols::splice::Splice
• polyAla() : protocols::flexpep_docking::FlexPepDockingProtocol
• polymer_direction() : core::kinematics::Edge
• PolymerBondedEnergyContainer() : core::scoring::PolymerBondedEnergyContainer
• PolymerBondedNeighborConstIterator() : core::scoring::PolymerBondedNeighborConstIterator
• PolymerBondedNeighborIterator() : core::scoring::PolymerBondedNeighborIterator
• polymeric_oriented_sequence_distance() : core::conformation::Residue
• polymeric_sequence_distance() : core::conformation::Residue
• polynom_by_z() : core::scoring::membrane::MPResidueLipophilicityEnergy
• Polynomial_1d() : core::scoring::hbonds::Polynomial_1d
• Pool_ConvergenceCheck() : protocols::canonical_sampling::mc_convergence_checks::Pool_ConvergenceCheck
• Pool_Evaluator() : protocols::canonical_sampling::mc_convergence_checks::Pool_Evaluator
• pool_exists() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• Pool_RMSD() : protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD
• pool_size() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• PoolData() : protocols::canonical_sampling::mc_convergence_checks::PoolData
• PoolEvaluatorCreator() : protocols::simple_filters::PoolEvaluatorCreator
• pop() : protocols::electron_density::ResultDB< T, Tcomp > , protocols::forge::remodel::RemodelAccumulator , protocols::ligand_docking::ga_ligand_dock::OutputStructureStore , protocols::pack_daemon::TopEntitySet
• pop_back() : protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD , protocols::evaluation::MetaPoseEvaluator
• pop_back_CA_xyz() : protocols::toolbox::DecoySetEvaluation
• pop_job_from_queue() : protocols::jd3::job_distributors::JobExtractor
• pop_mutation() : protocols::pmut_scan::Mutant
• pop_next() : protocols::wum::WorkUnitQueue
• pop_passport() : core::conformation::Conformation , protocols::environment::ClientMover , protocols::environment::ProtectedConformation
• populate_all_cdrs() : protocols::antibody_legacy::Antibody
• populate_batch_list_from_cmd() : protocols::jd2::JobDistributor
• populate_matrix() : core::scoring::bin_transitions::BinTransitionCalculator
• populate_next_n_jobs() : protocols::jd2::LargeNstructJobInputter
• population() : protocols::genetic_algorithm::GeneticAlgorithmBase
• population_size() : protocols::evolution::EvolutionaryDynamicsMover
• pore_center_x() : core::conformation::membrane::AqueousPoreParameters , core::conformation::membrane::ImplicitLipidInfo
• pore_center_x_deriv() : core::conformation::membrane::AqueousPoreParameters
• pore_center_y() : core::conformation::membrane::AqueousPoreParameters , core::conformation::membrane::ImplicitLipidInfo
• pore_center_y_deriv() : core::conformation::membrane::AqueousPoreParameters
• pore_major_radius() : core::conformation::membrane::AqueousPoreParameters , core::conformation::membrane::ImplicitLipidInfo
• pore_major_radius_deriv() : core::conformation::membrane::AqueousPoreParameters
• pore_minor_radius() : core::conformation::membrane::AqueousPoreParameters , core::conformation::membrane::ImplicitLipidInfo
• pore_minor_radius_deriv() : core::conformation::membrane::AqueousPoreParameters
• pore_radius() : core::select::util::SelectResiduesByLayer , protocols::flxbb::LayerDesignOperation
• pore_rotation() : core::conformation::membrane::AqueousPoreParameters , core::conformation::membrane::ImplicitLipidInfo
• pore_rotation_deriv() : core::conformation::membrane::AqueousPoreParameters
• pos() : core::fragment::NonContinuousFrame , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::mean_field::AAProb , protocols::mean_field::RotProb
• Pos1() : core::scoring::dssp::Pairing
• pos1() : protocols::environment::claims::JumpClaim
• Pos2() : core::scoring::dssp::Pairing
• pos2() : protocols::environment::claims::JumpClaim
• pos2select() : protocols::flxbb::LayerDesignOperation
• pose() : core::fragment::picking_old::vall::eval::EnergyEval , core::import_pose::PoseResource , core::import_pose::RNA_DeNovoSetup , core::optimization::AtomTreeMultifunc , core::optimization::CartesianMultifunc , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > , core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::SimpleInteractionGraph , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph , core::pose::datacache::CacheablePoseRawPtr
• Pose() : core::pose::Pose
• pose() : protocols::calc_taskop_filters::RelativePoseFilter , protocols::jd3::chunk_library::ChunkLibraryJobResult , protocols::jd3::chunk_library::MoverAndChunkLibraryJob , protocols::jd3::job_results::PoseJobResult , protocols::jd3::jobs::MoverJob , protocols::multistage_rosetta_scripts::MRSJob , protocols::multistate_design::SingleState , protocols::normalmode::NormalModeMultifunc , protocols::pack_daemon::PackDaemon , protocols::pack_daemon::QuickRepacker , protocols::pockets::PlaidFingerprint , protocols::sic_dock::Rose , protocols::simple_moves::AlignChainMover , protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker , protocols::stepwise::modeler::rna::o2prime::O2PrimePacker , protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler , protocols::stepwise::sampler::copy_dofs::ResidueAlternativeSet , protocols::stepwise::screener::SampleApplier
• pose0() : protocols::md::MDBase
• pose1() : core::scoring::motif::MotifHit , core::scoring::motif::ResPairMotifQuery
• pose1ptr() : core::scoring::motif::MotifHit
• pose2() : core::scoring::motif::MotifHit , core::scoring::motif::ResPairMotifQuery
• pose2pdb() : core::pose::PDBInfo
• pose2ptr() : core::scoring::motif::MotifHit
• pose_aligner() : protocols::rna::AlignmentEnergy
• pose_at_origin() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler
• pose_cache_real_data() : core::io::StructFileRep
• pose_cache_string_data() : core::io::StructFileRep
• pose_coords_are_same() : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• pose_cop() : core::pack::interaction_graph::SimpleInteractionGraph
• pose_deep_copy() : core::import_pose::PoseResource
• pose_energy() : protocols::cyclic_peptide_predict::HierarchicalHybridJD_JobResultsSummary
• pose_for_inner_job() : protocols::jd3::standard::StandardJobQueen
• pose_for_inner_job_derived() : protocols::multistage_rosetta_scripts::MRSJobQueen
• pose_for_job() : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::standard::StandardJobQueen
• pose_for_job_derived() : protocols::multistage_rosetta_scripts::MRSJobQueen
• pose_from_checkpoint_file() : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• pose_from_checkpoint_file_low() : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• pose_from_file() : protocols::jd2::SerializedPoseJobInputter
• pose_from_input_source() : protocols::jd3::pose_inputters::PDBPoseInputter , protocols::jd3::pose_inputters::PoseInputter , protocols::jd3::pose_inputters::SilentFilePoseInputter
• pose_from_job() : protocols::comparative_modeling::GenericJobInputter , protocols::comparative_modeling::ThreadingJobInputter , protocols::enzdes::EnzdesJobInputter , protocols::features::DatabaseJobInputter , protocols::jd2::AtomTreeDiffJobInputter , protocols::jd2::BatchJobInputter , protocols::jd2::EmptyPoseJobInputter , protocols::jd2::JobInputter , protocols::jd2::LargeNstructJobInputter , protocols::jd2::LazySilentFileJobInputter , protocols::jd2::PDBJobInputter , protocols::jd2::PoseInputStreamJobInputter , protocols::jd2::ScreeningJobInputter , protocols::jd2::SerializedPoseJobInputter , protocols::jd2::SilentFileJobInputter , protocols::make_rot_lib::MakeRotLibJobInputter , protocols::protein_interface_design::ParserJobInputter
• pose_from_posedata() : protocols::energy_based_clustering::EnergyBasedClusteringProtocol
• pose_from_res() : protocols::splice::SpliceManager
• pose_has_chainbreak() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer
• pose_id() : protocols::jd3::deallocation::InputPoseDeallocationMessage
• pose_index() : core::pose::ResidueIndexDescriptionPoseNum
• pose_input_sources_from_command_line() : protocols::jd3::pose_inputters::PDBPoseInputter , protocols::jd3::pose_inputters::PoseInputter , protocols::jd3::pose_inputters::SilentFilePoseInputter
• pose_input_sources_from_tag() : protocols::jd3::pose_inputters::PDBPoseInputter , protocols::jd3::pose_inputters::PoseInputter , protocols::jd3::pose_inputters::SilentFilePoseInputter
• pose_input_stream() : protocols::stepwise::modeler::protein::InputStreamWithResidueInfo
• pose_inputs_from_command_line() : protocols::jd3::pose_inputters::PoseInputterFactory
• pose_inputter_creators() : protocols::jd3::pose_inputters::PoseInputterFactory
• pose_inputter_for_job() : protocols::jd3::standard::StandardJobQueen
• pose_inputter_xml_schema_group_name() : protocols::jd3::pose_inputters::PoseInputterFactory
• pose_is_setup_for_density_scoring() : core::scoring::electron_density::FastDensEnergy
• pose_length() : protocols::denovo_design::components::StructureData
• pose_list() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection , protocols::stepwise::legacy::screener::SimplePoseSelection , protocols::stepwise::modeler::align::StepWiseClusterer , protocols::stepwise::modeler::StepWiseMinimizer , protocols::stepwise::sampler::copy_dofs::ResidueAlternativeSet
• pose_loop_anchors() : protocols::legacy_sewing::Assembly
• pose_minobj() : protocols::md::MDBase
• pose_name() : protocols::moves::StructureRestrictor
• pose_num() : protocols::legacy_sewing::Assembly
• pose_numb() : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• pose_number() : protocols::legacy_sewing::Model
• pose_outputter_creators() : protocols::jd3::pose_outputters::PoseOutputterFactory
• pose_outputter_for_job() : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::standard::StandardJobQueen
• pose_outputter_from_command_line() : protocols::jd3::pose_outputters::PoseOutputterFactory
• pose_outputter_xml_schema_group_name() : protocols::jd3::pose_outputters::PoseOutputterFactory
• pose_passes_ss_length_check() : protocols::frags::TorsionFragmentMover
• pose_preliminaries() : protocols::rna::movers::ErraserMinimizerMover
• pose_raw_unfolded_state_energymap() : core::scoring::UnfoldedStatePotential
• pose_ref() : protocols::simple_moves::CombinePoseMover
• pose_reporter_group_name() : protocols::rosetta_scripts::PosePropertyReporterFactory
• pose_res_no() : core::scoring::constraints::FabConstraint
• pose_residue() : protocols::denovo_design::components::StructureData
• pose_resnum() : protocols::pmut_scan::MutationData
• pose_right() : protocols::forge::build::ConnectRight
• pose_selection_by_full_score() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection
• pose_selector_group_name() : protocols::rosetta_scripts::PoseSelectorFactory
• pose_sequence() : core::scoring::electron_density_atomwise::PoseSequence
• pose_string() : protocols::simple_moves::CopyDofMover
• pose_tag() : protocols::jd3::pose_outputters::ScoreFileOutputSpecification , protocols::jd3::pose_outputters::SilentFilePoseOutputSpecification , protocols::simple_moves::CombinePoseMover
• pose_to_local() : protocols::denovo_design::components::Segment
• pose_to_res() : protocols::splice::SpliceManager
• pose_to_segment() : protocols::denovo_design::components::Segment
• PoseArchitect() : protocols::denovo_design::architects::PoseArchitect
• PoseBalls() : core::scoring::packing::PoseBalls
• PoseBallsLite() : core::scoring::packing::PoseBallsLite
• poseBfacts2multivec() : protocols::electron_density::BfactorMultifunc
• PoseComment() : protocols::simple_filters::PoseComment
• PoseCommentsFeatures() : protocols::features::PoseCommentsFeatures
• PoseCondition() : protocols::moves::PoseCondition
• PoseConformationFeatures() : protocols::features::PoseConformationFeatures
• PoseEvaluator() : protocols::evaluation::PoseEvaluator
• PoseFolder() : protocols::denovo_design::components::PoseFolder
• PoseForPoseID() : protocols::multistage_rosetta_scripts::PoseForPoseID
• PoseFoundResiduesCombination() : protocols::enzdes::PoseFoundResiduesCombination
• PoseFromPoseResourceMover() : protocols::simple_moves::PoseFromPoseResourceMover
• PoseFromSequenceMover() : protocols::pose_creation::PoseFromSequenceMover
• PoseFromSFRBuilder() : core::io::pose_from_sfr::PoseFromSFRBuilder
• PoseInfoFilter() : protocols::simple_filters::PoseInfoFilter
• PoseInputSource() : protocols::jd3::pose_inputters::PoseInputSource
• PoseInputStream() : core::import_pose::pose_stream::PoseInputStream
• PoseInputStreamJobInputter() : protocols::jd2::PoseInputStreamJobInputter
• PoseInputter() : protocols::jd3::pose_inputters::PoseInputter
• PoseInputterFactory() : protocols::jd3::pose_inputters::PoseInputterFactory
• PoseInputterRegistrator() : protocols::jd3::pose_inputters::PoseInputterRegistrator< T >
• PoseInserter() : protocols::match::output::PoseInserter
• PoseJobResult() : protocols::jd3::job_results::PoseJobResult
• PoseMatchOutputWriter() : protocols::match::output::PoseMatchOutputWriter
• PoseMetricCalculator() : core::pose::metrics::PoseMetricCalculator
• PoseMetricContainer() : core::pose::metrics::PoseMetricContainer
• PoseMetricEvaluator() : protocols::simple_filters::PoseMetricEvaluator< T >
• PoseNumberedLoopFileReader() : protocols::loops::PoseNumberedLoopFileReader
• PoseOutputSpecification() : protocols::jd3::pose_outputters::PoseOutputSpecification , protocols::jd3::standard::PoseOutputSpecification
• PoseOutputter() : protocols::jd3::pose_outputters::PoseOutputter
• PoseOutputterFactory() : protocols::jd3::pose_outputters::PoseOutputterFactory
• PoseOutputterRegistrator() : protocols::jd3::pose_outputters::PoseOutputterRegistrator< T >
• PosePropertyReporter() : protocols::rosetta_scripts::PosePropertyReporter
• PosePropertyReporterCreator() : protocols::rosetta_scripts::PosePropertyReporterCreator
• PosePropertyReporterFactory() : protocols::rosetta_scripts::PosePropertyReporterFactory
• PosePropertyReporterRegistrator() : protocols::rosetta_scripts::PosePropertyReporterRegistrator< T >
• PoseResidueTypeSet() : core::chemical::PoseResidueTypeSet
• PoseResource() : core::import_pose::PoseResource
• PoseResourceLoader() : core::import_pose::PoseResourceLoader
• poses_from_cmd_line() : protocols::comparative_modeling::AlignmentClustering
• PoseSelectionScreener() : protocols::stepwise::screener::PoseSelectionScreener
• PoseSelector() : protocols::rosetta_scripts::PoseSelector
• PoseSelectorCreator() : protocols::rosetta_scripts::PoseSelectorCreator
• PoseSelectorFactory() : protocols::rosetta_scripts::PoseSelectorFactory
• PoseSelectorRegistrator() : protocols::rosetta_scripts::PoseSelectorRegistrator< T >
• PoseSequence() : core::scoring::electron_density_atomwise::PoseSequence
• poseSphericalSamples() : protocols::electron_density::DockIntoDensityMover
• PoseToStructFileRepConverter() : core::io::pose_to_sfr::PoseToStructFileRepConverter
• position() : core::chemical::sdf::MolFileIOAtom , core::environment::LocalPosition , core::kinematics::tree::Atom , core::kinematics::tree::Atom_ , core::pose::rna::RNA_Datum , core::pose::rna::RNA_Reactivity , core::scoring::motif::Xfrag , protocols::optimize_weights::PNatAAOptEPositionData
• position_ala_ddG() : protocols::task_operations::RestrictConservedLowDdgOperation
• position_backbone_is_randomizable() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• position_data_begin() : protocols::optimize_weights::OptEData
• position_data_end() : protocols::optimize_weights::OptEData
• position_index() : core::fragment::picking_old::vall::VallResidue
• position_membrane_at_topology_com() : protocols::symmetric_docking::membrane::MPSymDockMover
• position_stub() : protocols::protein_interface_design::movers::PlaceOnLoop
• position_untouchable() : protocols::task_operations::RestrictConservedLowDdgOperation
• position_vector_setup() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• PositionConservedResiduesStore() : core::pose::datacache::PositionConservedResiduesStore
• PositionDdGInfo() : core::io::PositionDdGInfo::PositionDdGInfo
• positions() : protocols::dna::DnaChains , protocols::enzdes::EnzdesFlexibleRegion , protocols::forge::build::BuildManager
• PositionType() : protocols::dna::PositionType
• positive_states() : protocols::multistate_design::MultiStateFitnessFunction
• possible_root() : core::kinematics::FoldTree
• PossibleAtomTypesForAtom() : core::chemical::gasteiger::PossibleAtomTypesForAtom
• PossibleLoop() : protocols::pose_length_moves::PossibleLoop
• post_catalog_op() : core::fragment::picking_old::vall::eval::VallFragmentEval
• post_catalog_ops() : core::fragment::picking_old::vall::VallLibrarian
• post_loop_closure_protocol() : protocols::abinitio::AbrelaxMover
• post_packing() : protocols::dna::DnaInterfacePacker
• post_process() : protocols::fold_from_loops::NubInitioMover , protocols::relax::WorkUnit_BatchRelax , protocols::relax::WorkUnit_BatchRelax_and_PostRescore
• post_relax_round_update_steps() : protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper , protocols::cyclic_peptide::crosslinker::TMA_Helper
• PostDockAssemblyScorer() : protocols::domain_assembly::PostDockAssemblyScorer
• postfold_ct_naming_func() : protocols::denovo_design::movers::BuildDeNovoBackboneMover
• postfold_movers() : protocols::denovo_design::movers::BuildDeNovoBackboneMover
• PosType() : protocols::multistate_design::PosType
• potential_energy() : protocols::md::MDBase
• potential_twobody_memory_use() : core::pack::interaction_graph::DoubleLazyEdge
• potential_valid_ss_strings() : protocols::indexed_structure_store::SSHashedFragmentStore
• potentially_discard_some_job_results() : protocols::jd3::job_distributors::VanillaJobDistributor
• potentially_output_some_job_results() : protocols::jd3::job_distributors::VanillaJobDistributor
• power() : core::scoring::PDvertex , core::scoring::power_diagram::PDvertex
• PowerDiagram() : core::scoring::power_diagram::PowerDiagram
• PowExpression() : protocols::pack_daemon::PowExpression
• PQR() : core::scoring::PQR
• pre_align() : protocols::constraints_additional::BindingSiteConstraint
• pre_catalog_op() : core::fragment::picking_old::vall::eval::ABEGOEval , core::fragment::picking_old::vall::eval::EnergyEval , core::fragment::picking_old::vall::eval::IdentityEval , core::fragment::picking_old::vall::eval::VallFragmentEval
• pre_catalog_ops() : core::fragment::picking_old::vall::VallLibrarian
• pre_chitip_transform() : protocols::match::upstream::UpstreamResTypeGeometry
• pre_compute_grid_points() : protocols::topology_broker::TMHTopologySamplerClaimer
• PRE_Curie_prefactor() : core::scoring::nmr::pre::PREMultiSet
• pre_data_to_distances() : protocols::nmr::pre::PREMover
• PRE_DD_prefactor() : core::scoring::nmr::pre::PREMultiSet
• pre_load_data() : protocols::antibody::task_operations::AddCDRProfileSetsOperation , protocols::antibody::task_operations::AddCDRProfilesOperation
• pre_loop_closure_protocol() : protocols::abinitio::AbrelaxMover
• pre_nresidue_change() : core::conformation::Conformation
• pre_process() : protocols::relax::WorkUnit_BatchRelax , protocols::relax::WorkUnit_BatchRelax_and_PostRescore , protocols::topology_broker::MembraneTopologyClaimer , protocols::topology_broker::TMHTopologySamplerClaimer , protocols::topology_broker::TopologyClaimer
• pre_rate_type_to_string() : core::scoring::nmr::pre::PRESingleSet
• pre_relax_round_update_steps() : protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper , protocols::cyclic_peptide::crosslinker::TMA_Helper
• pre_scoring() : protocols::flexpack::OtherContextScoreFunction
• pre_talaris_2013_behavior_settings() : core::init::pre_talaris_2013_behavior_settings
• preallocate() : core::fragment::picking_old::vall::VallLibrarian
• preamble() : protocols::ligand_docking::rdf::RDFBase , protocols::ligand_docking::rdf::RDFBinaryOrbitalFunction , protocols::ligand_docking::rdf::RDFHbondFunction , protocols::ligand_docking::rdf::RDFOrbitalFunction
• preapply() : protocols::monte_carlo::GenericMonteCarloMover
• precalc_context() : core::scoring::elec::FA_GrpElecEnergy
• precalc_etable_coefficients() : core::scoring::etable::Etable , core::scoring::etable::MembEtable
• precalculate_bb_bb_energy_for_design() : core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• precision() : core::io::silent::SilentStruct
• precompute_all_energies() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• precompute_energies() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• precompute_ig() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• precompute_transforms() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• precompute_unweighted_score() : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• precomputed_library_mover() : protocols::stepwise::modeler::StepWiseModeler
• PrecomputedLibraryMover() : protocols::stepwise::modeler::precomputed::PrecomputedLibraryMover
• PrecomputedPairEnergiesEdge() : core::pack::interaction_graph::PrecomputedPairEnergiesEdge
• PrecomputedPairEnergiesInteractionGraph() : core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph
• PrecomputedPairEnergiesNode() : core::pack::interaction_graph::PrecomputedPairEnergiesNode
• PREData() : core::scoring::nmr::pre::PREData
• predefine_search() : protocols::electron_density::DockIntoDensityMover
• PredesignPerturbMover() : protocols::enzdes::PredesignPerturbMover
• Predicate() : core::scoring::Predicate
• predict_H3_base_type() : protocols::antibody::AntibodyInfo
• predict_pos_rd1() : protocols::ss_prediction::SS_predictor
• predict_pos_rd2() : protocols::ss_prediction::SS_predictor
• predict_rd1() : protocols::ss_prediction::SS_predictor
• predict_rd2() : protocols::ss_prediction::SS_predictor
• predict_region() : protocols::mpi_refinement::StructAvrgMover
• predict_ss() : protocols::ss_prediction::SS_predictor
• PredictedBurialEvaluator() : protocols::simple_filters::PredictedBurialEvaluator
• PredictedBurialFnEvaluatorCreator() : protocols::simple_filters::PredictedBurialFnEvaluatorCreator
• PREDistanceRecord() : protocols::nmr::pre::PREDistanceRecord
• PREEnergy() : protocols::nmr::pre::PREEnergy
• preexisting_positions() : protocols::forge::build::Bridge , protocols::forge::build::BuildInstruction , protocols::forge::build::BuildManager , protocols::forge::build::ConnectRight , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap
• preferred_properties() : core::chemical::ResidueTypeFinder
• preferred_root_res() : core::pose::full_model_info::FullModelInfo
• prefix() : protocols::constraint_movers::CstInfoMover , protocols::fold_from_loops::NubInitioMover , protocols::match::output::PDBWriter
• prefix_each_output_pdb() : protocols::recces::options::RECCES_Options
• prefold_ct_naming_func() : protocols::denovo_design::movers::BuildDeNovoBackboneMover
• prefold_movers() : protocols::denovo_design::movers::BuildDeNovoBackboneMover
• preliminary_job_node() : protocols::jd3::standard::StandardInnerLarvalJob
• preliminary_job_nodes() : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen
• PreliminaryLarvalJob() : protocols::jd3::standard::PreliminaryLarvalJob
• PreliminaryLarvalJobTracker() : protocols::jd3::standard::PreliminaryLarvalJobTracker
• PreloadedPDB() : protocols::cluster::calibur::PreloadedPDB
• premin_ligand() : protocols::ligand_docking::ga_ligand_dock::GALigandDock
• preminimize() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• preminimize_pose() : protocols::stepwise::monte_carlo::mover::StepWiseMasterMover
• PREMover() : protocols::nmr::pre::PREMover
• PREMultiSet() : core::scoring::nmr::pre::PREMultiSet
• prep_aa_submatrix() : core::pack::interaction_graph::DoubleLazyEdge
• prep_for_neighbors_perturbation() : core::pack::interaction_graph::FASTERNode
• prep_grid() : protocols::match::downstream::ActiveSiteGrid
• prep_restype() : core::chemical::ResidueTypeSet
• prepack() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• prepack_only() : protocols::flexpep_docking::FlexPepDockingProtocol
• PrepackMover() : protocols::protein_interface_design::movers::PrepackMover
• prepare() : protocols::abinitio::abscript::ConstraintPreparer , protocols::abinitio::abscript::StagePreparer
• prepare_constraint_target_pose() : protocols::constraint_generator::CoordinateConstraintGenerator
• prepare_constraints_energy_container() : core::scoring::constraints::ConstraintsEnergy
• prepare_coord() : protocols::normalmode::NormalMode
• prepare_correlation_lists() : core::scoring::sc::ElectrostaticComplementarityCalculator
• prepare_enrich_stage() : protocols::mpi_refinement::Scheduler
• prepare_fold_tree_for_erraser() : protocols::stepwise::monte_carlo::mover::TransientCutpointHandler
• prepare_foldtree() : protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover
• prepare_for_altbb_move_to_closest_state() : protocols::flexpack::interaction_graph::MinimalistFlexbbNode
• prepare_for_altbb_move_to_state() : protocols::flexpack::interaction_graph::MinimalistFlexbbNode
• prepare_for_FASTER() : core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::FASTERNode
• prepare_for_hit_generation() : protocols::match::downstream::SecondaryMatcherToDownstreamResidue , protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• prepare_for_hit_generation_at_target_build_point() : protocols::match::downstream::SecondaryMatcherToDownstreamResidue , protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• prepare_for_hit_generation_for_constraint() : protocols::match::Matcher
• prepare_for_hit_generation_for_geomcst() : protocols::match::downstream::SecondaryMatcherToDownstreamResidue
• prepare_for_match_enumeration() : protocols::match::downstream::DownstreamAlgorithm , protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• prepare_for_neighbors_substitution() : core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G > , core::pack::interaction_graph::NPDHBondNode< V, E, G > , core::pack::interaction_graph::NPDHBSimpleNode
• prepare_for_new_residue_type() : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• prepare_for_output_writing() : protocols::match::output::CloudPDBWriter , protocols::match::output::OutputWriter , protocols::match::output::PDBWriter
• prepare_for_packing() : protocols::legacy_sewing::Assembly
• prepare_for_perturbation() : core::pack::interaction_graph::FASTERNode
• prepare_for_query() : protocols::indexed_structure_store::search::StructureData
• prepare_for_residue_pair() : core::scoring::etable::BaseEtableEnergy< Derived >
• prepare_for_scoring() : core::scoring::NeighborList
• prepare_for_simulated_annealing() : core::pack::hbonds::BareMinimumPDEdge , core::pack::interaction_graph::BackgroundNode< V, E, G > , core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G > , core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::EdgeBase , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G > , core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchEdge< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::NodeBase , core::pack::interaction_graph::NPDHBondBackgroundEdge< V, E, G > , core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G > , core::pack::interaction_graph::NPDHBondEdge< V, E, G > , core::pack::interaction_graph::NPDHBondNode< V, E, G > , core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G > , core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceEdge< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistEdge , core::pack::interaction_graph::SymmMinimalistNode , protocols::flexpack::interaction_graph::FlexbbNode , protocols::flexpack::interaction_graph::MinimalistFlexbbEdge , protocols::flexpack::interaction_graph::MinimalistFlexbbNode , protocols::flexpack::interaction_graph::OTFFlexbbEdge
• prepare_for_simulated_annealing_no_deletion() : core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::PDEdge
• prepare_from_prior_sampled_sugar_jobs() : protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator
• prepare_from_prior_sampled_sugar_jobs_for_chain_break() : protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator
• prepare_ghost_pose() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• prepare_graph_for_simulated_annealing() : core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > , core::pack::interaction_graph::AnnealableGraphBase , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::MultiplexedAnnealableGraph , core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > , core::pack::interaction_graph::ResidueArrayAnnealingEvaluator , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistInteractionGraph
• prepare_grid() : protocols::ligand_docking::ga_ligand_dock::GridScorer
• prepare_hashing_packer_task_() : protocols::hotspot_hashing::HotspotStubSet
• prepare_loop_in_stage3() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints , protocols::abinitio::FragmentSampler , protocols::abinitio::KinematicAbinitio , protocols::abinitio::MembraneAbinitio
• prepare_loop_in_stage4() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints , protocols::abinitio::FragmentSampler , protocols::abinitio::KinematicAbinitio , protocols::abinitio::MembraneAbinitio
• prepare_neighbor_graphs() : core::scoring::Energies
• prepare_otf_graph() : core::pack::rotamer_set::RotamerSets
• prepare_output() : protocols::hbnet::HBNet , protocols::hbnet::HBNetStapleInterface
• prepare_output_torsion_ids() : protocols::recces::RECCES_Mover
• prepare_pose() : protocols::constraints_additional::ConstraintEvaluator , protocols::peptide_deriver::PeptideDeriverFilter
• prepare_pose_for_sampling() : protocols::abinitio::KinematicControl
• prepare_push_back() : protocols::toolbox::DecoySetEvaluation
• prepare_rotamers_for_packing() : core::scoring::elec::FA_ElecEnergy , core::scoring::elec::FA_ElecEnergyAroAll , core::scoring::elec::FA_ElecEnergyAroAro , core::scoring::elec::FA_GrpElecEnergy , core::scoring::elec::RNA_FA_ElecEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::hbonds::HBondEnergy , core::scoring::lkball::LK_BallEnergy , core::scoring::methods::CustomAtomPairEnergy , core::scoring::methods::EnergyMethod , core::scoring::methods::FACTSEnergy , core::scoring::methods::GenBornEnergy , core::scoring::methods::MMLJEnergyInter , core::scoring::methods::MultipoleElecEnergy , core::scoring::methods::PairEnergy , core::scoring::methods::SASAEnergy , core::scoring::methods::VdWTinkerEnergy , core::scoring::orbitals::OrbitalsScore , core::scoring::ScoreFunction , core::scoring::vdwaals::VDW_Energy
• prepare_scoring() : protocols::noesy_assign::DistanceScoreMover
• prepare_search_stage() : protocols::mpi_refinement::Scheduler
• prepare_sets_for_packing() : core::pack::rotamer_set::RotamerSets
• prepare_simulation() : protocols::canonical_sampling::MetropolisHastingsMover
• prepare_single_ligand_pose() : protocols::ligand_docking::HighResEnsemble , protocols::ligand_docking::ProtLigEnsemble
• prepare_stage1() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints , protocols::abinitio::FragmentSampler , protocols::abinitio::KinematicAbinitio , protocols::abinitio::MembraneAbinitio
• prepare_stage2() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints , protocols::abinitio::FragmentSampler , protocols::abinitio::KinematicAbinitio , protocols::abinitio::MembraneAbinitio
• prepare_stage3() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::KinematicAbinitio , protocols::abinitio::MembraneAbinitio
• prepare_stage4() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FoldConstraints , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• prepare_stage5() : protocols::abinitio::ClassicAbinitio
• prepare_symm_otf_interaction_graph() : core::pack::rotamer_set::symmetry::SymmetricRotamerSets
• prepare_task_poses() : protocols::mean_field::GenMeanFieldMover
• prepare_termini_for_remodel() : protocols::denovo_design::movers::FoldTreeFromFoldGraphMover
• prepare_to_note_hits_for_completed_round() : protocols::match::OccupiedSpaceHash
• prepare_xml_text() : protocols::rosetta_scripts::XmlObjects
• PrepareForCentroid() : protocols::loop_modeling::utilities::PrepareForCentroid
• PrepareForFullatom() : protocols::loop_modeling::utilities::PrepareForFullatom
• prepend_Aform_residue() : core::import_pose::RNA_HelixAssembler
• prepend_edge() : core::kinematics::FoldTree
• prepend_other_pose() : protocols::stepwise::monte_carlo::mover::AddMover
• prepend_output_name() : protocols::canonical_sampling::MetricRecorder
• prepend_polymer_residue_before_seqpos() : core::conformation::Conformation , core::conformation::symmetry::SymmetricConformation , core::pose::Pose , protocols::environment::ProtectedConformation
• prepend_res() : core::pose::PDBInfo
• prepend_residue() : protocols::stepwise::monte_carlo::mover::AddMover
• PrependMainchainAtom() : core::chemical::PrependMainchainAtom
• preprocess_data() : core::scoring::ResidualDipolarCoupling
• preprocess_pose() : core::import_pose::pose_stream::PoseInputStream
• PreProlineFilter() : protocols::denovo_design::filters::PreProlineFilter
• presample_virtual_sugars() : protocols::stepwise::modeler::StepWiseConnectionSampler
• prescoring_filter_exists() : protocols::helical_bundle::BackboneGridSampler
• prescoring_mover_exists() : protocols::helical_bundle::BackboneGridSampler
• PreSelectedResidRange() : core::select::PreSelectedResidRange
• preselection_filter_exists() : protocols::helical_bundle::BundleGridSampler
• preselection_mover_exists() : protocols::generalized_kinematic_closure::GeneralizedKIC , protocols::helical_bundle::BundleGridSampler
• preserve_atom_coords() : protocols::simple_moves::MutateResidue
• preserve_buried_contacts() : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• preserve_c_beta() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• preserve_crystinfo() : core::io::StructFileRepOptions
• preserve_detailed_balance() : protocols::backrub::BackrubMover , protocols::backrub::BackrubSidechainMover , protocols::canonical_sampling::ThermodynamicMover , protocols::kinematic_closure::BalancedKicMover , protocols::rigid::RigidBodyMover , protocols::rigid::UniformRigidBodyMover , protocols::simple_moves::BackboneMover , protocols::simple_moves::BBGaussianMover , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• preserve_header() : core::io::StructFileRepOptions
• preserve_old_mainchain_torsions() : protocols::cyclic_peptide::PeptideStubMover
• PreserveCBetaRLT() : core::pack::task::operation::PreserveCBetaRLT
• presetClass() : protocols::sparta::GDB
• PRESingle() : core::scoring::nmr::pre::PRESingle
• PRESingleSet() : core::scoring::nmr::pre::PRESingleSet
• pretty_print() : core::scoring::mm::MMBondAngleLibrary , core::scoring::mm::MMBondLengthLibrary
• preturb_rot_and_dunbrack_eval() : protocols::simple_moves::sidechain_moves::SidechainMover
• prev_residue_skipping_merges() : core::io::pose_from_sfr::PoseFromSFRBuilder
• prev_residue_skipping_null_residue_types() : core::io::pose_from_sfr::PoseFromSFRBuilder
• prevent_repacking() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_ , protocols::calc_taskop_movers::DesignRepackMover , protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation , protocols::task_operations::RestrictIdentitiesOperation , protocols::task_operations::RestrictNativeResiduesOperation
• PreventChainFromRepackingOperation() : protocols::task_operations::PreventChainFromRepackingOperation
• PreventResiduesFromRepackingOperation() : protocols::task_operations::PreventResiduesFromRepackingOperation
• previous() : protocols::legacy_sewing::SegmentGraph
• previous_child() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• previous_round_geometry_still_matchable() : protocols::match::OccupiedSpaceHash
• previous_sibling() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• previous_working_pack_res() : protocols::stepwise::modeler::packer::StepWisePacker
• previously_builded_res_clash_filter() : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• previously_builded_res_contact_filter() : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• previously_builded_res_VDW_filter() : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• PrimarySequenceNeighborhoodSelector() : core::select::residue_selector::PrimarySequenceNeighborhoodSelector
• principal_component() : protocols::features::helixAssembly::HelicalFragment
• PrincipalQuantumNumber_strings() : core::chemical::ElectronConfiguration
• print() : core::chemical::AtomType , core::chemical::Bond , core::chemical::Orbital , core::io::raw_data::ScoreMap , core::pack::interaction_graph::BackgroundNode< V, E, G > , core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DotSphere , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::NodeBase , core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G > , core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > , core::pack::interaction_graph::NPDHBondNode< V, E, G > , core::pack::interaction_graph::NPDHBSimpleNode , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::RotamerDots , core::pack::interaction_graph::RotamerDotsCache , core::pack::interaction_graph::SimpleNode , core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode , core::pose::metrics::EnergyDependentCalculator , core::pose::metrics::PoseMetricCalculator , core::pose::metrics::PoseMetricContainer , core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator , core::pose::metrics::simple_calculators::InterfaceDeltaEnergeticsCalculator , core::pose::metrics::simple_calculators::InterfaceNeighborDefinitionCalculator , core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator , core::pose::metrics::simple_calculators::SasaCalculator2 , core::pose::metrics::simple_calculators::SasaCalculatorLegacy , core::pose::metrics::StructureDependentCalculator , core::scoring::elec::electrie::ElecAtom , core::scoring::EMapVector , core::scoring::EnergyNode , core::scoring::etable::etrie::CountPairData_1_1 , core::scoring::etable::etrie::CountPairData_1_2 , core::scoring::etable::etrie::CountPairData_1_3 , core::scoring::etable::etrie::CountPairDataGeneric , core::scoring::etable::etrie::EtableAtom , core::scoring::etable::etrie::TrieCountPair1BC3 , core::scoring::etable::etrie::TrieCountPairAll , core::scoring::etable::etrie::TrieCountPairGeneric , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::hbonds::graph::HBondNode , core::scoring::hbonds::hbtrie::HBAtom , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::hbonds::hbtrie::HBCPData , core::scoring::lkball::lkbtrie::LKBAtom , core::scoring::MembraneTopology , core::scoring::MinimizationNode , core::scoring::mm::mmtrie::MMEnergyTableAtom , core::scoring::trie::RotamerTrie< AT, CPDATA > , core::scoring::trie::RotamerTrieBase , core::scoring::trie::TrieNode< AT, CPDATA > , core::scoring::vdwaals::VDWAtom , protocols::constel::ChainTerm , protocols::constel::ResidueMask , protocols::denovo_design::calculators::CavityCalculator , protocols::dna::DnaChains , protocols::fldsgn::NcontactsCalculator , protocols::flexpack::interaction_graph::FlexbbNode , protocols::flexpack::interaction_graph::MinimalistFlexbbNode , protocols::flexpack::interaction_graph::OTFFlexbbNode , protocols::frag_picker::nonlocal::NonlocalPair , protocols::frags::TorsionFragmentLibrary , protocols::loophash::BackboneSegment , protocols::match::downstream::AtomAngleSecMatchRPE , protocols::match::downstream::AtomDihedralSecMatchRPE , protocols::match::downstream::AtomDistanceSecMatchRPE , protocols::match::downstream::AtomGeometrySecMatchRPE , protocols::mean_field::EnergiesByTaskCalculator , protocols::motifs::Motif , protocols::moves::MoverStatistics , protocols::moves::PyMOLMover , protocols::pockets::PocketGrid , protocols::pose_creation::MakeJunctionsMover::Design , protocols::pose_creation::MergePDBMover::Overlap , protocols::pose_metric_calculators::CatPiCalculator , protocols::pose_metric_calculators::ChargeCalculator , protocols::pose_metric_calculators::ClashCountCalculator , protocols::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator , protocols::pose_metric_calculators::FragQualCalculator , protocols::pose_metric_calculators::HPatchCalculator , protocols::pose_metric_calculators::InterGroupNeighborsCalculator , protocols::pose_metric_calculators::NeighborhoodByDistanceCalculator , protocols::pose_metric_calculators::NeighborsByDistanceCalculator , protocols::pose_metric_calculators::NonlocalContactsCalculator , protocols::pose_metric_calculators::PackstatCalculator , protocols::pose_metric_calculators::PiPiCalculator , protocols::pose_metric_calculators::ResidueDecompositionCalculator , protocols::pose_metric_calculators::RotamerBoltzCalculator , protocols::pose_metric_calculators::SaltBridgeCalculator , protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator , protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator , protocols::pose_metric_calculators::SurfaceCalculator , protocols::rbsegment_relax::RBSegmentMover , protocols::scoring::Interface , protocols::simple_moves::Hit , protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator , protocols::simple_pose_metric_calculators::NumberHBondsCalculator , protocols::splice::RotLibOut , protocols::vardist_solaccess::VarSolDistSasaCalculator , protocols::wum::SilentStructStore , protocols::wum::WorkUnitBase
• print_additional_headers() : protocols::hbnet::HBNet , protocols::hbnet::HBNetStapleInterface
• print_additional_info_for_net() : protocols::hbnet::HBNet , protocols::hbnet::HBNetStapleInterface
• print_address() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• print_addresses_at_level() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• print_all_bond_lengths() : core::chemical::IdealBondLengthSet
• print_all_info() : protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator
• print_all_nodes() : protocols::jd3::JobGenealogist
• print_all_score_headers() : core::io::silent::SilentFileOptions
• print_all_types() : core::chemical::MMAtomTypeSet
• print_allowed_types() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• print_alt_energies() : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• print_atom_info() : protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator
• print_atom_subset() : protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator
• print_avg_cluster_centroid_dist() : protocols::make_rot_lib::MakeRotLibMover
• print_best_rms() : protocols::electron_density::DockIntoDensityMover
• print_bit_string() : core::pack::interaction_graph::RotamerDotsCache
• print_bondangles() : core::chemical::ResidueType
• print_cache() : protocols::genetic_algorithm::GeneticAlgorithmBase
• print_cluster_assignment() : protocols::cluster::ClusterBase , protocols::toolbox::ClusterBase
• print_cluster_PDBs() : protocols::cluster::ClusterBase
• print_clusters_silentfile() : protocols::cluster::ClusterBase
• print_comments() : core::io::silent::SilentStruct
• print_conformation() : core::import_pose::PDBSilentStruct , core::io::raw_data::DecoyStruct , core::io::raw_data::RawStruct , core::io::raw_data::ScoreStructJSON , core::io::raw_data::ScoreStructText , core::io::silent::BinarySilentStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RigidBodySilentStruct , core::io::silent::RNA_SilentStruct , core::io::silent::ScoreFileSilentStruct , core::io::silent::ScoreJumpFileSilentStruct , core::io::silent::SilentStruct
• print_current_energy() : core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmMinimalistEdge
• print_current_state_assignment() : core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistInteractionGraph , protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph
• print_data() : protocols::fold_from_loops::movers::DisplayPoseLabelsMover
• print_debug() : protocols::abinitio::MembraneAbinitio
• print_definitions() : protocols::make_rot_lib::MakeRotLibMover
• print_dofs() : protocols::optimize_weights::WrapperOptEMultifunc
• print_dot_bit_string() : core::pack::interaction_graph::InvRotamerDots , core::scoring::sasa::LeGrandSasa
• print_dunbrack02_rotlib() : protocols::make_rot_lib::MakeRotLibMover
• print_dunbrack10_rotlib() : protocols::make_rot_lib::MakeRotLibMover
• print_energies() : protocols::optimize_weights::IterativeOptEDriver
• print_entity_history() : protocols::pack_daemon::PackDaemon
• print_fragment() : protocols::frag_picker::FragmentCandidate
• print_fragment_index() : protocols::frag_picker::FragmentCandidate
• print_fragment_seq() : protocols::frag_picker::FragmentCandidate
• print_generation_statistics() : protocols::genetic_algorithm::GeneticAlgorithmBase
• print_grid_param() : protocols::scoring::methods::pcs::PCS_Energy_parameters_manager , protocols::scoring::methods::pcsTs1::PCS_Energy_parameters_manager_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_parameters_manager_Ts4
• print_header() : core::import_pose::PDBSilentStruct , core::io::raw_data::RawStruct , core::io::raw_data::ScoreStructJSON , core::io::silent::BinarySilentStruct , core::io::silent::RNA_SilentStruct , core::io::silent::ScoreFileSilentStruct , core::io::silent::ScoreJumpFileSilentStruct , core::io::silent::SilentStruct , core::scoring::motif::ResPairMotif
• print_histogram() : core::scoring::epr_deer::DEERData
• print_hpatch_avoidance_stats() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• print_info() : core::pose::rna::BasePair
• print_internal_energies() : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode , protocols::flexpack::interaction_graph::FlexbbNode
• print_internal_energies_for_current_state_assignment() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• print_job_lineage() : protocols::multistage_rosetta_scripts::MRSJobQueen
• print_lib_to_file() : protocols::splice::RotLibOut
• print_library() : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• print_metric() : core::pose::Pose
• print_movemap() : protocols::fold_from_loops::movers::DisplayPoseLabelsMover
• print_mut_string() : protocols::ligand_docking::ProtLigPair_info
• print_mutation_data() : protocols::pmut_scan::MutationData
• print_ngb_mask() : protocols::neighbor::Neighborhood
• print_nmap() : protocols::constel::NeighTeller
• print_npd_hbond_avoidance_stats() : core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >
• print_pack_report() : protocols::vip::VIP_Mover
• print_parent_remarks() : core::io::silent::SilentStruct
• print_particles() : core::optimization::ParticleSwarmMinimizer
• print_peak_info() : protocols::noesy_assign::CrossPeak
• print_population() : protocols::genetic_algorithm::GeneticAlgorithmBase
• print_pretty_path_distances() : core::chemical::ResidueType
• print_pymol_selection_of_hbond_unsat() : protocols::analysis::InterfaceAnalyzerMover
• print_pymol_selection_of_interface_residues() : protocols::analysis::InterfaceAnalyzerMover
• print_pymol_selection_of_packing() : protocols::analysis::InterfaceAnalyzerMover
• print_quantiles() : core::scoring::motif::XformScore
• print_raw_numbers() : protocols::cluster::ClusterBase
• print_relax_report() : protocols::vip::VIP_Mover
• print_report() : protocols::frag_picker::BoundedCollector< StrictWeakOrdering > , protocols::frag_picker::CandidatesCollector , protocols::frag_picker::GrabAllCollector , protocols::frag_picker::quota::ABEGO_SS_Pool , protocols::frag_picker::quota::QuotaCollector , protocols::frag_picker::quota::SecondaryStructurePool
• print_residue_numbers() : core::io::silent::SilentStruct
• print_rot_data() : protocols::make_rot_lib::MakeRotLibMover
• print_rot_data_vec() : protocols::make_rot_lib::MakeRotLibMover
• print_rot_vec() : protocols::pose_metric_calculators::RotamerRecovery
• print_sc_results() : protocols::simple_filters::ShapeComplementarityFilter
• print_score() : protocols::optimize_weights::ConstraintedOptimizationWeightFunc , protocols::optimize_weights::DDGBindOptEData , protocols::optimize_weights::DDGMutationOptEData , protocols::optimize_weights::DGBindOptEData , protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData , protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData , protocols::optimize_weights::OptEPositionData , protocols::optimize_weights::PNatAAOptEPositionData , protocols::optimize_weights::PNatLigPoseOptEData , protocols::optimize_weights::PNatRotOptEPositionData , protocols::optimize_weights::PNatStructureOptEData , protocols::optimize_weights::PSSMOptEPositionData , protocols::relax::RangeRelaxMover
• print_score_functions() : core::scoring::disulfides::FullatomDisulfidePotential
• print_score_header() : core::io::silent::SilentStruct
• print_scores() : core::io::raw_data::RawStruct , core::io::raw_data::ScoreStructJSON , core::io::silent::SilentStruct , core::scoring::motif::XformScore
• print_scores_norm() : core::scoring::motif::XformScore
• print_sequence() : protocols::frag_picker::CSTalosIO , protocols::frag_picker::PhiPsiTalosIO
• print_sho_energies() : protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator
• print_statistics() : protocols::sewing::movers::AssemblyMover
• print_stats() : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement , protocols::wum::MPI_WorkUnitManager
• print_stats_auto() : protocols::wum::MPI_WorkUnitManager
• print_str_vec() : protocols::antibody::design::AntibodyDesignMover
• print_string() : protocols::ligand_docking::ProtLigPair_info
• print_string_to_PDBfile() : protocols::pockets::GenPharmacophore
• print_submotif_info() : core::io::silent::SilentStruct
• print_summary() : protocols::cluster::ClusterBase , protocols::mpi_refinement::MPI_Refinement , protocols::toolbox::ClusterBase
• print_surface_avoidance_stats() : core::pack::interaction_graph::SurfaceNode< V, E, G >
• print_task_operators() : protocols::fold_from_loops::movers::DisplayPoseLabelsMover
• print_timing_stats() : protocols::wum::MPI_WorkUnitManager
• print_to_file() : protocols::pockets::FingerprintBase
• print_to_oegrid() : protocols::pockets::ElectrostaticpotentialGrid
• print_to_pdb() : protocols::pockets::FingerprintBase
• print_verbose_ddgs() : protocols::ddg::ddGMover
• print_vertex_groups() : core::pack::interaction_graph::InteractionGraphBase
• print_vertices() : core::pack::interaction_graph::InteractionGraphBase
• print_water_weight_grid_xz_plane() : core::scoring::geometric_solvation::WaterWeightGridSet
• print_xyz() : protocols::ligand_docking::TransformEnsemble
• printContent() : protocols::pockets::SmallMol
• printCoordinates() : protocols::pockets::SmallMol
• PrintErrorAndQuit() : protocols::hybridization::TMalign
• printGrishinFormat() : core::sequence::SequenceAlignment
• prioritize_rosetta_types_over_pdb_components() : core::chemical::ResidueTypeFinder
• priority() : protocols::topology_broker::claims::SequenceClaim
• private_data_to_public_array() : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• pro_cd_cprev_n_ca_interres_improper_params() : core::scoring::methods::ResidueCartBondedParameters
• pro_CD_index() : core::scoring::methods::ResidueCartBondedParameters
• prob() : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• prob_random_pert_current() : protocols::backrub::BackrubSidechainMover , protocols::simple_moves::sidechain_moves::SidechainMover
• prob_sum_of_gaussians() : core::scoring::func::SOGFunc_Impl
• prob_to_accumulate() : core::pack::dunbrack::SingleResidueDunbrackLibrary
• prob_to_accumulate_buried() : core::pack::dunbrack::SingleResidueDunbrackLibrary
• prob_to_accumulate_nonburied() : core::pack::dunbrack::SingleResidueDunbrackLibrary
• prob_uniform() : protocols::backrub::BackrubSidechainMover , protocols::simple_moves::sidechain_moves::SidechainMover
• prob_withinrot() : protocols::backrub::BackrubSidechainMover , protocols::simple_moves::sidechain_moves::SidechainMover
• probA() : core::scoring::packstat::PackingScore
• probabilistically_commit_relaxation() : core::pack::interaction_graph::FASTERInteractionGraph
• probability() : core::pack::dunbrack::DunbrackRotamerSampleData , protocols::frag_picker::quota::ABEGO_SS_Config , protocols::mean_field::AAProb , protocols::mean_field::RotProb , protocols::noesy_assign::CrossPeak
• probability_limit() : protocols::match::upstream::BuildSet
• probability_matrix() : core::scoring::bin_transitions::BinTransitionData
• probability_row() : core::sequence::SequenceProfile
• probability_to_accumulate_while_building_rotamers() : core::pack::dunbrack::SingleResidueDunbrackLibrary
• probabilty_row() : core::sequence::SequenceProfile
• probB() : core::scoring::packstat::PackingScore
• probe_radius() : protocols::match::BumpGrid , protocols::simple_filters::TaskAwareSASAFilter
• proceed() : protocols::mpi_refinement::Scheduler
• process() : protocols::mean_field::DesignMeanField , protocols::mean_field::FlexBBDesignMeanField , protocols::mean_field::FlexBBMeanField , protocols::mean_field::MeanField
• process_AA_SET_line() : protocols::pack_daemon::EntityFunc
• process_add_daemon_message() : protocols::pack_daemon::DaemonSet
• process_algorithm_info() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• process_continuous_design_string() : protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover
• process_data() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• process_deallocation_message() : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::JobQueen , protocols::jd3::standard::StandardJobQueen
• process_decoy() : protocols::abinitio::AbrelaxApplication
• process_deletions() : protocols::rna::movers::RNAThreadAndMinimizeMover
• process_discard_entity_message() : protocols::pack_daemon::DaemonSet
• process_elements() : protocols::environment::EnvClaimBroker
• process_energy_change() : core::pose::metrics::PoseMetricContainer
• process_entire_pose() : protocols::rna::movers::ErraserMinimizerMover
• process_ENTITY_FUNCTION_line() : protocols::pack_daemon::DynamicAggregateFunction
• process_FITNESS_line() : protocols::pack_daemon::DynamicAggregateFunction
• process_fragments() : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• process_hit() : protocols::match::downstream::SecondaryMatcherToUpstreamResidue , protocols::match::downstream::SecondaryMatchUpstreamResProcessor , protocols::match::output::PoseInserter , protocols::match::output::UpstreamHitCacher , protocols::match::output::WriteUpstreamHitKinemage , protocols::match::upstream::UpstreamResidueProcessor
• process_inbound_wus() : protocols::loophash::MPI_LoopHashRefine_Emperor , protocols::loophash::MPI_LoopHashRefine_Master , protocols::mpi_refinement::MPI_Refine_Emperor , protocols::mpi_refinement::MPI_Refine_Master , protocols::wum::MPI_WorkUnitManager , protocols::wum::MPI_WorkUnitManager_Slave
• process_incoming_msgs() : protocols::wum::MPI_WorkUnitManager
• process_input_line_tokens() : protocols::toolbox::match_enzdes_util::ResInteractions
• process_insert_design_string() : protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover
• process_insertions() : protocols::rna::movers::RNAThreadAndMinimizeMover
• process_match() : protocols::match::output::MatchConsolidator , protocols::match::output::MatchOutputter , protocols::match::output::MatchProcessor
• process_match_list() : protocols::canonical_sampling::AsyncMPITemperingBase
• process_matches() : protocols::match::Matcher
• process_matches_all_hit_combos_for_hit_subsets() : protocols::match::Matcher
• process_matches_main_loop_enumerating_all_hit_combos() : protocols::match::Matcher
• process_matches_where_one_geomcst_defines_downstream_location() : protocols::match::Matcher
• process_matching_exchange_requests() : protocols::canonical_sampling::AsyncMPITemperingBase
• process_message() : protocols::jd2::archive::MPIArchiveJobDistributor , protocols::jd2::MPIFileBufJobDistributor
• process_motifs() : protocols::simple_filters::SymmetricMotifFilter
• process_NPD_PROPERTY_line() : protocols::pack_daemon::DynamicAggregateFunction
• process_outbound_wus() : protocols::loophash::MPI_LoopHashRefine_Emperor , protocols::loophash::MPI_LoopHashRefine_Master , protocols::mpi_refinement::MPI_Refine_Emperor , protocols::mpi_refinement::MPI_Refine_Master , protocols::wum::MPI_WorkUnitManager , protocols::wum::MPI_WorkUnitManager_Slave
• process_pdb_header() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• process_pose() : protocols::denovo_design::DisulfidizeMover , protocols::match::MatcherMover , protocols::rosetta_scripts::MultiplePoseMover
• process_POSE_ENERGY_line() : protocols::pack_daemon::DynamicAggregateFunction
• process_POSE_ENERGY_VECTOR_line() : protocols::pack_daemon::DynamicAggregateFunction
• process_pose_request_for_entity() : protocols::pack_daemon::DaemonSet
• process_poses() : protocols::rosetta_scripts::MultiplePoseMover
• process_rotamers() : protocols::optimize_weights::PNatAAOptEPositionData
• process_round() : protocols::mpi_refinement::MPI_Refine_Master
• process_SCALAR_EXPRESSION_line() : protocols::pack_daemon::DynamicAggregateFunction
• process_score() : protocols::optimize_weights::DDGBindOptEData , protocols::optimize_weights::DDGMutationOptEData , protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData , protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData , protocols::optimize_weights::PNatRotOptEPositionData , protocols::optimize_weights::PNatStructureOptEData
• process_SCORE_line() : protocols::pack_daemon::EntityFunc
• process_SET_CONDITION_line() : protocols::pack_daemon::EntityFunc
• process_state_energy_evaluations_for_entity() : protocols::pack_daemon::DaemonSet
• process_STATE_line() : protocols::pack_daemon::DynamicAggregateFunction
• process_STATE_VECTOR_line() : protocols::pack_daemon::DynamicAggregateFunction
• process_structure_change() : core::pose::metrics::PoseMetricContainer
• process_SUB_EXPRESSION_line() : protocols::pack_daemon::EntityFunc
• process_symmdef_file() : protocols::symmetry::SetupForSymmetryMover
• process_termination() : protocols::mpi_refinement::MPI_Refine_Emperor , protocols::mpi_refinement::MPI_Refine_Master
• process_VECTOR_EXPRESSION_line() : protocols::pack_daemon::DynamicAggregateFunction
• process_VECTOR_VARIABLE_line() : protocols::pack_daemon::DynamicAggregateFunction
• process_work_unit() : protocols::network::NetworkQueue
• processed_jobs() : protocols::jd3::full_model::FullModelJobQueen
• ProcessorFactory() : protocols::match::output::ProcessorFactory
• ProClosureEnergy() : core::scoring::methods::ProClosureEnergy
• prof_row() : core::sequence::SequenceProfile , protocols::frag_picker::LAMBEGO_IO , protocols::frag_picker::TorsionBinIO
• profile() : core::fragment::picking_old::vall::VallResidue , core::sequence::SequenceProfile , protocols::frag_picker::VallResidue
• profile_config() : protocols::indexed_structure_store::movers::SegmentSequenceProfileMover
• profile_feature() : core::scoring::methods::ProQ_Energy
• profile_index_to_aa() : core::scoring::methods::ProQ_Energy
• profile_mapping() : core::scoring::constraints::SequenceProfileConstraint
• profile_struct() : protocols::frag_picker::VallResidue
• profile_weight_away_from_interface() : protocols::splice::Splice , protocols::splice::SpliceManager
• ProfilerMover() : protocols::moves::ProfilerMover
• ProfileScore() : protocols::frag_picker::scores::ProfileScore
• ProfileScoreBlosum62() : protocols::frag_picker::scores::ProfileScoreBlosum62
• ProfileScoreDistWeight() : protocols::frag_picker::scores::ProfileScoreDistWeight
• ProfileScoreL1() : protocols::frag_picker::scores::ProfileScoreL1
• ProfileScoreStructL1() : protocols::frag_picker::scores::ProfileScoreStructL1
• ProfileScoreSubMatrix() : protocols::frag_picker::scores::ProfileScoreSubMatrix
• ProfSimScoringScheme() : core::sequence::ProfSimScoringScheme
• progress_file() : protocols::monte_carlo::GenericMonteCarloMover
• ProgressBarObserver() : protocols::canonical_sampling::ProgressBarObserver
• prohibit_property_i() : core::scoring::bin_transitions::BinTransitionData
• prohibit_property_iplus1() : core::scoring::bin_transitions::BinTransitionData
• prohibit_res_identity_i() : core::scoring::bin_transitions::BinTransitionData
• prohibit_res_identity_iplus1() : core::scoring::bin_transitions::BinTransitionData
• prohibit_single_residue_loops() : protocols::loops::LoopFromFileData
• ProhibitResidueProperties() : core::pack::task::operation::ProhibitResidueProperties
• ProhibitSpecifiedBaseResidueTypes() : core::pack::task::operation::ProhibitSpecifiedBaseResidueTypes
• project_deltaE_for_substitution() : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode , protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph , protocols::flexpack::interaction_graph::MinimalistFlexbbNode
• project_deltaE_for_substitution_surface() : core::pack::interaction_graph::SurfaceNode< V, E, G >
• project_point_to_3d() : protocols::match::OccupiedSpaceHash
• project_surface_deltaE() : core::pack::interaction_graph::SurfaceNode< V, E, G >
• project_surface_deltaE_for_substitution() : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >
• ProlineFixMover() : protocols::simple_moves::ProlineFixMover
• ProlinePhiScore() : protocols::frag_picker::scores::ProlinePhiScore
• promote_sameresidue_nonjump_child() : core::kinematics::AtomTree
• propagate_best_from_previous_generation() : protocols::genetic_algorithm::GeneticAlgorithmBase
• PropagateClashCheckFilter() : protocols::dna_dock::PropagateClashCheckFilter
• propeller() : protocols::dna::DNABasepair
• properties() : core::chemical::Atom , core::chemical::ResidueTypeBase , core::chemical::ResidueTypeFinder , core::pack::task::operation::ProhibitResidueProperties , core::pack::task::operation::RestrictToResidueProperties , protocols::ligand_docking::ga_ligand_dock::ConstraintInfo
• properties_match_this() : core::scoring::aa_composition_energy::AACompositionPropertiesSet
• property() : core::pack::task::operation::ResidueHasProperty , core::pack::task::operation::ResiduePDBInfoHasLabel
• PROPERTY() : core::pack::task::PROPERTY
• property_from_string() : core::chemical::AtomPropertiesManager
• property_penalty() : core::scoring::aa_composition_energy::AACompositionEnergySetup
• property_set_indices_matching_residue() : core::scoring::aa_composition_energy::AACompositionEnergySetup
• property_to_string_map() : core::chemical::AtomPropertiesManager
• proposal_density() : protocols::simple_moves::sidechain_moves::SidechainMover
• proposal_density_ratio() : protocols::stepwise::monte_carlo::mover::StepWiseMasterMover
• proposal_probability() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• proposed_one_body_energy() : core::pack::interaction_graph::SimpleNode
• proposed_since_last_batch() : protocols::jd2::archive::ArchiveBase
• props() : protocols::ligand_docking::ga_ligand_dock::Pharmacophore
• ProQ_Energy() : core::scoring::methods::ProQ_Energy
• ProQPotential() : core::scoring::ProQPotential
• ProtectedConformation() : protocols::environment::ProtectedConformation
• protein_calculate() : protocols::scoring::Interface
• protein_dielectric() : core::scoring::methods::EnergyMethodOptions
• protein_dna_motif() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• protein_DNA_motif_build_positions_JA() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• protein_DNA_motif_target_positions_JA() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• protein_family() : protocols::splice::Splice
• protein_in_membrane() : protocols::membrane::MPLipidAccessibility
• protein_interface_design() : protocols::task_operations::SeqprofConsensusOperation
• protein_neighbors() : protocols::dna::DnaInterfaceFinder
• protein_pack_all() : core::import_pose::options::RNA_MinimizerOptions
• protein_packing() : core::import_pose::options::RNA_MinimizerOptions
• protein_packing_distance() : core::import_pose::options::RNA_MinimizerOptions
• protein_patches_can_apply() : protocols::mainchain_potential::GenerateMainchainPotential
• protein_position_equal_within() : core::scoring::methods::PoissonBoltzmannEnergy
• protein_positions() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• protein_prepack() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• protein_protein_rdf() : protocols::ligand_docking::ComputeLigandRDF
• protein_residue() : protocols::ligand_docking::ga_ligand_dock::LigandConformer
• protein_rot() : protocols::simple_moves::WaterRotsDB
• protein_scan() : protocols::dna::DnaInterfacePacker
• protein_sidechain_packing() : protocols::rna::denovo::movers::RNP_HighResMover
• ProteinAtrRepChecker() : protocols::stepwise::modeler::protein::checker::ProteinAtrRepChecker
• ProteinAtrRepScreener() : protocols::stepwise::legacy::screener::ProteinAtrRepScreener
• ProteinBackboneAtomAtomPairFeatures() : protocols::features::ProteinBackboneAtomAtomPairFeatures
• ProteinBackboneBuildPoint() : protocols::match::upstream::ProteinBackboneBuildPoint
• ProteinBackboneTorsionAngleFeatures() : protocols::features::ProteinBackboneTorsionAngleFeatures
• ProteinBetaAntiParallelStepWiseSampler() : protocols::stepwise::sampler::protein::ProteinBetaAntiParallelStepWiseSampler
• ProteinBondGeometryFeatures() : protocols::features::ProteinBondGeometryFeatures
• ProteinCCD_ClosureScreener() : protocols::stepwise::screener::ProteinCCD_ClosureScreener
• ProteinCore() : protocols::task_operations::ProteinCore
• ProteinFragmentStepWiseSampler() : protocols::stepwise::sampler::protein::ProteinFragmentStepWiseSampler
• ProteinInterfaceDesignOperation() : protocols::task_operations::ProteinInterfaceDesignOperation
• ProteinInterfaceMultiStateDesignMover() : protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• ProteinLigandInterfaceUpweighter() : protocols::enzdes::ProteinLigandInterfaceUpweighter
• ProteinMainChainStepWiseSampler() : protocols::stepwise::sampler::protein::ProteinMainChainStepWiseSampler
• ProteinProteinInterfaceUpweighter() : protocols::pack_interface::ProteinProteinInterfaceUpweighter
• ProteinResidueConformationFeatures() : protocols::features::ProteinResidueConformationFeatures
• ProteinResidueSelector() : protocols::fold_from_loops::selectors::ProteinResidueSelector
• ProteinRMSDFeatures() : protocols::features::ProteinRMSDFeatures
• ProteinRMSDNoSuperpositionFeatures() : protocols::features::ProteinRMSDNoSuperpositionFeatures
• ProteinSilentReport() : protocols::features::ProteinSilentReport
• ProteinSilentStruct_SinglePrecCreator() : core::io::silent::ProteinSilentStruct_SinglePrecCreator
• ProteinSilentStruct_Template() : core::io::silent::ProteinSilentStruct_Template< T >
• ProteinSilentStructCreator() : core::io::silent::ProteinSilentStructCreator
• ProteinUpstreamBuilder() : protocols::match::upstream::ProteinUpstreamBuilder
• ProtLigEnsemble() : protocols::ligand_docking::ProtLigEnsemble
• ProtLigPair_info() : protocols::ligand_docking::ProtLigPair_info
• Protocol() : protocols::abinitio::Protocol
• protocol_option_set() : protocols::rosetta_scripts::RosettaScriptsParser
• ProtocolFeatures() : protocols::features::ProtocolFeatures
• protocols() : protocols::multistage_rosetta_scripts::MRSJob
• protocols_subelement_mangler() : protocols::multistage_rosetta_scripts::MRSJobQueen
• ProtocolSettingsMetric() : core::simple_metrics::composite_metrics::ProtocolSettingsMetric
• proton() : protocols::noesy_assign::CrossPeak
• proton_chi_2_chi() : core::chemical::ResidueType
• proton_chi_extra_samples() : core::chemical::MutableChiRecord , core::chemical::ResidueType
• proton_chi_extra_samples_for_chi() : core::chemical::MutableResidueType
• proton_chi_samples() : core::chemical::MutableChiRecord , core::chemical::ResidueType
• proton_chi_samples_for_chi() : core::chemical::MutableResidueType
• proton_index() : protocols::noesy_assign::MethylNames
• proton_indices() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup
• proton_tolerance() : protocols::noesy_assign::CrossPeakInfo
• protonated_H1_adenosine_list() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• ProtonResonance() : protocols::noesy_assign::ProtonResonance
• provide_attributes() : protocols::simple_task_operations::RestrictToLoops
• provide_attributes_and_subelements() : protocols::fldsgn::MatchResidues
• provide_authorship_info_for_unpublished() : core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty , core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty , core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy , core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyEnergy , core::pack::palette::NCAADefaultPackerPalette , core::pack::palette::PackerPalette , core::pack::task::operation::TaskOperation , core::scoring::methods::EnergyMethod , core::scoring::netcharge_energy::NetChargeEnergy , core::scoring::ScoreFunction , core::select::residue_selector::AndResidueSelector , core::select::residue_selector::NeighborhoodResidueSelector , core::select::residue_selector::NotResidueSelector , core::select::residue_selector::OrResidueSelector , core::select::residue_selector::ResidueSelector , core::select::residue_selector::SliceResidueSelector , core::simple_metrics::metrics::CalculatorMetric , core::simple_metrics::metrics::DihedralDistanceMetric , core::simple_metrics::metrics::InteractionEnergyMetric , core::simple_metrics::metrics::ResidueSummaryMetric , core::simple_metrics::metrics::RMSDMetric , core::simple_metrics::metrics::SasaMetric , core::simple_metrics::metrics::SecondaryStructureMetric , core::simple_metrics::metrics::SelectedResidueCountMetric , core::simple_metrics::metrics::SelectedResiduesMetric , core::simple_metrics::metrics::SelectedResiduesPyMOLMetric , core::simple_metrics::metrics::SequenceMetric , core::simple_metrics::metrics::SequenceSimilarityMetric , core::simple_metrics::metrics::TimingProfileMetric , core::simple_metrics::metrics::TotalEnergyMetric , core::simple_metrics::SimpleMetric , protocols::analysis::GlycanInfoMover , protocols::analysis::simple_metrics::RunSimpleMetricsMover , protocols::antibody::AntibodyCDRGrafter , protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover , protocols::antibody::constraints::ParatopeSiteConstraintMover , protocols::antibody::design::AntibodyDesignMover , protocols::antibody::design::MutateFrameworkForCluster , protocols::calc_taskop_movers::CreateSequenceMotifMover , protocols::carbohydrates::CreateGlycanSequonMover , protocols::carbohydrates::GlycanSampler , protocols::carbohydrates::GlycanTreeMinMover , protocols::carbohydrates::GlycanTreeModeler , protocols::carbohydrates::LinkageConformerMover , protocols::carbohydrates::RingPlaneFlipMover , protocols::carbohydrates::SimpleGlycosylateMover , protocols::carbohydrates::TautomerizeAnomerMover , protocols::cyclic_peptide::PeptideInternalHbondsFilter , protocols::cyclic_peptide::PeptideInternalHbondsMetric , protocols::cyclic_peptide::SymmetricCycpepAlign , protocols::cyclic_peptide::TryDisulfPermutations , protocols::denovo_design::filters::CavityVolumeFilter , protocols::enzymatic_movers::EnzymaticMover , protocols::enzymatic_movers::GlycosyltransferaseMover , protocols::enzymatic_movers::KinaseMover , protocols::filters::Filter , protocols::generalized_kinematic_closure::GeneralizedKIC , protocols::grafting::AnchoredGraftMover , protocols::grafting::CCDEndsGraftMover , protocols::grafting::simple_movers::DeleteRegionMover , protocols::helical_bundle::BackboneGridSampler , protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::PerturbBundle , protocols::ligand_docking::FinalMinimizer , protocols::ligand_docking::HighResDocker , protocols::ligand_docking::HighResEnsemble , protocols::ligand_docking::InterfaceScoreCalculator , protocols::ligand_docking::ProtLigEnsemble , protocols::monte_carlo::GenericMonteCarloMover , protocols::moves::Mover , protocols::moves::MoverContainer , protocols::protein_interface_design::movers::LoopOver , protocols::relax::RelaxProtocolBase , protocols::rosetta_scripts::ParsedProtocol , protocols::simple_moves::BBDihedralSamplerMover , protocols::simple_moves::ConvertRealToVirtualMover , protocols::simple_moves::ConvertVirtualToRealMover , protocols::simple_moves::SetupMetalsMover , protocols::simple_moves::SimpleThreadingMover
• provide_citation_info() : core::pack::palette::CustomBaseTypePackerPalette , core::pack::palette::DefaultPackerPalette , core::pack::palette::PackerPalette , core::pack::task::operation::TaskOperation , core::scoring::aa_composition_energy::AACompositionEnergy , core::scoring::methods::EnergyMethod , core::scoring::ScoreFunction , core::select::residue_selector::AndResidueSelector , core::select::residue_selector::LayerSelector , core::select::residue_selector::NeighborhoodResidueSelector , core::select::residue_selector::NotResidueSelector , core::select::residue_selector::OrResidueSelector , core::select::residue_selector::ResidueSelector , core::select::residue_selector::SliceResidueSelector , core::simple_metrics::metrics::DihedralDistanceMetric , core::simple_metrics::metrics::InteractionEnergyMetric , core::simple_metrics::metrics::ResidueSummaryMetric , core::simple_metrics::metrics::RMSDMetric , core::simple_metrics::metrics::SasaMetric , core::simple_metrics::metrics::SecondaryStructureMetric , core::simple_metrics::metrics::SelectedResidueCountMetric , core::simple_metrics::metrics::SelectedResiduesMetric , core::simple_metrics::metrics::SelectedResiduesPyMOLMetric , core::simple_metrics::metrics::SequenceMetric , core::simple_metrics::metrics::SequenceSimilarityMetric , core::simple_metrics::metrics::TotalEnergyMetric , core::simple_metrics::SimpleMetric , protocols::antibody::AntibodyCDRGrafter , protocols::antibody::AntibodyNumberingConverterMover , protocols::antibody::constraints::CDRDihedralConstraintMover , protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover , protocols::antibody::constraints::ParatopeSiteConstraintMover , protocols::antibody::design::AntibodyDesignMover , protocols::antibody::design::MutateFrameworkForCluster , protocols::calc_taskop_movers::CreateSequenceMotifMover , protocols::carbohydrates::IdealizeAnomericHydrogens , protocols::carbohydrates::LinkageConformerMover , protocols::cyclic_peptide::PeptideInternalHbondsFilter , protocols::cyclic_peptide::PeptideInternalHbondsMetric , protocols::denovo_design::movers::FastDesign , protocols::features::ReportToDB , protocols::filters::Filter , protocols::generalized_kinematic_closure::GeneralizedKIC , protocols::grafting::AnchoredGraftMover , protocols::grafting::CCDEndsGraftMover , protocols::grafting::simple_movers::DeleteRegionMover , protocols::grafting::simple_movers::InsertPoseIntoPoseMover , protocols::grafting::simple_movers::KeepRegionMover , protocols::grafting::simple_movers::ReplaceRegionMover , protocols::helical_bundle::BackboneGridSampler , protocols::helical_bundle::BundleGridSampler , protocols::indexed_structure_store::filters::FragmentLookupFilter , protocols::ligand_docking::FinalMinimizer , protocols::ligand_docking::HighResDocker , protocols::ligand_docking::HighResEnsemble , protocols::ligand_docking::InterfaceScoreCalculator , protocols::ligand_docking::ProtLigEnsemble , protocols::ligand_docking::StartFrom , protocols::ligand_docking::Transform , protocols::ligand_docking::TransformEnsemble , protocols::loop_grower::FragmentExtension , protocols::loop_grower::LoopGrower , protocols::loop_grower::SheetSampler , protocols::monte_carlo::GenericMonteCarloMover , protocols::moves::Mover , protocols::moves::MoverContainer , protocols::protein_interface_design::movers::LoopOver , protocols::relax::FastRelax , protocols::relax::RelaxProtocolBase , protocols::rosetta_scripts::ParsedProtocol , protocols::simple_moves::BBDihedralSamplerMover , protocols::simple_moves::ConvertRealToVirtualMover , protocols::simple_moves::ConvertVirtualToRealMover , protocols::simple_moves::DeleteChainsMover , protocols::simple_moves::RingConformationMover , protocols::simple_moves::SetupMetalsMover
• provide_pymol_commands_to_show_groups() : core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty , core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph
• provide_shared_xml_schema_elements() : protocols::cyclic_peptide::PeptideInternalHbondsMetric
• provide_stored_derivatives() : core::optimization::ArmijoLineMinimization , core::optimization::LineMinimizationAlgorithm , core::optimization::StrongWolfeLineMinimization
• provide_xml_definition() : protocols::fold_from_loops::utils::Nub
• provide_xml_schema() : core::conformation::symmetry::SymmDataLoader , core::conformation::symmetry::SymmDataLoaderCreator , core::fragment::FragmentSetLoader , core::fragment::FragmentSetLoaderCreator , core::import_pose::PoseResourceLoader , core::import_pose::PoseResourceLoaderCreator , core::pack::palette::CustomBaseTypePackerPalette , core::pack::palette::CustomBaseTypePackerPaletteCreator , core::pack::palette::DefaultPackerPalette , core::pack::palette::DefaultPackerPaletteCreator , core::pack::palette::NCAADefaultPackerPalette , core::pack::palette::NCAADefaultPackerPaletteCreator , core::pack::palette::NoDesignPackerPalette , core::pack::palette::NoDesignPackerPaletteCreator , core::pack::palette::PackerPaletteCreator , core::pack::palette::PackerPaletteFactory , core::pack::task::operation::AddBehaviorRLT , core::pack::task::operation::AddBehaviorRLTCreator , core::pack::task::operation::AllResFilter , core::pack::task::operation::AllResFilterCreator , core::pack::task::operation::AnyResFilter , core::pack::task::operation::AnyResFilterCreator , core::pack::task::operation::AppendResidueRotamerSet , core::pack::task::operation::AppendResidueRotamerSetCreator , core::pack::task::operation::AppendRotamer , core::pack::task::operation::AppendRotamerCreator , core::pack::task::operation::AppendRotamerSet , core::pack::task::operation::AppendRotamerSetCreator , core::pack::task::operation::ChainIs , core::pack::task::operation::ChainIsCreator , core::pack::task::operation::ChainIsnt , core::pack::task::operation::ChainIsntCreator , core::pack::task::operation::ClashBasedRepackShell , core::pack::task::operation::ClashBasedRepackShellCreator , core::pack::task::operation::DesignRestrictions , core::pack::task::operation::DesignRestrictionsCreator , core::pack::task::operation::DisallowIfNonnative , core::pack::task::operation::DisallowIfNonnativeCreator , core::pack::task::operation::DisallowIfNonnativeRLT , core::pack::task::operation::DisallowIfNonnativeRLTCreator , core::pack::task::operation::EnableMultiCoolAnnealer , core::pack::task::operation::EnableMultiCoolAnnealerCreator , core::pack::task::operation::EnableSmartAnnealer , core::pack::task::operation::EnableSmartAnnealerCreator , core::pack::task::operation::ExtraChiCutoff , core::pack::task::operation::ExtraChiCutoffCreator , core::pack::task::operation::ExtraChiCutoffRLT , core::pack::task::operation::ExtraChiCutoffRLTCreator , core::pack::task::operation::ExtraRotamers , core::pack::task::operation::ExtraRotamersCreator , core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::operation::ExtraRotamersGenericCreator , core::pack::task::operation::ExtraRotamersGenericRLT , core::pack::task::operation::ExtraRotamersGenericRLTCreator , core::pack::task::operation::FillAUTOTaskOperation , core::pack::task::operation::FillAUTOTaskOperationCreator , core::pack::task::operation::IncludeCurrent , core::pack::task::operation::IncludeCurrentCreator , core::pack::task::operation::IncludeCurrentRLT , core::pack::task::operation::IncludeCurrentRLTCreator , core::pack::task::operation::InitializeExtraRotsFromCommandline , core::pack::task::operation::InitializeExtraRotsFromCommandlineCreator , core::pack::task::operation::InitializeFromCommandline , core::pack::task::operation::InitializeFromCommandlineCreator , core::pack::task::operation::InitializeFromOptionCollection , core::pack::task::operation::InitializeFromOptionCollectionCreator , core::pack::task::operation::KeepSequenceSymmetry , core::pack::task::operation::KeepSequenceSymmetryCreator , core::pack::task::operation::NoRepackDisulfides , core::pack::task::operation::NoRepackDisulfidesCreator , core::pack::task::operation::NoResFilter , core::pack::task::operation::NoResFilterCreator , core::pack::task::operation::OperateOnCertainResidues , core::pack::task::operation::OperateOnCertainResiduesCreator , core::pack::task::operation::OperateOnResidueSubset , core::pack::task::operation::OperateOnResidueSubsetCreator , core::pack::task::operation::OptCysHG , core::pack::task::operation::OptCysHGCreator , core::pack::task::operation::OptH , core::pack::task::operation::OptHCreator , core::pack::task::operation::PreserveCBeta , core::pack::task::operation::PreserveCBetaCreator , core::pack::task::operation::PreserveCBetaRLT , core::pack::task::operation::PreserveCBetaRLTCreator , core::pack::task::operation::PreventRepacking , core::pack::task::operation::PreventRepackingCreator , core::pack::task::operation::PreventRepackingRLT , core::pack::task::operation::PreventRepackingRLTCreator , core::pack::task::operation::ProhibitResidueProperties , core::pack::task::operation::ProhibitResiduePropertiesCreator , core::pack::task::operation::ProhibitSpecifiedBaseResidueTypes , core::pack::task::operation::ProhibitSpecifiedBaseResidueTypesCreator , core::pack::task::operation::ReadResfile , core::pack::task::operation::ReadResfileAndObeyLengthEvents , core::pack::task::operation::ReadResfileAndObeyLengthEventsCreator , core::pack::task::operation::ReadResfileCreator , core::pack::task::operation::ResFilterCreator , core::pack::task::operation::ResidueHasProperty , core::pack::task::operation::ResidueHasPropertyCreator , core::pack::task::operation::ResidueIndexIs , core::pack::task::operation::ResidueIndexIsCreator , core::pack::task::operation::ResidueIndexIsnt , core::pack::task::operation::ResidueIndexIsntCreator , core::pack::task::operation::ResidueLacksProperty , core::pack::task::operation::ResidueLacksPropertyCreator , core::pack::task::operation::ResidueName3Is , core::pack::task::operation::ResidueName3IsCreator , core::pack::task::operation::ResidueName3Isnt , core::pack::task::operation::ResidueName3IsntCreator , core::pack::task::operation::ResiduePDBIndexIs , core::pack::task::operation::ResiduePDBIndexIsCreator , core::pack::task::operation::ResiduePDBIndexIsnt , core::pack::task::operation::ResiduePDBIndexIsntCreator , core::pack::task::operation::ResiduePDBInfoHasLabel , core::pack::task::operation::ResiduePDBInfoHasLabelCreator , core::pack::task::operation::ResiduePDBInfoLacksLabel , core::pack::task::operation::ResiduePDBInfoLacksLabelCreator , core::pack::task::operation::ResidueTypeFilter , core::pack::task::operation::ResidueTypeFilterCreator , core::pack::task::operation::ResLvlTaskOperationCreator , core::pack::task::operation::ResLvlTaskOperationFactory , core::pack::task::operation::RestrictAbsentCanonicalAAS , core::pack::task::operation::RestrictAbsentCanonicalAASCreator , core::pack::task::operation::RestrictAbsentCanonicalAASExceptNativeRLT , core::pack::task::operation::RestrictAbsentCanonicalAASExceptNativeRLTCreator , core::pack::task::operation::RestrictAbsentCanonicalAASRLT , core::pack::task::operation::RestrictAbsentCanonicalAASRLTCreator , core::pack::task::operation::RestrictInteractionGraphThreadsOperation , core::pack::task::operation::RestrictInteractionGraphThreadsOperationCreator , core::pack::task::operation::RestrictResidueToRepacking , core::pack::task::operation::RestrictResidueToRepackingCreator , core::pack::task::operation::RestrictToRepacking , core::pack::task::operation::RestrictToRepackingCreator , core::pack::task::operation::RestrictToRepackingRLT , core::pack::task::operation::RestrictToRepackingRLTCreator , core::pack::task::operation::RestrictToResidueProperties , core::pack::task::operation::RestrictToResiduePropertiesCreator , core::pack::task::operation::RestrictToSpecifiedBaseResidueTypes , core::pack::task::operation::RestrictToSpecifiedBaseResidueTypesCreator , core::pack::task::operation::RestrictYSDesign , core::pack::task::operation::RestrictYSDesignCreator , core::pack::task::operation::RotamerExplosion , core::pack::task::operation::RotamerExplosionCreator , core::pack::task::operation::SetRotamerCouplings , core::pack::task::operation::SetRotamerCouplingsCreator , core::pack::task::operation::SetRotamerLinks , core::pack::task::operation::SetRotamerLinksCreator , core::pack::task::operation::TaskOperationCreator , core::pack::task::operation::TaskOperationFactory , core::pack::task::operation::UseMultiCoolAnnealer , core::pack::task::operation::UseMultiCoolAnnealerCreator , core::pack::task::residue_selector::ClashBasedShellSelector , core::pack::task::residue_selector::ClashBasedShellSelectorCreator , core::select::jump_selector::AndJumpSelector , core::select::jump_selector::AndJumpSelectorCreator , core::select::jump_selector::InterchainJumpSelector , core::select::jump_selector::InterchainJumpSelectorCreator , core::select::jump_selector::JumpIndexSelector , core::select::jump_selector::JumpIndexSelectorCreator , core::select::jump_selector::JumpSelectorCreator , core::select::jump_selector::JumpSelectorFactory , core::select::jump_selector::NotJumpSelector , core::select::jump_selector::NotJumpSelectorCreator , core::select::jump_selector::OrJumpSelector , core::select::jump_selector::OrJumpSelectorCreator , core::select::movemap::MoveMapFactory , core::select::residue_selector::AndResidueSelector , core::select::residue_selector::AndResidueSelectorCreator , core::select::residue_selector::AsymmetricUnitSelector , core::select::residue_selector::AsymmetricUnitSelectorCreator , core::select::residue_selector::BinSelector , core::select::residue_selector::BinSelectorCreator , core::select::residue_selector::BondedResidueSelector , core::select::residue_selector::BondedResidueSelectorCreator , core::select::residue_selector::ChainSelector , core::select::residue_selector::ChainSelectorCreator , core::select::residue_selector::CloseContactResidueSelector , core::select::residue_selector::CloseContactResidueSelectorCreator , core::select::residue_selector::DensityFitResidueSelector , core::select::residue_selector::DensityFitResidueSelectorCreator , core::select::residue_selector::FalseResidueSelector , core::select::residue_selector::FalseResidueSelectorCreator , core::select::residue_selector::GlycanLayerSelector , core::select::residue_selector::GlycanLayerSelectorCreator , core::select::residue_selector::GlycanPositionSelector , core::select::residue_selector::GlycanPositionSelectorCreator , core::select::residue_selector::GlycanResidueSelector , core::select::residue_selector::GlycanResidueSelectorCreator , core::select::residue_selector::GlycanSequonsSelector , core::select::residue_selector::GlycanSequonsSelectorCreator , core::select::residue_selector::InterGroupInterfaceByVectorSelector , core::select::residue_selector::InterGroupInterfaceByVectorSelectorCreator , core::select::residue_selector::JumpDownstreamSelector , core::select::residue_selector::JumpDownstreamSelectorCreator , core::select::residue_selector::JumpUpstreamSelector , core::select::residue_selector::JumpUpstreamSelectorCreator , core::select::residue_selector::LayerSelector , core::select::residue_selector::LayerSelectorCreator , core::select::residue_selector::NeighborhoodResidueSelector , core::select::residue_selector::NeighborhoodResidueSelectorCreator , core::select::residue_selector::NotResidueSelector , core::select::residue_selector::NotResidueSelectorCreator , core::select::residue_selector::NumNeighborsSelector , core::select::residue_selector::NumNeighborsSelectorCreator , core::select::residue_selector::OrResidueSelector , core::select::residue_selector::OrResidueSelectorCreator , core::select::residue_selector::PhiSelector , core::select::residue_selector::PhiSelectorCreator , core::select::residue_selector::PrimarySequenceNeighborhoodSelector , core::select::residue_selector::PrimarySequenceNeighborhoodSelectorCreator , core::select::residue_selector::RandomGlycanFoliageSelector , core::select::residue_selector::RandomGlycanFoliageSelectorCreator , core::select::residue_selector::RandomResidueSelector , core::select::residue_selector::RandomResidueSelectorCreator , core::select::residue_selector::ResidueIndexSelector , core::select::residue_selector::ResidueIndexSelectorCreator , core::select::residue_selector::ResidueInMembraneSelector , core::select::residue_selector::ResidueInMembraneSelectorCreator , core::select::residue_selector::ResidueInSequenceMotifSelector , core::select::residue_selector::ResidueInSequenceMotifSelectorCreator , core::select::residue_selector::ResidueNameSelector , core::select::residue_selector::ResidueNameSelectorCreator , core::select::residue_selector::ResiduePDBInfoHasLabelSelector , core::select::residue_selector::ResiduePDBInfoHasLabelSelectorCreator , core::select::residue_selector::ResiduePropertySelector , core::select::residue_selector::ResiduePropertySelectorCreator , core::select::residue_selector::ResidueSelectorCreator , core::select::residue_selector::ResidueSelectorFactory , core::select::residue_selector::ResidueSpanSelector , core::select::residue_selector::ResidueSpanSelectorCreator , core::select::residue_selector::ReturnResidueSubsetSelector , core::select::residue_selector::ScoreTermValueBasedSelector , core::select::residue_selector::ScoreTermValueBasedSelectorCreator , core::select::residue_selector::SecondaryStructureSelector , core::select::residue_selector::SecondaryStructureSelectorCreator , core::select::residue_selector::SliceResidueSelector , core::select::residue_selector::SliceResidueSelectorCreator , core::select::residue_selector::SSElementSelector , core::select::residue_selector::SSElementSelectorCreator , core::select::residue_selector::SymmetricalResidueSelector , core::select::residue_selector::SymmetricalResidueSelectorCreator , core::select::residue_selector::TrueResidueSelector , core::select::residue_selector::TrueResidueSelectorCreator , core::simple_metrics::composite_metrics::CompositeEnergyMetric , core::simple_metrics::composite_metrics::CompositeEnergyMetricCreator , core::simple_metrics::composite_metrics::ElectrostaticComplementarityMetric , core::simple_metrics::composite_metrics::ElectrostaticComplementarityMetricCreator , core::simple_metrics::composite_metrics::ProtocolSettingsMetric , core::simple_metrics::composite_metrics::ProtocolSettingsMetricCreator , core::simple_metrics::metrics::CalculatorMetric , core::simple_metrics::metrics::CalculatorMetricCreator , core::simple_metrics::metrics::DihedralDistanceMetric , core::simple_metrics::metrics::DihedralDistanceMetricCreator , core::simple_metrics::metrics::InteractionEnergyMetric , core::simple_metrics::metrics::InteractionEnergyMetricCreator , core::simple_metrics::metrics::ResidueSummaryMetric , core::simple_metrics::metrics::ResidueSummaryMetricCreator , core::simple_metrics::metrics::RMSDMetric , core::simple_metrics::metrics::RMSDMetricCreator , core::simple_metrics::metrics::SasaMetric , core::simple_metrics::metrics::SasaMetricCreator , core::simple_metrics::metrics::SecondaryStructureMetric , core::simple_metrics::metrics::SecondaryStructureMetricCreator , core::simple_metrics::metrics::SelectedResidueCountMetric , core::simple_metrics::metrics::SelectedResidueCountMetricCreator , core::simple_metrics::metrics::SelectedResiduesMetric , core::simple_metrics::metrics::SelectedResiduesMetricCreator , core::simple_metrics::metrics::SelectedResiduesPyMOLMetric , core::simple_metrics::metrics::SelectedResiduesPyMOLMetricCreator , core::simple_metrics::metrics::SequenceMetric , core::simple_metrics::metrics::SequenceMetricCreator , core::simple_metrics::metrics::SequenceSimilarityMetric , core::simple_metrics::metrics::SequenceSimilarityMetricCreator , core::simple_metrics::metrics::TimingProfileMetric , core::simple_metrics::metrics::TimingProfileMetricCreator , core::simple_metrics::metrics::TotalEnergyMetric , core::simple_metrics::metrics::TotalEnergyMetricCreator , core::simple_metrics::per_residue_metrics::HbondMetric , core::simple_metrics::per_residue_metrics::HbondMetricCreator , core::simple_metrics::per_residue_metrics::PerResidueClashMetric , core::simple_metrics::per_residue_metrics::PerResidueClashMetricCreator , core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric , core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetricCreator , core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric , core::simple_metrics::per_residue_metrics::PerResidueEnergyMetricCreator , core::simple_metrics::per_residue_metrics::PerResidueGlycanLayerMetric , core::simple_metrics::per_residue_metrics::PerResidueGlycanLayerMetricCreator , core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric , core::simple_metrics::per_residue_metrics::PerResidueRMSDMetricCreator , core::simple_metrics::per_residue_metrics::PerResidueSasaMetric , core::simple_metrics::per_residue_metrics::PerResidueSasaMetricCreator , core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric , core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetricCreator , core::simple_metrics::SimpleMetricCreator , core::simple_metrics::SimpleMetricFactory , core::simple_metrics::TestCompositeRealMetric , core::simple_metrics::TestCompositeRealMetricCreator , core::simple_metrics::TestCompositeStringMetric , core::simple_metrics::TestCompositeStringMetricCreator , core::simple_metrics::TestPerResidueRealMetric , core::simple_metrics::TestPerResidueRealMetricCreator , core::simple_metrics::TestPerResidueStringMetric , core::simple_metrics::TestPerResidueStringMetricCreator , core::simple_metrics::TestRealMetric , core::simple_metrics::TestRealMetricCreator , core::simple_metrics::TestStringMetric , core::simple_metrics::TestStringMetricCreator , protocols::aa_composition::AddCompositionConstraintMover , protocols::aa_composition::AddCompositionConstraintMoverCreator , protocols::aa_composition::AddHelixSequenceConstraintsMover , protocols::aa_composition::AddHelixSequenceConstraintsMoverCreator , protocols::aa_composition::AddMHCEpitopeConstraintMover , protocols::aa_composition::AddMHCEpitopeConstraintMoverCreator , protocols::aa_composition::AddNetChargeConstraintMover , protocols::aa_composition::AddNetChargeConstraintMoverCreator , protocols::aa_composition::ClearCompositionConstraintsMover , protocols::aa_composition::ClearCompositionConstraintsMoverCreator , protocols::abinitio::abscript::AbscriptLoopCloserCM , protocols::abinitio::abscript::AbscriptLoopCloserCMCreator , protocols::abinitio::abscript::AbscriptMover , protocols::abinitio::abscript::AbscriptMoverCreator , protocols::abinitio::abscript::ConstraintPreparer , protocols::abinitio::abscript::ConstraintPreparerCreator , protocols::abinitio::abscript::FragmentCM , protocols::abinitio::abscript::FragmentCMCreator , protocols::abinitio::abscript::FragmentJumpCM , protocols::abinitio::abscript::FragmentJumpCMCreator , protocols::abinitio::abscript::RigidChunkCM , protocols::abinitio::abscript::RigidChunkCMCreator , protocols::abinitio::abscript::StructPerturberCM , protocols::abinitio::abscript::StructPerturberCMCreator , protocols::abinitio::DomainAssembly , protocols::abinitio::DomainAssemblyCreator , protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric , protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetricCreator , protocols::analysis::GlycanInfoMover , protocols::analysis::GlycanInfoMoverCreator , protocols::analysis::InterfaceAnalyzerMover , protocols::analysis::InterfaceAnalyzerMoverCreator , protocols::analysis::LoopAnalyzerMover , protocols::analysis::LoopAnalyzerMoverCreator , protocols::analysis::simple_metrics::RunSimpleMetricsMover , protocols::analysis::simple_metrics::RunSimpleMetricsMoverCreator , protocols::analysis::simple_metrics::SequenceRecoveryMetric , protocols::analysis::simple_metrics::SequenceRecoveryMetricCreator , protocols::antibody::AntibodyCDRGrafter , protocols::antibody::AntibodyCDRGrafterCreator , protocols::antibody::AntibodyFeatures , protocols::antibody::AntibodyFeaturesCreator , protocols::antibody::AntibodyNumberingConverterMover , protocols::antibody::AntibodyNumberingConverterMoverCreator , protocols::antibody::clusters::CDRClusterFeatures , protocols::antibody::clusters::CDRClusterFeaturesCreator , protocols::antibody::constraints::CDRDihedralConstraintMover , protocols::antibody::constraints::CDRDihedralConstraintMoverCreator , protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover , protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMoverCreator , protocols::antibody::constraints::ParatopeSiteConstraintMover , protocols::antibody::constraints::ParatopeSiteConstraintMoverCreator , protocols::antibody::design::AntibodyDesignMover , protocols::antibody::design::AntibodyDesignMoverCreator , protocols::antibody::design::ResnumFromStringsWithRangesSelector , protocols::antibody::residue_selector::AntibodyRegionSelector , protocols::antibody::residue_selector::AntibodyRegionSelectorCreator , protocols::antibody::residue_selector::CDRResidueSelector , protocols::antibody::residue_selector::CDRResidueSelectorCreator , protocols::antibody::snugdock::SnugDock , protocols::antibody::snugdock::SnugDockCreator , protocols::antibody::task_operations::AddCDRProfileSetsOperation , protocols::antibody::task_operations::AddCDRProfileSetsOperationCreator , protocols::antibody::task_operations::AddCDRProfilesOperation , protocols::antibody::task_operations::AddCDRProfilesOperationCreator , protocols::antibody::task_operations::DisableAntibodyRegionOperation , protocols::antibody::task_operations::DisableAntibodyRegionOperationCreator , protocols::antibody::task_operations::DisableCDRsOperation , protocols::antibody::task_operations::DisableCDRsOperationCreator , protocols::antibody::task_operations::RestrictToCDRsAndNeighbors , protocols::antibody::task_operations::RestrictToCDRsAndNeighborsCreator , protocols::backbone_moves::local_backbone_mover::LocalBackboneMover , protocols::backbone_moves::local_backbone_mover::LocalBackboneMoverCreator , protocols::backbone_moves::RandomizeBBByRamaPrePro , protocols::backbone_moves::RandomizeBBByRamaPreProCreator , protocols::backrub::BackrubMover , protocols::backrub::BackrubMoverCreator , protocols::backrub::BackrubProtocol , protocols::backrub::BackrubProtocolCreator , protocols::backrub::BackrubSidechainMover , protocols::backrub::BackrubSidechainMoverCreator , protocols::calc_taskop_filters::ConservedPosMutationFilter , protocols::calc_taskop_filters::ConservedPosMutationFilterCreator , protocols::calc_taskop_filters::MultipleSigmoids , protocols::calc_taskop_filters::MultipleSigmoidsFilterCreator , protocols::calc_taskop_filters::Operator , protocols::calc_taskop_filters::OperatorFilterCreator , protocols::calc_taskop_filters::RelativePoseFilter , protocols::calc_taskop_filters::RelativePoseFilterCreator , protocols::calc_taskop_filters::RotamerBoltzmannWeight2 , protocols::calc_taskop_filters::RotamerBoltzmannWeight2Creator , protocols::calc_taskop_filters::RotamerBoltzmannWeight , protocols::calc_taskop_filters::RotamerBoltzmannWeightFilterCreator , protocols::calc_taskop_filters::Sigmoid , protocols::calc_taskop_filters::SigmoidFilterCreator , protocols::calc_taskop_movers::ConsensusDesignMover , protocols::calc_taskop_movers::ConsensusDesignMoverCreator , protocols::calc_taskop_movers::CreateSequenceMotifMover , protocols::calc_taskop_movers::CreateSequenceMotifMoverCreator , protocols::calc_taskop_movers::ForceDisulfidesMover , protocols::calc_taskop_movers::ForceDisulfidesMoverCreator , protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::HamiltonianExchangeCreator , protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::MetricRecorderCreator , protocols::canonical_sampling::MetropolisHastingsMover , protocols::canonical_sampling::MetropolisHastingsMoverCreator , protocols::canonical_sampling::ParallelTempering , protocols::canonical_sampling::ParallelTemperingCreator , protocols::canonical_sampling::PDBTrajectoryRecorder , protocols::canonical_sampling::PDBTrajectoryRecorderCreator , protocols::canonical_sampling::SilentTrajectoryRecorder , protocols::canonical_sampling::SilentTrajectoryRecorderCreator , protocols::canonical_sampling::SimulatedTempering , protocols::canonical_sampling::SimulatedTemperingCreator , protocols::canonical_sampling::TrialCounterObserver , protocols::canonical_sampling::TrialCounterObserverCreator , protocols::carbohydrates::CreateGlycanSequonMover , protocols::carbohydrates::CreateGlycanSequonMoverCreator , protocols::carbohydrates::GlycanSampler , protocols::carbohydrates::GlycanSamplerCreator , protocols::carbohydrates::GlycanTreeMinMover , protocols::carbohydrates::GlycanTreeMinMoverCreator , protocols::carbohydrates::GlycanTreeModeler , protocols::carbohydrates::GlycanTreeModelerCreator , protocols::carbohydrates::IdealizeAnomericHydrogens , protocols::carbohydrates::IdealizeAnomericHydrogensCreator , protocols::carbohydrates::LinkageConformerMover , protocols::carbohydrates::LinkageConformerMoverCreator , protocols::carbohydrates::RingPlaneFlipMover , protocols::carbohydrates::RingPlaneFlipMoverCreator , protocols::carbohydrates::SimpleGlycosylateMover , protocols::carbohydrates::SimpleGlycosylateMoverCreator , protocols::carbohydrates::TautomerizeAnomerMover , protocols::carbohydrates::TautomerizeAnomerMoverCreator , protocols::chemically_conjugated_docking::UBQ_GTPaseMover , protocols::chemically_conjugated_docking::UBQ_GTPaseMoverCreator , protocols::comparative_modeling::LoopRelaxMover , protocols::comparative_modeling::LoopRelaxMoverCreator , protocols::constraint_filters::ConstraintScoreFilter , protocols::constraint_filters::ConstraintScoreFilterCreator , protocols::constraint_filters::SavePoseConstraintToFileFilter , protocols::constraint_filters::SavePoseConstraintToFileFilterCreator , protocols::constraint_filters::ShowConstraintsFilter , protocols::constraint_filters::ShowConstraintsFilterCreator , protocols::constraint_generator::AddConstraints , protocols::constraint_generator::AddConstraintsCreator , protocols::constraint_generator::AtomPairConstraintGenerator , protocols::constraint_generator::AtomPairConstraintGeneratorCreator , protocols::constraint_generator::ConstraintGeneratorCreator , protocols::constraint_generator::CoordinateConstraintGenerator , protocols::constraint_generator::CoordinateConstraintGeneratorCreator , protocols::constraint_generator::DihedralConstraintGenerator , protocols::constraint_generator::DihedralConstraintGeneratorCreator , protocols::constraint_generator::DistanceConstraintGenerator , protocols::constraint_generator::DistanceConstraintGeneratorCreator , protocols::constraint_generator::HydrogenBondConstraintGenerator , protocols::constraint_generator::HydrogenBondConstraintGeneratorCreator , protocols::constraint_generator::MembraneSpanConstraintGenerator , protocols::constraint_generator::MembraneSpanConstraintGeneratorCreator , protocols::constraint_generator::MetalContactsConstraintGenerator , protocols::constraint_generator::MetalContactsConstraintGeneratorCreator , protocols::constraint_generator::RemoveConstraints , protocols::constraint_generator::RemoveConstraintsCreator , protocols::constraint_generator::ResidueTypeConstraintGenerator , protocols::constraint_generator::ResidueTypeConstraintGeneratorCreator , protocols::constraint_generator::TerminiConstraintGenerator , protocols::constraint_generator::TerminiConstraintGeneratorCreator , protocols::constraint_movers::AddConstraintsToCurrentConformationMover , protocols::constraint_movers::AddConstraintsToCurrentConformationMoverCreator , protocols::constraint_movers::ClearConstraintsMover , protocols::constraint_movers::ClearConstraintsMoverCreator , protocols::constraint_movers::ConstraintSetMover , protocols::constraint_movers::ConstraintSetMoverCreator , protocols::constraint_movers::CstInfoMover , protocols::constraint_movers::CstInfoMoverCreator , protocols::constraint_movers::ResidueTypeConstraintMover , protocols::constraint_movers::ResidueTypeConstraintMoverCreator , protocols::contact_map::ContactMap , protocols::contact_map::ContactMapCreator , protocols::coupled_moves::CoupledMovesProtocol , protocols::coupled_moves::CoupledMovesProtocolCreator , protocols::cryst::CrystRMS , protocols::cryst::CrystRMSCreator , protocols::cryst::DockLatticeMover , protocols::cryst::DockLatticeMoverCreator , protocols::cryst::FitBfactorsMover , protocols::cryst::FitBfactorsMoverCreator , protocols::cryst::LoadDensityMapMover , protocols::cryst::LoadDensityMapMoverCreator , protocols::cryst::MakeLatticeMover , protocols::cryst::MakeLatticeMoverCreator , protocols::cryst::MakeLayerMover , protocols::cryst::MakeLayerMoverCreator , protocols::cryst::RecomputeDensityMapMover , protocols::cryst::RecomputeDensityMapMoverCreator , protocols::cryst::ReportGradientsMover , protocols::cryst::ReportGradientsMoverCreator , protocols::cryst::SetCrystWeightMover , protocols::cryst::SetCrystWeightMoverCreator , protocols::cryst::SetRefinementOptionsMover , protocols::cryst::SetRefinementOptionsMoverCreator , protocols::cryst::TagPoseWithRefinementStatsMover , protocols::cryst::TagPoseWithRefinementStatsMoverCreator , protocols::cryst::UpdateCrystInfo , protocols::cryst::UpdateCrystInfoCreator , protocols::cryst::UpdateSolventMover , protocols::cryst::UpdateSolventMoverCreator , protocols::cutoutdomain::CutOutDomain , protocols::cutoutdomain::CutOutDomainCreator , protocols::cyclic_peptide::CreateAngleConstraint , protocols::cyclic_peptide::CreateAngleConstraintCreator , protocols::cyclic_peptide::CreateDistanceConstraint , protocols::cyclic_peptide::CreateDistanceConstraintCreator , protocols::cyclic_peptide::CreateTorsionConstraint , protocols::cyclic_peptide::CreateTorsionConstraintCreator , protocols::cyclic_peptide::CrosslinkerMover , protocols::cyclic_peptide::CrosslinkerMoverCreator , protocols::cyclic_peptide::CycpepSymmetryFilter , protocols::cyclic_peptide::CycpepSymmetryFilterCreator , protocols::cyclic_peptide::DeclareBond , protocols::cyclic_peptide::DeclareBondCreator , protocols::cyclic_peptide::FlipChiralityMover , protocols::cyclic_peptide::FlipChiralityMoverCreator , protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter , protocols::cyclic_peptide::OversaturatedHbondAcceptorFilterCreator , protocols::cyclic_peptide::PeptideCyclizeMover , protocols::cyclic_peptide::PeptideCyclizeMoverCreator , protocols::cyclic_peptide::PeptideInternalHbondsFilter , protocols::cyclic_peptide::PeptideInternalHbondsFilterCreator , protocols::cyclic_peptide::PeptideInternalHbondsMetric , protocols::cyclic_peptide::PeptideInternalHbondsMetricCreator , protocols::cyclic_peptide::PeptideStubMover , protocols::cyclic_peptide::PeptideStubMoverCreator , protocols::cyclic_peptide::RamaMutationSelector , protocols::cyclic_peptide::RamaMutationSelectorCreator , protocols::cyclic_peptide::SymmetricCycpepAlign , protocols::cyclic_peptide::SymmetricCycpepAlignCreator , protocols::cyclic_peptide::TryDisulfPermutations , protocols::cyclic_peptide::TryDisulfPermutationsCreator , protocols::denovo_design::architects::BetaSheetArchitect , protocols::denovo_design::architects::BetaSheetArchitectCreator , protocols::denovo_design::architects::BlueprintArchitect , protocols::denovo_design::architects::BlueprintArchitectCreator , protocols::denovo_design::architects::CompoundArchitect , protocols::denovo_design::architects::CompoundArchitectCreator , protocols::denovo_design::architects::DeNovoArchitectCreator , protocols::denovo_design::architects::DeNovoMotifArchitect , protocols::denovo_design::architects::HelixArchitect , protocols::denovo_design::architects::HelixArchitectCreator , protocols::denovo_design::architects::PoseArchitect , protocols::denovo_design::architects::PoseArchitectCreator , protocols::denovo_design::architects::StrandArchitect , protocols::denovo_design::architects::StrandArchitectCreator , protocols::denovo_design::components::HelixPairing , protocols::denovo_design::components::HelixSheetPairing , protocols::denovo_design::components::StrandPairing , protocols::denovo_design::constraints::FileConstraintGenerator , protocols::denovo_design::constraints::FileConstraintGeneratorCreator , protocols::denovo_design::DisulfidizeMover , protocols::denovo_design::DisulfidizeMoverCreator , protocols::denovo_design::filters::CavityVolumeFilter , protocols::denovo_design::filters::CavityVolumeFilterCreator , protocols::denovo_design::filters::ExposedHydrophobicsFilter , protocols::denovo_design::filters::ExposedHydrophobicsFilterCreator , protocols::denovo_design::filters::PreProlineFilter , protocols::denovo_design::filters::PreProlineFilterCreator , protocols::denovo_design::filters::SSPredictionFilter , protocols::denovo_design::filters::SSPredictionFilterCreator , protocols::denovo_design::filters::SSShapeComplementarityFilter , protocols::denovo_design::filters::SSShapeComplementarityFilterCreator , protocols::denovo_design::movers::AddSegmentDataMover , protocols::denovo_design::movers::AddSegmentDataMoverCreator , protocols::denovo_design::movers::AlignResiduesMover , protocols::denovo_design::movers::AlignResiduesMoverCreator , protocols::denovo_design::movers::BridgeChainsCreator , protocols::denovo_design::movers::BridgeChainsMover , protocols::denovo_design::movers::BridgeChainsMoverCreator , protocols::denovo_design::movers::BuildDeNovoBackboneMover , protocols::denovo_design::movers::BuildDeNovoBackboneMoverCreator , protocols::denovo_design::movers::DeclareStructureDataCovalentBondMover , protocols::denovo_design::movers::DeclareStructureDataCovalentBondMoverCreator , protocols::denovo_design::movers::ExtendChainMover , protocols::denovo_design::movers::ExtendChainMoverCreator , protocols::denovo_design::movers::FastDesign , protocols::denovo_design::movers::FastDesignCreator , protocols::denovo_design::movers::MakeAsymmetricStructureDataMover , protocols::denovo_design::movers::MakeAsymmetricStructureDataMoverCreator , protocols::denovo_design::movers::SetResidueAliasMover , protocols::denovo_design::movers::SetResidueAliasMoverCreator , protocols::denovo_design::residue_selectors::NamedSegmentSelector , protocols::denovo_design::residue_selectors::NamedSegmentSelectorCreator , protocols::denovo_design::residue_selectors::PairedSheetResidueSelector , protocols::denovo_design::residue_selectors::PairedSheetResidueSelectorCreator , protocols::denovo_design::task_operations::ConsensusLoopDesignOperation , protocols::denovo_design::task_operations::ConsensusLoopDesignOperationCreator , protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::GreedyOptMutationMoverCreator , protocols::dna::DesignProteinBackboneAroundDNA , protocols::dna::DesignProteinBackboneAroundDNACreator , protocols::dna::DnaInterfaceMinMover , protocols::dna::DnaInterfaceMinMoverCreator , protocols::dna::DnaInterfaceMultiStateDesign , protocols::dna::DnaInterfaceMultiStateDesignCreator , protocols::dna::DnaInterfacePacker , protocols::dna::DnaInterfacePackerCreator , protocols::dna::RestrictDesignToProteinDNAInterface , protocols::dna::RestrictDesignToProteinDNAInterfaceCreator , protocols::dna::SeparateDnaFromNonDna , protocols::dna::SeparateDnaFromNonDnaCreator , protocols::dna::WatsonCrickRotamerCouplings , protocols::dna::WatsonCrickRotamerCouplingsCreator , protocols::dna_dock::DNAClashCheckFilterCreator , protocols::dna_dock::PropagateClashCheckFilterCreator , protocols::docking::ConformerSwitchMover , protocols::docking::ConformerSwitchMoverCreator , protocols::docking::DockingHighResLegacy , protocols::docking::DockingHighResLegacyCreator , protocols::docking::DockingInitialPerturbation , protocols::docking::DockingInitialPerturbationCreator , protocols::docking::DockingPrepackProtocol , protocols::docking::DockingPrepackProtocolCreator , protocols::docking::DockingProtocol , protocols::docking::DockingProtocolCreator , protocols::docking::DockingSlideIntoContact , protocols::docking::DockingSlideIntoContactCreator , protocols::docking::DockMCMProtocol , protocols::docking::DockMCMProtocolCreator , protocols::docking::DockMinMover , protocols::docking::DockMinMoverCreator , protocols::docking::DockSetupMover , protocols::docking::DockSetupMoverCreator , protocols::docking::membrane::MPDockingMover , protocols::docking::membrane::MPDockingMoverCreator , protocols::docking::membrane::MPDockingSetupMover , protocols::docking::membrane::MPDockingSetupMoverCreator , protocols::electron_density::BfactorFittingMover , protocols::electron_density::BfactorFittingMoverCreator , protocols::electron_density::ReportFSC , protocols::electron_density::ReportFSCCreator , protocols::electron_density::ScaleMapIntensities , protocols::electron_density::ScaleMapIntensitiesCreator , protocols::electron_density::SetupForDensityScoringMover , protocols::electron_density::SetupForDensityScoringMoverCreator , protocols::electron_density::VoxelSpacingRefinementMover , protocols::electron_density::VoxelSpacingRefinementMoverCreator , protocols::environment::claims::CutBiasClaim , protocols::environment::claims::JumpClaim , protocols::environment::claims::TorsionClaim , protocols::environment::claims::VirtResClaim , protocols::environment::claims::XYZClaim , protocols::environment::CoMTrackerCM , protocols::environment::CoMTrackerCMCreator , protocols::environment::EnvMover , protocols::environment::EnvMoverCreator , protocols::environment::ScriptCM , protocols::environment::ScriptCMCreator , protocols::enzdes::AddLigandMotifRotamers , protocols::enzdes::AddLigandMotifRotamersOperationCreator , protocols::enzdes::AddOrRemoveMatchCsts , protocols::enzdes::AddOrRemoveMatchCstsCreator , protocols::enzdes::AddRigidBodyLigandConfs , protocols::enzdes::AddRigidBodyLigandConfsCreator , protocols::enzdes::BackboneSampler , protocols::enzdes::BackboneSamplerCreator , protocols::enzdes::DetectProteinLigandInterface , protocols::enzdes::DetectProteinLigandInterfaceOperationCreator , protocols::enzdes::DiffAtomSasaFilter , protocols::enzdes::DiffAtomSasaFilterCreator , protocols::enzdes::EnzdesScorefileFilter , protocols::enzdes::EnzdesScorefileFilterCreator , protocols::enzdes::EnzRepackMinimize , protocols::enzdes::EnzRepackMinimizeCreator , protocols::enzdes::EnzScoreFilter , protocols::enzdes::EnzScoreFilterCreator , protocols::enzdes::LigBurialFilter , protocols::enzdes::LigBurialFilterCreator , protocols::enzdes::LigDSasaFilter , protocols::enzdes::LigDSasaFilterCreator , protocols::enzdes::LigInterfaceEnergyFilter , protocols::enzdes::LigInterfaceEnergyFilterCreator , protocols::enzdes::PackRotamersMoverPartGreedy , protocols::enzdes::PackRotamersMoverPartGreedyCreator , protocols::enzdes::PredesignPerturbMover , protocols::enzdes::PredesignPerturbMoverCreator , protocols::enzdes::ProteinLigandInterfaceUpweighter , protocols::enzdes::ProteinLigandInterfaceUpweighterOperationCreator , protocols::enzdes::RemoveLigandFilter , protocols::enzdes::RemoveLigandFilterCreator , protocols::enzdes::RepackWithoutLigandFilter , protocols::enzdes::RepackWithoutLigandFilterCreator , protocols::enzdes::ResidueConformerFilter , protocols::enzdes::ResidueConformerFilterCreator , protocols::enzdes::SetCatalyticResPackBehavior , protocols::enzdes::SetCatalyticResPackBehaviorCreator , protocols::enzdes::UpdateEnzdesHeaderMover , protocols::enzdes::UpdateEnzdesHeaderMoverCreator , protocols::enzymatic_movers::DNAMethyltransferaseMover , protocols::enzymatic_movers::DNAMethyltransferaseMoverCreator , protocols::enzymatic_movers::GlycosyltransferaseMover , protocols::enzymatic_movers::GlycosyltransferaseMoverCreator , protocols::enzymatic_movers::KinaseMover , protocols::enzymatic_movers::KinaseMoverCreator , protocols::enzymatic_movers::NTerminalAcetyltransferaseMover , protocols::enzymatic_movers::NTerminalAcetyltransferaseMoverCreator , protocols::evolution::AASynthesisFitnessCost , protocols::evolution::AASynthesisFitnessCostFilterCreator , protocols::evolution::AlignmentAAFinder , protocols::evolution::AlignmentAAFinderFilterCreator , protocols::evolution::AlignmentGapInserter , protocols::evolution::AlignmentGapInserterFilterCreator , protocols::evolution::EvolutionaryDynamicsMover , protocols::evolution::EvolutionaryDynamicsMoverCreator , protocols::evolution::NucleotideMutation , protocols::evolution::NucleotideMutationCreator , protocols::farnesyl::InstallFarnesylMover , protocols::farnesyl::InstallFarnesylMoverCreator , protocols::farnesyl::SampleFarnesylMover , protocols::farnesyl::SampleFarnesylMoverCreator , protocols::features::AtomAtomPairFeatures , protocols::features::AtomAtomPairFeaturesCreator , protocols::features::AtomInResidueAtomInResiduePairFeatures , protocols::features::AtomInResidueAtomInResiduePairFeaturesCreator , protocols::features::AtomTypesFeatures , protocols::features::AtomTypesFeaturesCreator , protocols::features::BetaTurnDetectionFeatures , protocols::features::BetaTurnDetectionFeaturesCreator , protocols::features::ChargeChargeFeatures , protocols::features::ChargeChargeFeaturesCreator , protocols::features::DdGFeatures , protocols::features::DdGFeaturesCreator , protocols::features::FeaturesReporterCreator , protocols::features::GeometricSolvationFeatures , protocols::features::GeometricSolvationFeaturesCreator , protocols::features::HBondFeatures , protocols::features::HBondFeaturesCreator , protocols::features::HBondParameterFeatures , protocols::features::HBondParameterFeaturesCreator , protocols::features::helixAssembly::ConcurrencyTest , protocols::features::helixAssembly::ConcurrencyTestCreator , protocols::features::helixAssembly::HelixBundleFeatures , protocols::features::helixAssembly::HelixBundleFeaturesCreator , protocols::features::HelixCapFeatures , protocols::features::HelixCapFeaturesCreator , protocols::features::InterfaceDdGMover , protocols::features::InterfaceDdGMoverCreator , protocols::features::InterfaceFeatures , protocols::features::InterfaceFeaturesCreator , protocols::features::JobDataFeatures , protocols::features::JobDataFeaturesCreator , protocols::features::LoopAnchorFeatures , protocols::features::LoopAnchorFeaturesCreator , protocols::features::ModelFeatures , protocols::features::ModelFeaturesCreator , protocols::features::OrbitalsFeatures , protocols::features::OrbitalsFeaturesCreator , protocols::features::PairFeatures , protocols::features::PairFeaturesCreator , protocols::features::PdbDataFeatures , protocols::features::PdbDataFeaturesCreator , protocols::features::PoseCommentsFeatures , protocols::features::PoseCommentsFeaturesCreator , protocols::features::PoseConformationFeatures , protocols::features::PoseConformationFeaturesCreator , protocols::features::ProteinBackboneAtomAtomPairFeatures , protocols::features::ProteinBackboneAtomAtomPairFeaturesCreator , protocols::features::ProteinBackboneTorsionAngleFeatures , protocols::features::ProteinBackboneTorsionAngleFeaturesCreator , protocols::features::ProteinBondGeometryFeatures , protocols::features::ProteinBondGeometryFeaturesCreator , protocols::features::ProteinResidueConformationFeatures , protocols::features::ProteinResidueConformationFeaturesCreator , protocols::features::ProteinRMSDFeatures , protocols::features::ProteinRMSDFeaturesCreator , protocols::features::ProteinRMSDNoSuperpositionFeatures , protocols::features::ProteinRMSDNoSuperpositionFeaturesCreator , protocols::features::RadiusOfGyrationFeatures , protocols::features::RadiusOfGyrationFeaturesCreator , protocols::features::ReportToDB , protocols::features::ReportToDBCreator , protocols::features::ResidueBurialFeatures , protocols::features::ResidueBurialFeaturesCreator , protocols::features::ResidueConformationFeatures , protocols::features::ResidueConformationFeaturesCreator , protocols::features::ResidueFeatures , protocols::features::ResidueFeaturesCreator , protocols::features::ResidueGridScoresFeatures , protocols::features::ResidueGridScoresFeaturesCreator , protocols::features::ResidueScoresFeatures , protocols::features::ResidueScoresFeaturesCreator , protocols::features::ResidueSecondaryStructureFeatures , protocols::features::ResidueSecondaryStructureFeaturesCreator , protocols::features::ResidueTotalScoresFeatures , protocols::features::ResidueTotalScoresFeaturesCreator , protocols::features::ResidueTypesFeatures , protocols::features::ResidueTypesFeaturesCreator , protocols::features::RotamerBoltzmannWeightFeatures , protocols::features::RotamerBoltzmannWeightFeaturesCreator , protocols::features::RotamerFeatures , protocols::features::RotamerFeaturesCreator , protocols::features::RotamerRecoveryFeatures , protocols::features::RotamerRecoveryFeaturesCreator , protocols::features::RuntimeFeatures , protocols::features::RuntimeFeaturesCreator , protocols::features::SaltBridgeFeatures , protocols::features::SaltBridgeFeaturesCreator , protocols::features::ScoreFunctionFeatures , protocols::features::ScoreFunctionFeaturesCreator , protocols::features::ScoreTypeFeatures , protocols::features::ScoreTypeFeaturesCreator , protocols::features::ScreeningFeatures , protocols::features::ScreeningFeaturesCreator , protocols::features::SecondaryStructureSegmentFeatures , protocols::features::SecondaryStructureSegmentFeaturesCreator , protocols::features::SimpleMetricFeatures , protocols::features::SimpleMetricFeaturesCreator , protocols::features::SmotifFeatures , protocols::features::SmotifFeaturesCreator , protocols::features::strand_assembly::SandwichFeatures , protocols::features::strand_assembly::SandwichFeaturesCreator , protocols::features::strand_assembly::StrandBundleFeatures , protocols::features::strand_assembly::StrandBundleFeaturesCreator , protocols::features::StructureFeatures , protocols::features::StructureFeaturesCreator , protocols::features::StructureScoresFeatures , protocols::features::StructureScoresFeaturesCreator , protocols::features::TaskOperationFeatures , protocols::features::TaskOperationFeaturesCreator , protocols::features::TotalScoreFeatures , protocols::features::TotalScoreFeaturesCreator , protocols::features::TrajectoryMapFeatures , protocols::features::TrajectoryMapFeaturesCreator , protocols::features::TrajectoryReportToDB , protocols::features::TrajectoryReportToDBCreator , protocols::features::UnrecognizedAtomFeatures , protocols::features::UnrecognizedAtomFeaturesCreator , protocols::features::WaterFeatures , protocols::features::WaterFeaturesCreator , protocols::filters::CalculatorFilter , protocols::filters::CalculatorFilterCreator , protocols::filters::CombinedFilter , protocols::filters::CombinedFilterCreator , protocols::filters::CompoundFilter , protocols::filters::CompoundFilterCreator , protocols::filters::ContingentFilter , protocols::filters::ContingentFilterCreator , protocols::filters::FalseFilter , protocols::filters::FalseFilterCreator , protocols::filters::FilterCreator , protocols::filters::FilterFactory , protocols::filters::FilterValueMetric , protocols::filters::FilterValueMetricCreator , protocols::filters::IfThenFilter , protocols::filters::IfThenFilterCreator , protocols::filters::MoveBeforeFilter , protocols::filters::MoveBeforeFilterCreator , protocols::filters::ReplicateFilter , protocols::filters::ReplicateFilterCreator , protocols::filters::StochasticFilter , protocols::filters::StochasticFilterCreator , protocols::filters::TimeFilter , protocols::filters::TimeFilterCreator , protocols::filters::TrueFilter , protocols::filters::TrueFilterCreator , protocols::fldsgn::BluePrintBDR , protocols::fldsgn::BluePrintBDRCreator , protocols::fldsgn::CircularPermutation , protocols::fldsgn::CircularPermutationCreator , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::filters::CoreDunbrackFilterCreator , protocols::fldsgn::filters::FragQualFilter , protocols::fldsgn::filters::FragQualFilterCreator , protocols::fldsgn::filters::HelixBendFilter , protocols::fldsgn::filters::HelixBendFilterCreator , protocols::fldsgn::filters::HelixKinkFilter , protocols::fldsgn::filters::HelixKinkFilterCreator , protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::filters::HelixPairingFilterCreator , protocols::fldsgn::filters::HSSTripletFilter , protocols::fldsgn::filters::HSSTripletFilterCreator , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::fldsgn::filters::InterlockingAromaFilterCreator , protocols::fldsgn::filters::NcontactsFilter , protocols::fldsgn::filters::NcontactsFilterCreator , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilterCreator , protocols::fldsgn::filters::SecondaryStructureCountFilter , protocols::fldsgn::filters::SecondaryStructureCountFilterCreator , protocols::fldsgn::filters::SecondaryStructureFilter , protocols::fldsgn::filters::SecondaryStructureFilterCreator , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilterCreator , protocols::fldsgn::filters::SheetTopologyFilter , protocols::fldsgn::filters::SheetTopologyFilterCreator , protocols::fldsgn::filters::StrandCurvatureByLevels , protocols::fldsgn::filters::StrandCurvatureByLevelsCreator , protocols::fldsgn::filters::StrandHelixGeometryFilter , protocols::fldsgn::filters::StrandHelixGeometryFilterCreator , protocols::fldsgn::MatchResiduesMover , protocols::fldsgn::MatchResiduesMoverCreator , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::fldsgn::potentials::SetAACompositionPotentialCreator , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::fldsgn::potentials::SetSecStructEnergiesCreator , protocols::fldsgn::SheetConstraintGenerator , protocols::fldsgn::SheetConstraintGeneratorCreator , protocols::fldsgn::SheetRemodelConstraintGenerator , protocols::fldsgn::SheetRemodelConstraintGeneratorCreator , protocols::flexpep_docking::FlexPepDockingProtocol , protocols::flexpep_docking::FlexPepDockingProtocolCreator , protocols::flxbb::FlxbbDesign , protocols::flxbb::FlxbbDesignCreator , protocols::flxbb::InterlockAroma , protocols::flxbb::InterlockAromaCreator , protocols::flxbb::LayerDesignOperation , protocols::flxbb::LayerDesignOperationCreator , protocols::fold_from_loops::constraint_generator::AutomaticSheetConstraintGenerator , protocols::fold_from_loops::constraint_generator::AutomaticSheetConstraintGeneratorCreator , protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator , protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGeneratorCreator , protocols::fold_from_loops::filters::ConstraintFulfilmentFilter , protocols::fold_from_loops::filters::ConstraintFulfilmentFilterCreator , protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter , protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilterCreator , protocols::fold_from_loops::filters::ScorePoseSegmentFromResidueSelectorFilter , protocols::fold_from_loops::filters::ScorePoseSegmentFromResidueSelectorFilterCreator , protocols::fold_from_loops::movers::AlignByResidueSelectorMover , protocols::fold_from_loops::movers::AlignByResidueSelectorMoverCreator , protocols::fold_from_loops::movers::DisplayPoseLabelsMover , protocols::fold_from_loops::movers::DisplayPoseLabelsMoverCreator , protocols::fold_from_loops::movers::LabelPoseFromResidueSelectorMover , protocols::fold_from_loops::movers::LabelPoseFromResidueSelectorMoverCreator , protocols::fold_from_loops::movers::MoveMapFactoryToNamedMoveMapMover , protocols::fold_from_loops::movers::MoveMapFactoryToNamedMoveMapMoverCreator , protocols::fold_from_loops::movers::NubInitioLoopClosureMover , protocols::fold_from_loops::movers::NubInitioLoopClosureMoverCreator , protocols::fold_from_loops::movers::ReleaseConstraintFromResidueMover , protocols::fold_from_loops::movers::ReleaseConstraintFromResidueMoverCreator , protocols::fold_from_loops::movers::ResidueLabelsToPymolSelectionMover , protocols::fold_from_loops::movers::ResidueLabelsToPymolSelectionMoverCreator , protocols::fold_from_loops::movers::SavePDBInfoMover , protocols::fold_from_loops::movers::SavePDBInfoMoverCreator , protocols::fold_from_loops::movers::SplitAndMixPoseMover , protocols::fold_from_loops::movers::SplitAndMixPoseMoverCreator , protocols::fold_from_loops::NubInitioMover , protocols::fold_from_loops::NubInitioMoverCreator , protocols::fold_from_loops::selectors::ConstraintResidueSelector , protocols::fold_from_loops::selectors::ConstraintResidueSelectorCreator , protocols::fold_from_loops::selectors::CutpointResidueSelector , protocols::fold_from_loops::selectors::CutpointResidueSelectorCreator , protocols::fold_from_loops::selectors::ProteinResidueSelector , protocols::fold_from_loops::selectors::ProteinResidueSelectorCreator , protocols::forge::constraints::InverseRotamersCstGeneratorCreator , protocols::forge::constraints::InverseRotamersRCG , protocols::forge::constraints::InvrotTreeCstGeneratorCreator , protocols::forge::constraints::InvrotTreeRCG , protocols::forge::constraints::NtoCConstraintGenerator , protocols::forge::constraints::NtoCConstraintGeneratorCreator , protocols::forge::constraints::RemoveRemodelCsts , protocols::forge::constraints::RemoveRemodelCstsCreator , protocols::forge::remodel::RemodelMover , protocols::forge::remodel::RemodelMoverCreator , protocols::forge::remodel::RemodelRotamerLinks , protocols::forge::remodel::RemodelRotamerLinksCreator , protocols::forge::remodel::ResidueVicinityCstGeneratorCreator , protocols::forge::remodel::ResidueVicinityRCG , protocols::frag_picker::FragmentScoreFilter , protocols::frag_picker::FragmentScoreFilterCreator , protocols::generalized_kinematic_closure::GeneralizedKIC , protocols::generalized_kinematic_closure::GeneralizedKICCreator , protocols::grafting::AnchoredGraftMover , protocols::grafting::AnchoredGraftMoverCreator , protocols::grafting::CCDEndsGraftMover , protocols::grafting::CCDEndsGraftMoverCreator , protocols::grafting::simple_movers::DeleteRegionMover , protocols::grafting::simple_movers::DeleteRegionMoverCreator , protocols::grafting::simple_movers::InsertPoseIntoPoseMover , protocols::grafting::simple_movers::InsertPoseIntoPoseMoverCreator , protocols::grafting::simple_movers::KeepRegionMover , protocols::grafting::simple_movers::KeepRegionMoverCreator , protocols::grafting::simple_movers::ReplaceRegionMover , protocols::grafting::simple_movers::ReplaceRegionMoverCreator , protocols::hbnet::ConstrainHBondNetwork , protocols::hbnet::ConstrainHBondNetworkCreator , protocols::hbnet::HBNet , protocols::hbnet::HBNetCreator , protocols::hbnet::HBNetScore , protocols::hbnet::HBNetScoreFilterCreator , protocols::hbnet::HBNetStapleInterface , protocols::hbnet::HBNetStapleInterfaceCreator , protocols::hbnet::UnsatSelector , protocols::hbnet::UnsatSelectorCreator , protocols::helical_bundle::BackboneGridSampler , protocols::helical_bundle::BackboneGridSamplerCreator , protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::BundleGridSamplerCreator , protocols::helical_bundle::BundleReporterFilter , protocols::helical_bundle::BundleReporterFilterCreator , protocols::helical_bundle::FitSimpleHelix , protocols::helical_bundle::FitSimpleHelixCreator , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::MakeBundleCreator , protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::MakeBundleHelixCreator , protocols::helical_bundle::PerturbBundle , protocols::helical_bundle::PerturbBundleCreator , protocols::helical_bundle::PerturbBundleHelix , protocols::helical_bundle::PerturbBundleHelixCreator , protocols::hotspot_hashing::movers::PlaceSurfaceProbe , protocols::hotspot_hashing::movers::PlaceSurfaceProbeCreator , protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionPerturbationCreator , protocols::hybridization::BackboneTorsionSampler , protocols::hybridization::BackboneTorsionSamplerCreator , protocols::hybridization::CartesianSampler , protocols::hybridization::CartesianSamplerCreator , protocols::hybridization::HybridizeProtocol , protocols::hybridization::HybridizeProtocolCreator , protocols::idealize::IdealizeMover , protocols::idealize::IdealizeMoverCreator , protocols::indexed_structure_store::filters::FragmentLookupFilter , protocols::indexed_structure_store::filters::FragmentLookupFilterCreator , protocols::indexed_structure_store::movers::DirectSegmentLookupMover , protocols::indexed_structure_store::movers::DirectSegmentLookupMoverCreator , protocols::indexed_structure_store::movers::SegmentSequenceProfileMover , protocols::indexed_structure_store::movers::SegmentSequenceProfileMoverCreator , protocols::jd3::chunk_library_inputters::ChunkLibraryInputterCreator , protocols::jd3::chunk_library_inputters::PDBChunkLibraryInputter , protocols::jd3::chunk_library_inputters::PDBChunkLibraryInputterCreator , protocols::jd3::full_model_inputters::FullModelInputterCreator , protocols::jd3::full_model_inputters::PDBFullModelInputter , protocols::jd3::full_model_inputters::PDBFullModelInputterCreator , protocols::jd3::full_model_inputters::SilentFileFullModelInputter , protocols::jd3::full_model_inputters::SilentFileFullModelInputterCreator , protocols::jd3::pose_inputters::PDBPoseInputter , protocols::jd3::pose_inputters::PDBPoseInputterCreator , protocols::jd3::pose_inputters::PoseInputterCreator , protocols::jd3::pose_inputters::SilentFilePoseInputter , protocols::jd3::pose_inputters::SilentFilePoseInputterCreator , protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputter , protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputterCreator , protocols::jd3::pose_outputters::mmTFPoseOutputter , protocols::jd3::pose_outputters::mmTFPoseOutputterCreator , protocols::jd3::pose_outputters::PDBPoseOutputter , protocols::jd3::pose_outputters::PDBPoseOutputterCreator , protocols::jd3::pose_outputters::PoseOutputterCreator , protocols::jd3::pose_outputters::ScoreFileOutputter , protocols::jd3::pose_outputters::ScoreFileOutputterCreator , protocols::jd3::pose_outputters::SecondaryPoseOutputterCreator , protocols::jd3::pose_outputters::SilentFilePoseOutputter , protocols::jd3::pose_outputters::SilentFilePoseOutputterCreator , protocols::kinematic_closure::KicMover , protocols::kinematic_closure::KicMoverCreator , protocols::legacy_sewing::LegacyAddStartnodeFragments , protocols::legacy_sewing::LegacyAddStartnodeFragmentsCreator , protocols::legacy_sewing::LegacyAppendAssemblyMover , protocols::legacy_sewing::LegacyAppendAssemblyMoverCreator , protocols::legacy_sewing::LegacyAssemblyConstraintsMover , protocols::legacy_sewing::LegacyAssemblyConstraintsMoverCreator , protocols::legacy_sewing::LegacyAssemblyMover , protocols::legacy_sewing::LegacyEnumerateAssemblyMover , protocols::legacy_sewing::LegacyEnumerateAssemblyMoverCreator , protocols::legacy_sewing::LegacyGivenPathAssemblyMover , protocols::legacy_sewing::LegacyGivenPathAssemblyMoverCreator , protocols::legacy_sewing::LegacyGreedyAssemblyMover , protocols::legacy_sewing::LegacyGreedyAssemblyMoverCreator , protocols::legacy_sewing::LegacyMonteCarloAssemblyMover , protocols::legacy_sewing::LegacyMonteCarloAssemblyMoverCreator , protocols::legacy_sewing::LegacyReadNativeRotamersFile , protocols::legacy_sewing::LegacyReadNativeRotamersFileCreator , protocols::legacy_sewing::LegacyReadRepeatNativeRotamersFile , protocols::legacy_sewing::LegacyReadRepeatNativeRotamersFileCreator , protocols::legacy_sewing::LegacyRepeatAssemblyMover , protocols::legacy_sewing::LegacyRepeatAssemblyMoverCreator , protocols::legacy_sewing::sampling::requirements::LegacyGlobalLengthRequirement , protocols::legacy_sewing::sampling::requirements::LegacyGlobalLengthRequirementCreator , protocols::legacy_sewing::sampling::requirements::LegacyGlobalRequirementCreator , protocols::legacy_sewing::sampling::requirements::LegacyIntraSegmentRequirementCreator , protocols::legacy_sewing::sampling::requirements::LegacyResidueRetentionRequirement , protocols::legacy_sewing::sampling::requirements::LegacyResidueRetentionRequirementCreator , protocols::legacy_sewing::sampling::requirements::LegacySegmentDsspRequirement , protocols::legacy_sewing::sampling::requirements::LegacySegmentDsspRequirementCreator , protocols::legacy_sewing::sampling::requirements::LegacySegmentLengthRequirement , protocols::legacy_sewing::sampling::requirements::LegacySegmentLengthRequirementCreator , protocols::ligand_docking::AddHydrogens , protocols::ligand_docking::AddHydrogensCreator , protocols::ligand_docking::AtomCountFilter , protocols::ligand_docking::AtomCountFilterCreator , protocols::ligand_docking::ChainExistsFilter , protocols::ligand_docking::ChainExistsFilterCreator , protocols::ligand_docking::CompleteConnectionsFilter , protocols::ligand_docking::CompleteConnectionsFilterCreator , protocols::ligand_docking::CompoundTranslate , protocols::ligand_docking::CompoundTranslateCreator , protocols::ligand_docking::ComputeLigandRDF , protocols::ligand_docking::ComputeLigandRDFCreator , protocols::ligand_docking::FinalMinimizer , protocols::ligand_docking::FinalMinimizerCreator , protocols::ligand_docking::ga_ligand_dock::GALigandDock , protocols::ligand_docking::ga_ligand_dock::GALigandDockCreator , protocols::ligand_docking::GrowLigand , protocols::ligand_docking::GrowLigandCreator , protocols::ligand_docking::HBondAcceptorFilter , protocols::ligand_docking::HBondAcceptorFilterCreator , protocols::ligand_docking::HBondDonorFilter , protocols::ligand_docking::HBondDonorFilterCreator , protocols::ligand_docking::HeavyAtomFilter , protocols::ligand_docking::HeavyAtomFilterCreator , protocols::ligand_docking::HighResDocker , protocols::ligand_docking::HighResDockerCreator , protocols::ligand_docking::HighResEnsemble , protocols::ligand_docking::HighResEnsembleCreator , protocols::ligand_docking::InterfaceBuilder , protocols::ligand_docking::InterfaceBuilderLoader , protocols::ligand_docking::InterfaceBuilderLoaderCreator , protocols::ligand_docking::InterfaceScoreCalculator , protocols::ligand_docking::InterfaceScoreCalculatorCreator , protocols::ligand_docking::LigandArea , protocols::ligand_docking::LigandAreaLoader , protocols::ligand_docking::LigandAreaLoaderCreator , protocols::ligand_docking::LigandDesign , protocols::ligand_docking::LigandDesignCreator , protocols::ligand_docking::MinimizeBackbone , protocols::ligand_docking::MinimizeBackboneCreator , protocols::ligand_docking::MolarMassFilter , protocols::ligand_docking::MolarMassFilterCreator , protocols::ligand_docking::MolecularMassFilter , protocols::ligand_docking::MolecularMassFilterCreator , protocols::ligand_docking::MoveMapBuilder , protocols::ligand_docking::MoveMapBuilderLoader , protocols::ligand_docking::MoveMapBuilderLoaderCreator , protocols::ligand_docking::ProtLigEnsemble , protocols::ligand_docking::ProtLigEnsembleCreator , protocols::ligand_docking::RandomConformers , protocols::ligand_docking::RandomConformersCreator , protocols::ligand_docking::rdf::RDFBinaryHbondCreator , protocols::ligand_docking::rdf::RDFBinaryHbondFunction , protocols::ligand_docking::rdf::RDFBinaryOrbitalFunction , protocols::ligand_docking::rdf::RDFBinaryOrbitalFunctionCreator , protocols::ligand_docking::rdf::RDFChargeCreator , protocols::ligand_docking::rdf::RDFChargeFunction , protocols::ligand_docking::rdf::RDFElecCreator , protocols::ligand_docking::rdf::RDFElecFunction , protocols::ligand_docking::rdf::RDFEtableCreator , protocols::ligand_docking::rdf::RDFEtableFunction , protocols::ligand_docking::rdf::RDFFunctionCreator , protocols::ligand_docking::rdf::RDFHbondCreator , protocols::ligand_docking::rdf::RDFHbondFunction , protocols::ligand_docking::rdf::RDFOrbitalFunction , protocols::ligand_docking::rdf::RDFOrbitalFunctionCreator , protocols::ligand_docking::Rotate , protocols::ligand_docking::RotateCreator , protocols::ligand_docking::Rotates , protocols::ligand_docking::RotatesCreator , protocols::ligand_docking::SlideTogether , protocols::ligand_docking::SlideTogetherCreator , protocols::ligand_docking::StartFrom , protocols::ligand_docking::StartFromCreator , protocols::ligand_docking::Transform , protocols::ligand_docking::TransformCreator , protocols::ligand_docking::TransformEnsemble , protocols::ligand_docking::TransformEnsembleCreator , protocols::ligand_docking::Translate , protocols::ligand_docking::TranslateCreator , protocols::ligand_docking::WriteLigandMolFile , protocols::ligand_docking::WriteLigandMolFileCreator , protocols::loop_build::LoopmodelWrapper , protocols::loop_build::LoopmodelWrapperCreator , protocols::loop_build::LoopMover_SlidingWindow , protocols::loop_build::LoopMover_SlidingWindowCreator , protocols::loop_grower::FragmentExtension , protocols::loop_grower::FragmentExtensionCreator , protocols::loop_modeler::LoopModeler , protocols::loop_modeler::LoopModelerCreator , protocols::loop_modeling::LoopBuilder , protocols::loop_modeling::LoopBuilderCreator , protocols::loop_modeling::LoopProtocol , protocols::loop_modeling::LoopProtocolCreator , protocols::loop_modeling::refiners::MinimizationRefiner , protocols::loop_modeling::refiners::MinimizationRefinerCreator , protocols::loop_modeling::refiners::RepackingRefiner , protocols::loop_modeling::refiners::RepackingRefinerCreator , protocols::loop_modeling::refiners::RotamerTrialsRefiner , protocols::loop_modeling::refiners::RotamerTrialsRefinerCreator , protocols::loop_modeling::samplers::LegacyKicSampler , protocols::loop_modeling::samplers::LegacyKicSamplerCreator , protocols::loop_modeling::utilities::PrepareForCentroid , protocols::loop_modeling::utilities::PrepareForCentroidCreator , protocols::loop_modeling::utilities::PrepareForFullatom , protocols::loop_modeling::utilities::PrepareForFullatomCreator , protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashDiversifierCreator , protocols::loophash::LoopHashLibraryLoader , protocols::loophash::LoopHashLibraryLoaderCreator , protocols::loophash::LoopHashMoverWrapper , protocols::loophash::LoopHashMoverWrapperCreator , protocols::loops::filters::LoopAnalyzerFilter , protocols::loops::filters::LoopAnalyzerFilterCreator , protocols::loops::FoldTreeFromLoops , protocols::loops::FoldTreeFromLoopsCreator , protocols::loops::loop_closure::ccd::CCDLoopClosureMover , protocols::loops::loop_closure::ccd::CCDLoopClosureMoverCreator , protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover , protocols::loops::loop_closure::jacobi::JacobiLoopClosureMoverCreator , protocols::loops::loop_mover::LoopCM , protocols::loops::loop_mover::LoopCMCreator , protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD , protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCDCreator , protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC , protocols::loops::loop_mover::perturb::LoopMover_Perturb_KICCreator , protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD , protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves , protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_MovesCreator , protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCDCreator , protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub , protocols::loops::loop_mover::refine::LoopMover_Refine_BackrubCreator , protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::loops::loop_mover::refine::LoopMover_Refine_CCDCreator , protocols::loops::loop_mover::refine::LoopMover_Refine_KIC , protocols::loops::loop_mover::refine::LoopMover_Refine_KICCreator , protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer , protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainerCreator , protocols::loops::loop_mover::refine::RepackTrial , protocols::loops::loop_mover::refine::RepackTrialCreator , protocols::loops::loop_mover::refine::ShearMinCCDTrial , protocols::loops::loop_mover::refine::ShearMinCCDTrialCreator , protocols::loops::loop_mover::refine::SmallMinCCDTrial , protocols::loops::loop_mover::refine::SmallMinCCDTrialCreator , protocols::loops::loops_definers::LoopsDatabaseDefiner , protocols::loops::loops_definers::LoopsDatabaseDefinerCreator , protocols::loops::loops_definers::LoopsDefinerCreator , protocols::loops::loops_definers::LoopsDefinerLoader , protocols::loops::loops_definers::LoopsDefinerLoaderCreator , protocols::loops::loops_definers::LoopsExplicitDefiner , protocols::loops::loops_definers::LoopsExplicitDefinerCreator , protocols::loops::loops_definers::LoopsFileDefiner , protocols::loops::loops_definers::LoopsFileDefinerCreator , protocols::loops::loops_definers::LoopsStringDefiner , protocols::loops::loops_definers::LoopsStringDefinerCreator , protocols::loops::LoopsFileLoader , protocols::loops::LoopsFileLoaderCreator , protocols::match::MatcherMover , protocols::match::MatcherMoverCreator , protocols::matdes::BuildingBlockInterfaceOperation , protocols::matdes::BuildingBlockInterfaceOperationCreator , protocols::matdes::ClashCheckFilter , protocols::matdes::ClashCheckFilterCreator , protocols::matdes::ExtractSubposeMover , protocols::matdes::ExtractSubposeMoverCreator , protocols::matdes::GetRBDOFValues , protocols::matdes::GetRBDOFValuesCreator , protocols::matdes::InterfacePackingFilter , protocols::matdes::InterfacePackingFilterCreator , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMoverCreator , protocols::matdes::OligomericAverageDegreeFilter , protocols::matdes::OligomericAverageDegreeFilterCreator , protocols::matdes::SchemePlaceMotifsMover , protocols::matdes::SchemePlaceMotifsMoverCreator , protocols::matdes::SymDofMover , protocols::matdes::SymDofMoverCreator , protocols::matdes::SymUnsatHbondFilter , protocols::matdes::SymUnsatHbondFilterCreator , protocols::md::CartesianMD , protocols::md::CartesianMDCreator , protocols::mean_field::GenMeanFieldMover , protocols::mean_field::GenMeanFieldMoverCreator , protocols::membrane::AddMembraneMover , protocols::membrane::AddMembraneMoverCreator , protocols::membrane::AddMembraneSpanConstraint , protocols::membrane::AddMembraneSpanConstraintCreator , protocols::membrane::AddMembraneSpanTermZConstraint , protocols::membrane::AddMembraneSpanTermZConstraintCreator , protocols::membrane::AddMPLigandMover , protocols::membrane::AddMPLigandMoverCreator , protocols::membrane::AqueousPoreFinder , protocols::membrane::AqueousPoreFinderCreator , protocols::membrane::benchmark::MakeCanonicalHelix , protocols::membrane::benchmark::MakeCanonicalHelixCreator , protocols::membrane::benchmark::SampleTiltAngles , protocols::membrane::benchmark::SampleTiltAnglesCreator , protocols::membrane::FlipMover , protocols::membrane::FlipMoverCreator , protocols::membrane::MembranePositionFromTopologyMover , protocols::membrane::MembranePositionFromTopologyMoverCreator , protocols::membrane::MPLipidAccessibility , protocols::membrane::MPLipidAccessibilityCreator , protocols::membrane::OptimizeMembranePositionMover , protocols::membrane::OptimizeProteinEmbeddingMover , protocols::membrane::SetMembranePositionMover , protocols::membrane::SetMembranePositionMoverCreator , protocols::membrane::SpinAroundPartnerMover , protocols::membrane::symmetry::SymmetricAddMembraneMover , protocols::membrane::symmetry::SymmetricAddMembraneMoverCreator , protocols::membrane::TiltMover , protocols::membrane::TransformIntoMembraneMover , protocols::membrane::TransformIntoMembraneMoverCreator , protocols::membrane::visualize::VisualizeEmbeddingMover , protocols::membrane::visualize::VisualizeEmbeddingMoverCreator , protocols::membrane::visualize::VisualizeMembraneMover , protocols::membrane::visualize::VisualizeMembraneMoverCreator , protocols::membrane_benchmark::MembraneEnergyLandscapeSampler , protocols::membrane_benchmark::MembraneEnergyLandscapeSamplerCreator , protocols::membrane_benchmark::PeptideOrientationMover , protocols::membrane_benchmark::PeptideOrientationMoverCreator , protocols::minimization_packing::BoltzmannRotamerMover , protocols::minimization_packing::BoltzmannRotamerMoverCreator , protocols::minimization_packing::DisulfideOptimizationMover , protocols::minimization_packing::DisulfideOptimizationMoverCreator , protocols::minimization_packing::MinMover , protocols::minimization_packing::MinMoverCreator , protocols::minimization_packing::MinPackMover , protocols::minimization_packing::MinPackMoverCreator , protocols::minimization_packing::PackRotamersMover , protocols::minimization_packing::PackRotamersMoverCreator , protocols::minimization_packing::PertMinMover , protocols::minimization_packing::PertMinMoverCreator , protocols::minimization_packing::RotamerTrialsMinMover , protocols::minimization_packing::RotamerTrialsMinMoverCreator , protocols::minimization_packing::RotamerTrialsMover , protocols::minimization_packing::RotamerTrialsMoverCreator , protocols::minimization_packing::SaneMinMover , protocols::minimization_packing::SaneMinMoverCreator , protocols::minimization_packing::symmetry::SymMinMover , protocols::minimization_packing::symmetry::SymMinMoverCreator , protocols::minimization_packing::symmetry::SymPackRotamersMover , protocols::minimization_packing::symmetry::SymPackRotamersMoverCreator , protocols::minimization_packing::symmetry::SymRotamerTrialsMover , protocols::minimization_packing::symmetry::SymRotamerTrialsMoverCreator , protocols::minimization_packing::symmetry::TaskAwareSymMinMover , protocols::minimization_packing::symmetry::TaskAwareSymMinMoverCreator , protocols::minimization_packing::TaskAwareMinMover , protocols::minimization_packing::TaskAwareMinMoverCreator , protocols::monte_carlo::GenericMonteCarloMover , protocols::monte_carlo::GenericMonteCarloMoverCreator , protocols::monte_carlo::GenericSimulatedAnnealer , protocols::monte_carlo::GenericSimulatedAnnealerCreator , protocols::monte_carlo::MonteCarloRecover , protocols::monte_carlo::MonteCarloRecoverCreator , protocols::monte_carlo::MonteCarloReset , protocols::monte_carlo::MonteCarloResetCreator , protocols::monte_carlo::MonteCarloTest , protocols::monte_carlo::MonteCarloTestCreator , protocols::monte_carlo::ResetBaselineMover , protocols::monte_carlo::ResetBaselineMoverCreator , protocols::motif_grafting::movers::MotifGraftCreator , protocols::motif_grafting::movers::MotifGraftMover , protocols::motifs::MotifDnaPacker , protocols::motifs::MotifDnaPackerCreator , protocols::moves::DsspMover , protocols::moves::DsspMoverCreator , protocols::moves::FilterReportAsPoseExtraScoresMover , protocols::moves::FilterReportAsPoseExtraScoresMoverCreator , protocols::moves::IfMover , protocols::moves::IfMoverCreator , protocols::moves::IteratedConvergenceMover , protocols::moves::IteratedConvergenceMoverCreator , protocols::moves::MoverCreator , protocols::moves::MoverFactory , protocols::moves::PyMOLMover , protocols::moves::PyMOLMoverCreator , protocols::moves::RampingMover , protocols::moves::RampingMoverCreator , protocols::moves::RandomMover , protocols::moves::RandomMoverCreator , protocols::moves::SwitchMover , protocols::moves::SwitchMoverCreator , protocols::multistage_rosetta_scripts::cluster::ClusterMetricCreator , protocols::multistage_rosetta_scripts::cluster::ClusterMetricFactory , protocols::multistage_rosetta_scripts::cluster::metrics::JumpMetric , protocols::multistage_rosetta_scripts::cluster::metrics::JumpMetricCreator , protocols::multistage_rosetta_scripts::cluster::metrics::SequenceMetric , protocols::multistage_rosetta_scripts::cluster::metrics::SequenceMetricCreator , protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::NcbbDockDesignProtocolCreator , protocols::ncbb::oop::OopCreatorMover , protocols::ncbb::oop::OopCreatorMoverCreator , protocols::ncbb::oop::OopDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocolCreator , protocols::ncbb::ResidueReplacementRebuildMover , protocols::ncbb::ResidueReplacementRebuildMoverCreator , protocols::ncbb::SecStructMinimizeMover , protocols::ncbb::SecStructMinimizeMoverCreator , protocols::nmr::ParaNMRScoreMover , protocols::nmr::ParaNMRScoreMoverCreator , protocols::nmr::pcs::PCSLigandTransformMover , protocols::nmr::pcs::PCSLigandTransformMoverCreator , protocols::nmr::pre::PREMover , protocols::nmr::pre::PREMoverCreator , protocols::nonlocal::SingleFragmentMover , protocols::nonlocal::SingleFragmentMoverCreator , protocols::normalmode::NormalModeMinimizer , protocols::normalmode::NormalModeMinimizerCreator , protocols::normalmode::NormalModeRelaxMover , protocols::normalmode::NormalModeRelaxMoverCreator , protocols::pack_interface::ProteinProteinInterfaceUpweighter , protocols::pack_interface::ProteinProteinInterfaceUpweighterTaskOperationCreator , protocols::parser::ConstraintGeneratorLoader , protocols::parser::ConstraintGeneratorLoaderCreator , protocols::parser::DatabaseSessionLoader , protocols::parser::DatabaseSessionLoaderCreator , protocols::parser::DataLoaderCreator , protocols::parser::FragmentReader , protocols::parser::FragSetLoader , protocols::parser::FragSetLoaderCreator , protocols::parser::JumpSelectorLoader , protocols::parser::JumpSelectorLoaderCreator , protocols::parser::MonteCarloLoader , protocols::parser::MonteCarloLoaderCreator , protocols::parser::MoveMapFactoryLoader , protocols::parser::MoveMapFactoryLoaderCreator , protocols::parser::PackerPaletteLoader , protocols::parser::PackerPaletteLoaderCreator , protocols::parser::ResidueSelectorLoader , protocols::parser::ResidueSelectorLoaderCreator , protocols::parser::ResLvlTaskOperationLoader , protocols::parser::ResLvlTaskOperationLoaderCreator , protocols::parser::ScoreFunctionLoader , protocols::parser::ScoreFunctionLoaderCreator , protocols::parser::SimpleMetricLoader , protocols::parser::SimpleMetricLoaderCreator , protocols::parser::TaskOperationLoader , protocols::parser::TaskOperationLoaderCreator , protocols::pb_potential::SetupPoissonBoltzmannPotential , protocols::pb_potential::SetupPoissonBoltzmannPotentialCreator , protocols::pdbinfo_manipulations::AlignPDBInfoToSequences , protocols::pdbinfo_manipulations::AlignPDBInfoToSequencesCreator , protocols::peptide_deriver::PeptideDeriverFilter , protocols::peptide_deriver::PeptideDeriverFilterCreator , protocols::pose_creation::ExtendedPoseMover , protocols::pose_creation::ExtendedPoseMoverCreator , protocols::pose_creation::MakeJunctionsMover , protocols::pose_creation::MakeJunctionsMoverCreator , protocols::pose_creation::MakePolyXMover , protocols::pose_creation::MakePolyXMoverCreator , protocols::pose_creation::MergePDBatOverlapMover , protocols::pose_creation::MergePDBatOverlapMoverCreator , protocols::pose_creation::MergePDBMover , protocols::pose_creation::MergePDBMoverCreator , protocols::pose_creation::PoseFromSequenceMover , protocols::pose_creation::PoseFromSequenceMoverCreator , protocols::pose_creation::SliceToMiniProteinMover , protocols::pose_creation::SliceToMiniProteinMoverCreator , protocols::pose_length_moves::AnalyzeLoopModeling , protocols::pose_length_moves::AnalyzeLoopModelingCreator , protocols::pose_length_moves::ConnectChainsMover , protocols::pose_length_moves::ConnectChainsMoverCreator , protocols::pose_length_moves::FixAllLoopsMover , protocols::pose_length_moves::FixAllLoopsMoverCreator , protocols::pose_length_moves::InsertResMover , protocols::pose_length_moves::InsertResMoverCreator , protocols::pose_length_moves::NearNativeLoopCloser , protocols::pose_length_moves::NearNativeLoopCloserCreator , protocols::pose_reporters::EnergyReporter , protocols::pose_reporters::EnergyReporterCreator , protocols::pose_reporters::FilterReporter , protocols::pose_reporters::FilterReporterCreator , protocols::pose_reporters::RMSDReporter , protocols::pose_reporters::RMSDReporterCreator , protocols::pose_selectors::AndSelector , protocols::pose_selectors::AndSelectorCreator , protocols::pose_selectors::ClusterPoseSelector , protocols::pose_selectors::ClusterPoseSelectorCreator , protocols::pose_selectors::Filter , protocols::pose_selectors::FilterCreator , protocols::pose_selectors::OrSelector , protocols::pose_selectors::OrSelectorCreator , protocols::pose_selectors::TopNByProperty , protocols::pose_selectors::TopNByPropertyCreator , protocols::protein_interface_design::filters::AtomicContactCountFilter , protocols::protein_interface_design::filters::AtomicContactCountFilterCreator , protocols::protein_interface_design::filters::AverageDegreeFilter , protocols::protein_interface_design::filters::AverageDegreeFilterCreator , protocols::protein_interface_design::filters::BindingStrainFilter , protocols::protein_interface_design::filters::BindingStrainFilterCreator , protocols::protein_interface_design::filters::BoltzmannFilter , protocols::protein_interface_design::filters::BoltzmannFilterCreator , protocols::protein_interface_design::filters::ClashWithTargetFilter , protocols::protein_interface_design::filters::ClashWithTargetFilterCreator , protocols::protein_interface_design::filters::DesignableResiduesFilter , protocols::protein_interface_design::filters::DesignableResiduesFilterCreator , protocols::protein_interface_design::filters::DisulfideFilter , protocols::protein_interface_design::filters::DisulfideFilterCreator , protocols::protein_interface_design::filters::FilterScanFilter , protocols::protein_interface_design::filters::FilterScanFilterCreator , protocols::protein_interface_design::filters::FNatFilter , protocols::protein_interface_design::filters::FNatFilterCreator , protocols::protein_interface_design::filters::HbondsToAtomFilter , protocols::protein_interface_design::filters::HbondsToAtomFilterCreator , protocols::protein_interface_design::filters::HbondsToResidueFilter , protocols::protein_interface_design::filters::HbondsToResidueFilterCreator , protocols::protein_interface_design::filters::InterfaceHolesFilter , protocols::protein_interface_design::filters::InterfaceHolesFilterCreator , protocols::protein_interface_design::filters::IRmsdFilter , protocols::protein_interface_design::filters::IRmsdFilterCreator , protocols::protein_interface_design::filters::LRmsdFilter , protocols::protein_interface_design::filters::LRmsdFilterCreator , protocols::protein_interface_design::filters::RelativeSegmentFilter , protocols::protein_interface_design::filters::RelativeSegmentFilterCreator , protocols::protein_interface_design::filters::RmsdFilter , protocols::protein_interface_design::filters::RmsdFilterCreator , protocols::protein_interface_design::filters::RmsdSimpleFilter , protocols::protein_interface_design::filters::RmsdSimpleFilterCreator , protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::protein_interface_design::filters::SequenceRecoveryFilterCreator , protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter , protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilterCreator , protocols::protein_interface_design::filters::SSamountFilter , protocols::protein_interface_design::filters::SSamountFilterCreator , protocols::protein_interface_design::filters::StubScoreFilter , protocols::protein_interface_design::filters::StubScoreFilterCreator , protocols::protein_interface_design::filters::StubScoreLoopsFilter , protocols::protein_interface_design::filters::StubScoreLoopsFilterCreator , protocols::protein_interface_design::filters::Torsion , protocols::protein_interface_design::filters::TorsionCreator , protocols::protein_interface_design::movers::AddChainBreak , protocols::protein_interface_design::movers::AddChainBreakCreator , protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots , protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspotsCreator , protocols::protein_interface_design::movers::BackrubDDMover , protocols::protein_interface_design::movers::BackrubDDMoverCreator , protocols::protein_interface_design::movers::BestHotspotCstMover , protocols::protein_interface_design::movers::BestHotspotCstMoverCreator , protocols::protein_interface_design::movers::BuildAlaPose , protocols::protein_interface_design::movers::BuildAlaPoseCreator , protocols::protein_interface_design::movers::DesignMinimizeHbonds , protocols::protein_interface_design::movers::DesignMinimizeHbondsCreator , protocols::protein_interface_design::movers::DisulfideMover , protocols::protein_interface_design::movers::DisulfideMoverCreator , protocols::protein_interface_design::movers::DockAndRetrieveSidechains , protocols::protein_interface_design::movers::DockAndRetrieveSidechainsCreator , protocols::protein_interface_design::movers::DockWithHotspotMover , protocols::protein_interface_design::movers::DockWithHotspotMoverCreator , protocols::protein_interface_design::movers::FavorNativeResiduePreCycle , protocols::protein_interface_design::movers::FavorNativeResiduePreCycleCreator , protocols::protein_interface_design::movers::FavorNonNativeResiduePreCycle , protocols::protein_interface_design::movers::FavorNonNativeResiduePreCycleCreator , protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover , protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMoverCreator , protocols::protein_interface_design::movers::HotspotHasherMover , protocols::protein_interface_design::movers::HotspotHasherMoverCreator , protocols::protein_interface_design::movers::InterfaceRecapitulationMover , protocols::protein_interface_design::movers::InterfaceRecapitulationMoverCreator , protocols::protein_interface_design::movers::LoopFinder , protocols::protein_interface_design::movers::LoopFinderCreator , protocols::protein_interface_design::movers::LoopLengthChange , protocols::protein_interface_design::movers::LoopLengthChangeCreator , protocols::protein_interface_design::movers::LoopMoverFromCommandLine , protocols::protein_interface_design::movers::LoopMoverFromCommandLineCreator , protocols::protein_interface_design::movers::LoopOver , protocols::protein_interface_design::movers::LoopOverCreator , protocols::protein_interface_design::movers::LoopRemodel , protocols::protein_interface_design::movers::LoopRemodelCreator , protocols::protein_interface_design::movers::MapHotspot , protocols::protein_interface_design::movers::MapHotspotCreator , protocols::protein_interface_design::movers::PatchdockTransform , protocols::protein_interface_design::movers::PatchdockTransformCreator , protocols::protein_interface_design::movers::PeptideStapleDesignMover , protocols::protein_interface_design::movers::PeptideStapleDesignMoverCreator , protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::protein_interface_design::movers::PlacementAuctionMoverCreator , protocols::protein_interface_design::movers::PlacementMinimizationMover , protocols::protein_interface_design::movers::PlacementMinimizationMoverCreator , protocols::protein_interface_design::movers::PlaceOnLoop , protocols::protein_interface_design::movers::PlaceOnLoopCreator , protocols::protein_interface_design::movers::PlaceSimultaneouslyMover , protocols::protein_interface_design::movers::PlaceSimultaneouslyMoverCreator , protocols::protein_interface_design::movers::PlaceStubMover , protocols::protein_interface_design::movers::PlaceStubMoverCreator , protocols::protein_interface_design::movers::PrepackMover , protocols::protein_interface_design::movers::PrepackMoverCreator , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMoverCreator , protocols::protein_interface_design::movers::RandomMutation , protocols::protein_interface_design::movers::RandomMutationCreator , protocols::protein_interface_design::movers::RepackMinimize , protocols::protein_interface_design::movers::RepackMinimizeCreator , protocols::protein_interface_design::movers::SaveAndRetrieveSidechains , protocols::protein_interface_design::movers::SaveAndRetrieveSidechainsCreator , protocols::protein_interface_design::movers::SetAtomTree , protocols::protein_interface_design::movers::SetAtomTreeCreator , protocols::protein_interface_design::movers::SetTemperatureFactor , protocols::protein_interface_design::movers::SetTemperatureFactorCreator , protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover , protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMoverCreator , protocols::protein_interface_design::movers::SetupHotspotConstraintsMover , protocols::protein_interface_design::movers::SetupHotspotConstraintsMoverCreator , protocols::protein_interface_design::movers::ShoveResidueMover , protocols::protein_interface_design::movers::ShoveResidueMoverCreator , protocols::protein_interface_design::movers::SpinMover , protocols::protein_interface_design::movers::SpinMoverCreator , protocols::protein_interface_design::movers::SubroutineMover , protocols::protein_interface_design::movers::SubroutineMoverCreator , protocols::protein_interface_design::movers::TaskAwareCsts , protocols::protein_interface_design::movers::TaskAwareCstsCreator , protocols::protein_interface_design::movers::TopologyBrokerMover , protocols::protein_interface_design::movers::TopologyBrokerMoverCreator , protocols::protein_interface_design::movers::TryRotamers , protocols::protein_interface_design::movers::TryRotamersCreator , protocols::protein_interface_design::movers::VLB , protocols::protein_interface_design::movers::VLBCreator , protocols::qsar::RenderGridsToKinemage , protocols::qsar::RenderGridsToKinemageCreator , protocols::qsar::scoring_grid::AtrGrid , protocols::qsar::scoring_grid::AtrGridCreator , protocols::qsar::scoring_grid::ChargeGrid , protocols::qsar::scoring_grid::ChargeGridCreator , protocols::qsar::scoring_grid::ClassicGrid , protocols::qsar::scoring_grid::ClassicGridCreator , protocols::qsar::scoring_grid::GridCreator , protocols::qsar::scoring_grid::GridFactory , protocols::qsar::scoring_grid::HbaGrid , protocols::qsar::scoring_grid::HbaGridCreator , protocols::qsar::scoring_grid::HbdGrid , protocols::qsar::scoring_grid::HbdGridCreator , protocols::qsar::scoring_grid::LigandPropertyScore , protocols::qsar::scoring_grid::LigandPropertyScoreCreator , protocols::qsar::scoring_grid::PCSMultiGrid , protocols::qsar::scoring_grid::PCSMultiGridCreator , protocols::qsar::scoring_grid::PCSSingleGrid , protocols::qsar::scoring_grid::PCSSingleGridCreator , protocols::qsar::scoring_grid::RepGrid , protocols::qsar::scoring_grid::RepGridCreator , protocols::qsar::scoring_grid::ScoringGridLoader , protocols::qsar::scoring_grid::ScoringGridLoaderCreator , protocols::qsar::scoring_grid::ShapeGrid , protocols::qsar::scoring_grid::ShapeGridCreator , protocols::qsar::scoring_grid::SiteGrid , protocols::qsar::scoring_grid::SiteGridCreator , protocols::qsar::scoring_grid::SolvationGrid , protocols::qsar::scoring_grid::SolvationGridCreator , protocols::qsar::scoring_grid::SolvationMetaGrid , protocols::qsar::scoring_grid::SolvationMetaGridCreator , protocols::qsar::scoring_grid::VdwGrid , protocols::qsar::scoring_grid::VdwGridCreator , protocols::quantum_annealing::ExternalPackerResultLoader , protocols::quantum_annealing::ExternalPackerResultLoaderCreator , protocols::quantum_annealing::InteractionGraphSummaryMetric , protocols::quantum_annealing::InteractionGraphSummaryMetricCreator , protocols::rbsegment_relax::IdealizeHelicesMover , protocols::rbsegment_relax::IdealizeHelicesMoverCreator , protocols::rbsegment_relax::MakeStarTopologyMover , protocols::rbsegment_relax::MakeStarTopologyMoverCreator , protocols::rbsegment_relax::OptimizeThreadingMover , protocols::rbsegment_relax::OptimizeThreadingMoverCreator , protocols::recces::scratch::ThermalMinimizer , protocols::recces::scratch::ThermalMinimizerCreator , protocols::recces::scratch::ThermalSamplingMover , protocols::recces::scratch::ThermalSamplingMoverCreator , protocols::recon_design::FindConsensusSequence , protocols::recon_design::FindConsensusSequenceCreator , protocols::recon_design::FitnessFilter , protocols::recon_design::FitnessFilterCreator , protocols::recon_design::MSDMover , protocols::recon_design::MSDMoverCreator , protocols::relax::AcceptToBestMover , protocols::relax::AcceptToBestMoverCreator , protocols::relax::AtomCoordinateCstMover , protocols::relax::AtomCoordinateCstMoverCreator , protocols::relax::FastRelax , protocols::relax::FastRelaxCreator , protocols::relax::LocalRelax , protocols::relax::LocalRelaxCreator , protocols::relax::membrane::MPFastRelaxMover , protocols::relax::membrane::MPFastRelaxMoverCreator , protocols::relax::membrane::MPRangeRelaxMover , protocols::relax::RepeatProteinRelax , protocols::relax::RepeatProteinRelaxCreator , protocols::residue_selectors::HBondSelector , protocols::residue_selectors::HBondSelectorCreator , protocols::residue_selectors::LigandMetalContactSelector , protocols::residue_selectors::LigandMetalContactSelectorCreator , protocols::residue_selectors::NativeSelector , protocols::residue_selectors::NativeSelectorCreator , protocols::residue_selectors::StoredResidueSubsetSelector , protocols::residue_selectors::StoredResidueSubsetSelectorCreator , protocols::residue_selectors::StoreResidueSubsetMover , protocols::residue_selectors::StoreResidueSubsetMoverCreator , protocols::residue_selectors::TaskSelector , protocols::residue_selectors::TaskSelectorCreator , protocols::rigid::RigidBodyPerturbNoCenterMover , protocols::rigid::RigidBodyPerturbNoCenterMoverCreator , protocols::rigid::RigidBodyTiltMover , protocols::rigid::RigidBodyTiltMoverCreator , protocols::rigid::RigidBodyTransMover , protocols::rigid::RigidBodyTransMoverCreator , protocols::rigid::RollMover , protocols::rigid::RollMoverCreator , protocols::rigid::UniformRigidBodyCM , protocols::rigid::UniformRigidBodyCMCreator , protocols::rigid::UniformRigidBodyMover , protocols::rigid::UniformRigidBodyMoverCreator , protocols::rna::denovo::movers::RNA_DeNovoProtocolMover , protocols::rna::denovo::movers::RNA_DeNovoProtocolMoverCreator , protocols::rna::denovo::RNA_DeNovoProtocol , protocols::rna::denovo::RNA_DeNovoProtocolCreator , protocols::rna::movers::ERRASER2Protocol , protocols::rna::movers::ERRASER2ProtocolCreator , protocols::rna::movers::ErraserMinimizerMover , protocols::rna::movers::ErraserMinimizerMoverCreator , protocols::rna::movers::RNAIdealizeMover , protocols::rna::movers::RNAIdealizeMoverCreator , protocols::rosetta_scripts::MultipleOutputWrapper , protocols::rosetta_scripts::MultipleOutputWrapperCreator , protocols::rosetta_scripts::MultiplePoseMover , protocols::rosetta_scripts::MultiplePoseMoverCreator , protocols::rosetta_scripts::ParsedProtocol , protocols::rosetta_scripts::ParsedProtocolCreator , protocols::rosetta_scripts::PosePropertyReporterCreator , protocols::rosetta_scripts::PoseSelectorCreator , protocols::rosetta_scripts::SavePoseMover , protocols::rosetta_scripts::SavePoseMoverCreator , protocols::rotamer_recovery::RotamerRecoveryMover , protocols::rotamer_recovery::RotamerRecoveryMoverCreator , protocols::score_filters::GeometryFilter , protocols::score_filters::GeometryFilterCreator , protocols::score_filters::ScoreCutoffFilter , protocols::score_filters::ScoreCutoffFilterCreator , protocols::score_filters::ScoreTypeFilter , protocols::score_filters::ScoreTypeFilterCreator , protocols::seeded_abinitio::CAcstGenerator , protocols::seeded_abinitio::CAcstGeneratorCreator , protocols::seeded_abinitio::CloseFold , protocols::seeded_abinitio::CloseFoldCreator , protocols::seeded_abinitio::CoordinateCst , protocols::seeded_abinitio::CoordinateCstCreator , protocols::seeded_abinitio::DefineMovableLoops , protocols::seeded_abinitio::DefineMovableLoopsCreator , protocols::seeded_abinitio::GrowPeptides , protocols::seeded_abinitio::GrowPeptidesCreator , protocols::seeded_abinitio::SeedFoldTree , protocols::seeded_abinitio::SeedFoldTreeCreator , protocols::seeded_abinitio::SeedSetupMover , protocols::seeded_abinitio::SeedSetupMoverCreator , protocols::seeded_abinitio::SegmentHybridizer , protocols::seeded_abinitio::SegmentHybridizerCreator , protocols::seeded_abinitio::SwapSegment , protocols::seeded_abinitio::SwapSegmentCreator , protocols::sewing::hashing::AlignmentFileGeneratorMover , protocols::sewing::hashing::AlignmentFileGeneratorMoverCreator , protocols::sewing::movers::AppendAssemblyMover , protocols::sewing::movers::AppendAssemblyMoverCreator , protocols::sewing::movers::AssemblyMover , protocols::sewing::movers::AssemblyMoverCreator , protocols::sewing::movers::LigandBindingAssemblyMover , protocols::sewing::movers::LigandBindingAssemblyMoverCreator , protocols::sewing::requirements::AssemblyRequirementCreator , protocols::sewing::requirements::ClashRequirement , protocols::sewing::requirements::ClashRequirementCreator , protocols::sewing::requirements::DsspSpecificLengthRequirement , protocols::sewing::requirements::DsspSpecificLengthRequirementCreator , protocols::sewing::requirements::KeepLigandContactsRequirement , protocols::sewing::requirements::KeepLigandContactsRequirementCreator , protocols::sewing::requirements::LengthInResiduesRequirement , protocols::sewing::requirements::LengthInResiduesRequirementCreator , protocols::sewing::requirements::LigandClashRequirement , protocols::sewing::requirements::LigandClashRequirementCreator , protocols::sewing::requirements::NonTerminalStartingSegmentRequirement , protocols::sewing::requirements::NonTerminalStartingSegmentRequirementCreator , protocols::sewing::requirements::SizeInSegmentsRequirement , protocols::sewing::requirements::SizeInSegmentsRequirementCreator , protocols::sewing::scoring::AssemblyScorerCreator , protocols::sewing::scoring::InterModelMotifScorer , protocols::sewing::scoring::InterModelMotifScorerCreator , protocols::sewing::scoring::IntraDesignTerminusMotifScorer , protocols::sewing::scoring::IntraDesignTerminusMotifScorerCreator , protocols::sewing::scoring::LigandScorer , protocols::sewing::scoring::LigandScorerCreator , protocols::sewing::scoring::MotifScorer , protocols::sewing::scoring::MotifScorerCreator , protocols::sewing::scoring::PartnerMotifScorer , protocols::sewing::scoring::PartnerMotifScorerCreator , protocols::sewing::scoring::SegmentContactOrderScorer , protocols::sewing::scoring::SegmentContactOrderScorerCreator , protocols::sewing::scoring::StartingNodeMotifScorer , protocols::sewing::scoring::StartingNodeMotifScorerCreator , protocols::sewing::scoring::SubsetPartnerMotifScorer , protocols::sewing::scoring::SubsetPartnerMotifScorerCreator , protocols::sewing::scoring::TerminusMotifScorer , protocols::sewing::scoring::TerminusMotifScorerCreator , protocols::sewing::scoring::TopNMotifScorer , protocols::sewing::scoring::TopNMotifScorerCreator , protocols::simple_ddg::AlaScan , protocols::simple_ddg::AlaScanFilterCreator , protocols::simple_ddg::ddG , protocols::simple_ddg::ddGCreator , protocols::simple_ddg::DdgFilter , protocols::simple_ddg::DdgFilterCreator , protocols::simple_ddg::DdGScan , protocols::simple_ddg::DdGScanCreator , protocols::simple_ddg::InterfaceBindingEnergyDensityFilter , protocols::simple_ddg::InterfaceBindingEnergyDensityFilterCreator , protocols::simple_ddg::SSElementBisectddGFilter , protocols::simple_ddg::SSElementBisectddGFilterCreator , protocols::simple_filters::AngleToVector , protocols::simple_filters::AngleToVectorFilterCreator , protocols::simple_filters::AtomicContactFilter , protocols::simple_filters::AtomicContactFilterCreator , protocols::simple_filters::AtomicDistanceFilter , protocols::simple_filters::AtomicDistanceFilterCreator , protocols::simple_filters::AveragePathLengthFilter , protocols::simple_filters::AveragePathLengthFilterCreator , protocols::simple_filters::BuriedSurfaceAreaFilter , protocols::simple_filters::BuriedSurfaceAreaFilterCreator , protocols::simple_filters::BuriedUnsatHbondFilter , protocols::simple_filters::BuriedUnsatHbondFilterCreator , protocols::simple_filters::ChainBreak , protocols::simple_filters::ChainBreakFilterCreator , protocols::simple_filters::ChainCountFilter , protocols::simple_filters::ChainCountFilterCreator , protocols::simple_filters::ContactMolecularSurfaceFilter , protocols::simple_filters::ContactMolecularSurfaceFilterCreator , protocols::simple_filters::DeltaFilter , protocols::simple_filters::DeltaFilterCreator , protocols::simple_filters::DisulfideEntropyFilter , protocols::simple_filters::DisulfideEntropyFilterCreator , protocols::simple_filters::EnergyPerResidueFilter , protocols::simple_filters::EnergyPerResidueFilterCreator , protocols::simple_filters::ExpiryFilter , protocols::simple_filters::ExpiryFilterCreator , protocols::simple_filters::FileExistFilter , protocols::simple_filters::FileExistFilterCreator , protocols::simple_filters::FileRemoveFilter , protocols::simple_filters::FileRemoveFilterCreator , protocols::simple_filters::HelixHelixAngleFilter , protocols::simple_filters::HelixHelixAngleFilterCreator , protocols::simple_filters::HolesFilter , protocols::simple_filters::HolesFilterCreator , protocols::simple_filters::InterfaceHbondsFilter , protocols::simple_filters::InterfaceHbondsFilterCreator , protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter , protocols::simple_filters::InterfaceHydrophobicResidueContactsFilterCreator , protocols::simple_filters::InterfaceSasaFilter , protocols::simple_filters::InterfaceSasaFilterCreator , protocols::simple_filters::InterRepeatContactFilter , protocols::simple_filters::InterRepeatContactFilterCreator , protocols::simple_filters::IntraRepeatContactFilter , protocols::simple_filters::IntraRepeatContactFilterCreator , protocols::simple_filters::LeastNativeLike9merFilter , protocols::simple_filters::LeastNativeLike9merFilterCreator , protocols::simple_filters::LongestContinuousApolarSegmentFilter , protocols::simple_filters::LongestContinuousApolarSegmentFilterCreator , protocols::simple_filters::LongestContinuousPolarSegmentFilter , protocols::simple_filters::LongestContinuousPolarSegmentFilterCreator , protocols::simple_filters::MembAccesResidueLipophilicityFilter , protocols::simple_filters::MembAccesResidueLipophilicityFilterCreator , protocols::simple_filters::MotifScoreFilter , protocols::simple_filters::MotifScoreFilterCreator , protocols::simple_filters::MPSpanAngleFilter , protocols::simple_filters::MPSpanAngleFilterCreator , protocols::simple_filters::MutationsFilter , protocols::simple_filters::MutationsFilterCreator , protocols::simple_filters::NeighborTypeFilter , protocols::simple_filters::NeighborTypeFilterCreator , protocols::simple_filters::NetChargeFilter , protocols::simple_filters::NetChargeFilterCreator , protocols::simple_filters::NMerPSSMEnergyFilter , protocols::simple_filters::NMerPSSMEnergyFilterCreator , protocols::simple_filters::NMerSVMEnergyFilter , protocols::simple_filters::NMerSVMEnergyFilterCreator , protocols::simple_filters::NonSequentialNeighborsFilter , protocols::simple_filters::NonSequentialNeighborsFilterCreator , protocols::simple_filters::PackStatFilter , protocols::simple_filters::PackStatFilterCreator , protocols::simple_filters::PoseComment , protocols::simple_filters::PoseCommentFilterCreator , protocols::simple_filters::PoseInfoFilter , protocols::simple_filters::PoseInfoFilterCreator , protocols::simple_filters::RangeFilter , protocols::simple_filters::RangeFilterCreator , protocols::simple_filters::ReadPoseExtraScoreFilter , protocols::simple_filters::ReadPoseExtraScoreFilterCreator , protocols::simple_filters::RepeatParameterFilter , protocols::simple_filters::RepeatParameterFilterCreator , protocols::simple_filters::ReportFilter , protocols::simple_filters::ReportFilterCreator , protocols::simple_filters::ResidueBurialFilter , protocols::simple_filters::ResidueBurialFilterCreator , protocols::simple_filters::ResidueChiralityFilter , protocols::simple_filters::ResidueChiralityFilterCreator , protocols::simple_filters::ResidueCountFilter , protocols::simple_filters::ResidueCountFilterCreator , protocols::simple_filters::ResidueDepthFilter , protocols::simple_filters::ResidueDepthFilterCreator , protocols::simple_filters::ResidueDistanceFilter , protocols::simple_filters::ResidueDistanceFilterCreator , protocols::simple_filters::ResidueIEFilter , protocols::simple_filters::ResidueIEFilterCreator , protocols::simple_filters::ResidueLipophilicityFilter , protocols::simple_filters::ResidueLipophilicityFilterCreator , protocols::simple_filters::ResidueSelectionDistanceFilter , protocols::simple_filters::ResidueSelectionDistanceFilterCreator , protocols::simple_filters::ResidueSetChainEnergyFilter , protocols::simple_filters::ResidueSetChainEnergyFilterCreator , protocols::simple_filters::ResiduesInInterfaceFilter , protocols::simple_filters::ResiduesInInterfaceFilterCreator , protocols::simple_filters::SaveResfileToDiskFilter , protocols::simple_filters::SaveResfileToDiskFilterCreator , protocols::simple_filters::SecretionPredictionFilter , protocols::simple_filters::SecretionPredictionFilterCreator , protocols::simple_filters::SequenceDistance , protocols::simple_filters::SequenceDistanceFilterCreator , protocols::simple_filters::ShapeComplementarityFilter , protocols::simple_filters::ShapeComplementarityFilterCreator , protocols::simple_filters::SidechainRmsdFilter , protocols::simple_filters::SidechainRmsdFilterCreator , protocols::simple_filters::SimpleHbondsToAtomFilter , protocols::simple_filters::SimpleHbondsToAtomFilterCreator , protocols::simple_filters::SimpleMetricFilter , protocols::simple_filters::SimpleMetricFilterCreator , protocols::simple_filters::SpanTopologyMatchPoseFilter , protocols::simple_filters::SpanTopologyMatchPoseFilterCreator , protocols::simple_filters::SSElementLengthFilter , protocols::simple_filters::SSElementLengthFilterCreator , protocols::simple_filters::SSElementMotifContactFilter , protocols::simple_filters::SSElementMotifContactFilterCreator , protocols::simple_filters::SSMotifFinder , protocols::simple_filters::SSMotifFinderFilterCreator , protocols::simple_filters::StemFinder , protocols::simple_filters::StemFinderFilterCreator , protocols::simple_filters::SymmetricMotifFilter , protocols::simple_filters::SymmetricMotifFilterCreator , protocols::simple_filters::TaskAwareSASAFilter , protocols::simple_filters::TaskAwareSASAFilterCreator , protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::simple_filters::TaskAwareScoreTypeFilterCreator , protocols::simple_filters::TerminusDistanceFilter , protocols::simple_filters::TerminusDistanceFilterCreator , protocols::simple_filters::TMsAACompFilter , protocols::simple_filters::TMsAACompFilterCreator , protocols::simple_filters::TMsSpanMembraneFilter , protocols::simple_filters::TMsSpanMembraneFilterCreator , protocols::simple_filters::TotalSasaFilter , protocols::simple_filters::TotalSasaFilterCreator , protocols::simple_moves::AddChainMover , protocols::simple_moves::AddChainMoverCreator , protocols::simple_moves::AddJobPairData , protocols::simple_moves::AddJobPairDataCreator , protocols::simple_moves::AddPDBInfoMover , protocols::simple_moves::AddPDBInfoMoverCreator , protocols::simple_moves::AddResidueCouplingConstraint , protocols::simple_moves::AddResidueCouplingConstraintCreator , protocols::simple_moves::AddResidueLabelMoverCreator , protocols::simple_moves::AlignChainMover , protocols::simple_moves::AlignChainMoverCreator , protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockMoveRbJumpMover , protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockMoveRbJumpMoverCreator , protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockRbTrialMover , protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockRbTrialMoverCreator , protocols::simple_moves::BBGaussianMover , protocols::simple_moves::BBGaussianMoverCreator , protocols::simple_moves::bin_transitions::InitializeByBins , protocols::simple_moves::bin_transitions::InitializeByBinsCreator , protocols::simple_moves::bin_transitions::PerturbByBins , protocols::simple_moves::bin_transitions::PerturbByBinsCreator , protocols::simple_moves::ChangeAndResetFoldTreeMover , protocols::simple_moves::ChangeAndResetFoldTreeMoverCreator , protocols::simple_moves::ConcatenatePosesMover , protocols::simple_moves::ConcatenatePosesMoverCreator , protocols::simple_moves::ContingentAcceptMover , protocols::simple_moves::ContingentAcceptMoverCreator , protocols::simple_moves::ConvertRealToVirtualMover , protocols::simple_moves::ConvertRealToVirtualMoverCreator , protocols::simple_moves::ConvertVirtualToRealMover , protocols::simple_moves::ConvertVirtualToRealMoverCreator , protocols::simple_moves::CopyRotamerMover , protocols::simple_moves::CopyRotamerMoverCreator , protocols::simple_moves::CoupledMover , protocols::simple_moves::CoupledMoverCreator , protocols::simple_moves::DeleteChainMover , protocols::simple_moves::DeleteChainMoverCreator , protocols::simple_moves::DeleteChainsMover , protocols::simple_moves::DeleteChainsMoverCreator , protocols::simple_moves::DisulfideInsertionMover , protocols::simple_moves::DisulfideInsertionMoverCreator , protocols::simple_moves::DumpPdb , protocols::simple_moves::DumpPdbCreator , protocols::simple_moves::DumpSingleResidueRotamers , protocols::simple_moves::DumpSingleResidueRotamersCreator , protocols::simple_moves::ExplicitWaterMover , protocols::simple_moves::ExplicitWaterMoverCreator , protocols::simple_moves::FavorSequenceProfile , protocols::simple_moves::FavorSequenceProfileCreator , protocols::simple_moves::FavorSymmetricSequence , protocols::simple_moves::FavorSymmetricSequenceCreator , protocols::simple_moves::FoldTreeFromMotif , protocols::simple_moves::FoldTreeFromMotifCreator , protocols::simple_moves::LoadPDBMover , protocols::simple_moves::LoadPDBMoverCreator , protocols::simple_moves::LoadUnboundRotMover , protocols::simple_moves::LoadUnboundRotMoverCreator , protocols::simple_moves::MembraneTopology , protocols::simple_moves::MembraneTopologyCreator , protocols::simple_moves::ModifyVariantTypeMover , protocols::simple_moves::ModifyVariantTypeMoverCreator , protocols::simple_moves::MutateResidue , protocols::simple_moves::MutateResidueCreator , protocols::simple_moves::PDBReloadMover , protocols::simple_moves::PDBReloadMoverCreator , protocols::simple_moves::PeriodicBoxMover , protocols::simple_moves::PeriodicBoxMoverCreator , protocols::simple_moves::PoseFromPoseResourceMover , protocols::simple_moves::PoseFromPoseResourceMoverCreator , protocols::simple_moves::PSSM2BfactorMover , protocols::simple_moves::PSSM2BfactorMoverCreator , protocols::simple_moves::RandomOmegaFlipMover , protocols::simple_moves::RandomOmegaFlipMoverCreator , protocols::simple_moves::RandomTorsionMover , protocols::simple_moves::RandomTorsionMoverCreator , protocols::simple_moves::RepeatPropagationMover , protocols::simple_moves::RepeatPropagationMoverCreator , protocols::simple_moves::ReportEffectivePKA , protocols::simple_moves::ReportEffectivePKACreator , protocols::simple_moves::ReportXYZ , protocols::simple_moves::ReportXYZCreator , protocols::simple_moves::ResetFoldTree , protocols::simple_moves::ResetFoldTreeCreator , protocols::simple_moves::ResetFullModelInfoMover , protocols::simple_moves::ResetFullModelInfoMoverCreator , protocols::simple_moves::RingConformationMover , protocols::simple_moves::RingConformationMoverCreator , protocols::simple_moves::SaveSequenceToCommentsMover , protocols::simple_moves::SaveSequenceToCommentsMoverCreator , protocols::simple_moves::ScoreMover , protocols::simple_moves::ScoreMoverCreator , protocols::simple_moves::SequenceProfileMover , protocols::simple_moves::SequenceProfileMoverCreator , protocols::simple_moves::SetTorsion , protocols::simple_moves::SetTorsionCreator , protocols::simple_moves::SetupMetalsMover , protocols::simple_moves::SetupMetalsMoverCreator , protocols::simple_moves::ShearMover , protocols::simple_moves::ShearMoverCreator , protocols::simple_moves::ShortBackrubMover , protocols::simple_moves::ShortBackrubMoverCreator , protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover , protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMoverCreator , protocols::simple_moves::sidechain_moves::PerturbChiSidechainMover , protocols::simple_moves::sidechain_moves::PerturbChiSidechainMoverCreator , protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover , protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMoverCreator , protocols::simple_moves::sidechain_moves::SetChiMover , protocols::simple_moves::sidechain_moves::SetChiMoverCreator , protocols::simple_moves::sidechain_moves::SidechainMCMover , protocols::simple_moves::sidechain_moves::SidechainMCMoverCreator , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverCreator , protocols::simple_moves::SimpleThreadingMover , protocols::simple_moves::SimpleThreadingMoverCreator , protocols::simple_moves::SmallMover , protocols::simple_moves::SmallMoverCreator , protocols::simple_moves::StorePoseSnapshot , protocols::simple_moves::StorePoseSnapshotCreator , protocols::simple_moves::StructProfileMover , protocols::simple_moves::StructProfileMoverCreator , protocols::simple_moves::SuperimposeMover , protocols::simple_moves::SuperimposeMoverCreator , protocols::simple_moves::SwitchChainOrderMover , protocols::simple_moves::SwitchChainOrderMoverCreator , protocols::simple_moves::SwitchResidueTypeSetMover , protocols::simple_moves::SwitchResidueTypeSetMoverCreator , protocols::simple_moves::Tumble , protocols::simple_moves::TumbleCreator , protocols::simple_moves::VirtualRootMover , protocols::simple_moves::VirtualRootMoverCreator , protocols::simple_moves::WriteFiltersToPose , protocols::simple_moves::WriteFiltersToPoseCreator , protocols::simple_moves::WriteSSEMover , protocols::simple_moves::WriteSSEMoverCreator , protocols::simple_task_operations::DockingNoRepack1 , protocols::simple_task_operations::DockingNoRepack2 , protocols::simple_task_operations::InterfaceTaskOperation , protocols::simple_task_operations::RestrictToInterface , protocols::simple_task_operations::RestrictToInterfaceCreator , protocols::simple_task_operations::RestrictToLoops , protocols::simple_task_operations::RestrictToLoopsAndNeighbors , protocols::simple_task_operations::RestrictToLoopsAndNeighborsCreator , protocols::simple_task_operations::RestrictToLoopsCreator , protocols::splice::AlignEndsMover , protocols::splice::AlignEndsMoverCreator , protocols::splice::DesignInterfacesOperation , protocols::splice::DesignInterfacesOperationCreator , protocols::splice::FindEndpointsOperation , protocols::splice::FindEndpointsOperationCreator , protocols::splice::RBInMover , protocols::splice::RBInMoverCreator , protocols::splice::RBOutMover , protocols::splice::RBOutMoverCreator , protocols::splice::RotLibOut , protocols::splice::RotLibOutCreator , protocols::splice::SampleRotamersFromPDB , protocols::splice::SampleRotamersFromPDBCreator , protocols::splice::Splice , protocols::splice::SpliceCreator , protocols::splice::SpliceIn , protocols::splice::SpliceInAntibody , protocols::splice::SpliceInAntibodyCreator , protocols::splice::SpliceInCreator , protocols::splice::SpliceInTail , protocols::splice::SpliceInTailCreator , protocols::splice::SpliceOut , protocols::splice::SpliceOutAntibody , protocols::splice::SpliceOutAntibodyCreator , protocols::splice::SpliceOutCreator , protocols::splice::SpliceOutTail , protocols::splice::SpliceOutTailCreator , protocols::splice::TailSegmentMover , protocols::splice::TailSegmentMoverCreator , protocols::stepwise::monte_carlo::mover::AddMover , protocols::stepwise::monte_carlo::mover::AddMoverCreator , protocols::stepwise::monte_carlo::mover::DeleteMover , protocols::stepwise::monte_carlo::mover::DeleteMoverCreator , protocols::stepwise::monte_carlo::mover::FromScratchMover , protocols::stepwise::monte_carlo::mover::FromScratchMoverCreator , protocols::stepwise::monte_carlo::mover::ResampleMover , protocols::stepwise::monte_carlo::mover::ResampleMoverCreator , protocols::struct_fragment::StructFragmentMover , protocols::struct_fragment::StructFragmentMoverCreator , protocols::surface_docking::SurfaceVectorLoader , protocols::surface_docking::SurfaceVectorLoaderCreator , protocols::switches::GraftSwitchMover , protocols::switches::GraftSwitchMoverCreator , protocols::symmetric_docking::membrane::MPSymDockMover , protocols::symmetric_docking::membrane::MPSymDockMoverCreator , protocols::symmetric_docking::SymDockProtocol , protocols::symmetric_docking::SymDockProtocolCreator , protocols::symmetric_docking::SymFoldandDockMoveRbJumpMover , protocols::symmetric_docking::SymFoldandDockMoveRbJumpMoverCreator , protocols::symmetric_docking::SymFoldandDockRbTrialMover , protocols::symmetric_docking::SymFoldandDockRbTrialMoverCreator , protocols::symmetric_docking::SymFoldandDockSlideTrialMover , protocols::symmetric_docking::SymFoldandDockSlideTrialMoverCreator , protocols::symmetry::DetectSymmetry , protocols::symmetry::DetectSymmetryMoverCreator , protocols::symmetry::ExtractAsymmetricPoseMover , protocols::symmetry::ExtractAsymmetricPoseMoverCreator , protocols::symmetry::ExtractAsymmetricUnitMover , protocols::symmetry::ExtractAsymmetricUnitMoverCreator , protocols::symmetry::SetupForSequenceSymmetryMover , protocols::symmetry::SetupForSequenceSymmetryMoverCreator , protocols::symmetry::SetupForSymmetryMover , protocols::symmetry::SetupForSymmetryMoverCreator , protocols::symmetry::SetupNCSMover , protocols::symmetry::SetupNCSMoverCreator , protocols::task_operations::AlignedThreadOperation , protocols::task_operations::AlignedThreadOperationCreator , protocols::task_operations::ConservativeDesignOperation , protocols::task_operations::ConservativeDesignOperationCreator , protocols::task_operations::CrystalContactsOperation , protocols::task_operations::CrystalContactsOperationCreator , protocols::task_operations::DatabaseThread , protocols::task_operations::DatabaseThreadCreator , protocols::task_operations::DesignAroundOperation , protocols::task_operations::DesignAroundOperationCreator , protocols::task_operations::DsspDesignOperation , protocols::task_operations::DsspDesignOperationCreator , protocols::task_operations::ImportUnboundRotamersOperation , protocols::task_operations::ImportUnboundRotamersOperationCreator , protocols::task_operations::InteractingRotamerExplosion , protocols::task_operations::InteractingRotamerExplosionCreator , protocols::task_operations::JointSequenceOperation , protocols::task_operations::JointSequenceOperationCreator , protocols::task_operations::LimitAromaChi2Operation , protocols::task_operations::LimitAromaChi2OperationCreator , protocols::task_operations::LinkResidues , protocols::task_operations::LinkResiduesCreator , protocols::task_operations::ModifyAnnealer , protocols::task_operations::ModifyAnnealerCreator , protocols::task_operations::MutationSetDesignOperation , protocols::task_operations::pHVariantTaskOperation , protocols::task_operations::pHVariantTaskOperationCreator , protocols::task_operations::PreventChainFromRepackingOperation , protocols::task_operations::PreventChainFromRepackingOperationCreator , protocols::task_operations::PreventResiduesFromRepackingOperation , protocols::task_operations::PreventResiduesFromRepackingOperationCreator , protocols::task_operations::ProteinCore , protocols::task_operations::ProteinCoreFilterCreator , protocols::task_operations::ProteinInterfaceDesignOperation , protocols::task_operations::ProteinInterfaceDesignOperationCreator , protocols::task_operations::PruneBuriedUnsatsOperation , protocols::task_operations::PruneBuriedUnsatsOperationCreator , protocols::task_operations::ReadResfileFromDB , protocols::task_operations::ReadResfileFromDBCreator , protocols::task_operations::ResfileCommandOperation , protocols::task_operations::ResfileCommandOperationCreator , protocols::task_operations::ResidueProbDesignOperation , protocols::task_operations::ResidueProbDesignOperationCreator , protocols::task_operations::RestrictByCalculatorsOperation , protocols::task_operations::RestrictByCalculatorsOperationCreator , protocols::task_operations::RestrictChainToRepackingOperation , protocols::task_operations::RestrictChainToRepackingOperationCreator , protocols::task_operations::RestrictConservedLowDdgOperation , protocols::task_operations::RestrictConservedLowDdgOperationCreator , protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation , protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperationCreator , protocols::task_operations::RestrictIdentitiesOperation , protocols::task_operations::RestrictIdentitiesOperationCreator , protocols::task_operations::RestrictInterGroupVectorOperation , protocols::task_operations::RestrictInterGroupVectorOperationCreator , protocols::task_operations::RestrictNativeResiduesOperation , protocols::task_operations::RestrictNativeResiduesOperationCreator , protocols::task_operations::RestrictNonSurfaceToRepackingOperation , protocols::task_operations::RestrictNonSurfaceToRepackingOperationCreator , protocols::task_operations::RestrictResiduesToRepackingOperation , protocols::task_operations::RestrictResiduesToRepackingOperationCreator , protocols::task_operations::RestrictToAlignedSegmentsOperation , protocols::task_operations::RestrictToAlignedSegmentsOperationCreator , protocols::task_operations::RestrictToCDRH3Loop , protocols::task_operations::RestrictToCDRH3LoopCreator , protocols::task_operations::RestrictToInterfaceOperation , protocols::task_operations::RestrictToInterfaceOperationCreator , protocols::task_operations::RestrictToInterfaceVectorOperation , protocols::task_operations::RestrictToInterfaceVectorOperationCreator , protocols::task_operations::RestrictToMoveMapChiOperation , protocols::task_operations::RestrictToNeighborhoodOperation , protocols::task_operations::RestrictToNeighborhoodOperationCreator , protocols::task_operations::RestrictToTerminiOperation , protocols::task_operations::RestrictToTerminiOperationCreator , protocols::task_operations::RetrieveStoredTaskOperation , protocols::task_operations::RetrieveStoredTaskOperationCreator , protocols::task_operations::SelectByDeltaScoreOperation , protocols::task_operations::SelectByDeltaScoreOperationCreator , protocols::task_operations::SelectByDensityFitOperation , protocols::task_operations::SelectByDensityFitOperationCreator , protocols::task_operations::SelectBySASAOperation , protocols::task_operations::SelectBySASAOperationCreator , protocols::task_operations::SelectResiduesWithinChainOperation , protocols::task_operations::SelectResiduesWithinChainOperationCreator , protocols::task_operations::SeqprofConsensusOperation , protocols::task_operations::SeqprofConsensusOperationCreator , protocols::task_operations::SequenceMotifTaskOperation , protocols::task_operations::SequenceMotifTaskOperationCreator , protocols::task_operations::SetIGTypeOperation , protocols::task_operations::SetIGTypeOperationCreator , protocols::task_operations::StoreCombinedStoredTasksMover , protocols::task_operations::StoreCombinedStoredTasksMoverCreator , protocols::task_operations::StoreCompoundTaskMover , protocols::task_operations::StoreCompoundTaskMoverCreator , protocols::task_operations::StoreTaskMover , protocols::task_operations::StoreTaskMoverCreator , protocols::task_operations::ThreadSequenceOperation , protocols::task_operations::ThreadSequenceOperationCreator , protocols::testing::BenchmarkBuildRotamersMover , protocols::testing::BenchmarkBuildRotamersMoverCreator , protocols::vardist_solaccess::LoadVarSolDistSasaCalculatorMover , protocols::vardist_solaccess::LoadVarSolDistSasaCalculatorMoverCreator
• provide_xml_schema_attributes() : core::pack::task::residue_selector::ClashBasedShellSelector
• provide_xsd_copying_information() : core::conformation::parametric::RealValuedParameter
• provide_xsd_grid_sampling_information() : core::conformation::parametric::RealValuedParameter
• provide_xsd_information() : core::conformation::parametric::BooleanValuedParameter , core::conformation::parametric::Parameter , core::conformation::parametric::RealValuedParameter , core::conformation::parametric::RealVectorValuedParameter , core::conformation::parametric::SizeValuedParameter , core::conformation::parametric::SizeVectorValuedParameter , protocols::helical_bundle::parameters::OmegaBundleParameter
• provide_xsd_perturbation_information() : core::conformation::parametric::RealValuedParameter
• provide_xsd_pitch_copying_information() : protocols::helical_bundle::parameters::OmegaBundleParameter
• provide_xsd_setting_information() : core::conformation::parametric::RealValuedParameter
• prsa_feature() : core::scoring::methods::ProQ_Energy
• prune_donor_acceptor_groups_lacking_hbonds_to_packable() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode
• prune_extra_atoms() : protocols::generalized_kinematic_closure::GeneralizedKIC
• prune_small_bins() : core::scoring::motif::XformScore
• prune_symmetric_disulfides() : protocols::denovo_design::DisulfidizeMover
• prune_voxels_for_fixed_residues() : core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid
• PruneBuriedUnsats_RotamerSetsOperation() : protocols::task_operations::PruneBuriedUnsats_RotamerSetsOperation
• PruneBuriedUnsatsOperation() : protocols::task_operations::PruneBuriedUnsatsOperation
• PruneBuriedUnsatsOperationCreator() : protocols::task_operations::PruneBuriedUnsatsOperationCreator
• prv_eqxyz() : protocols::md::MDBase
• PseudoBond() : core::conformation::PseudoBond
• PseudoBondCollection() : core::conformation::PseudoBondCollection
• pseudobonds() : core::conformation::Residue
• PseudocontactShiftEnergyController() : protocols::topology_broker::PseudocontactShiftEnergyController
• PseudocontactShiftEnergyController_Ts1() : protocols::topology_broker::PseudocontactShiftEnergyController_Ts1
• PseudocontactShiftEnergyController_Ts2() : protocols::topology_broker::PseudocontactShiftEnergyController_Ts2
• PseudocontactShiftEnergyController_Ts3() : protocols::topology_broker::PseudocontactShiftEnergyController_Ts3
• PseudocontactShiftEnergyController_Ts4() : protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• pseudorotation() : protocols::dna::DNABase
• psi() : core::fragment::picking_old::vall::VallResidue , core::io::raw_data::DecoyStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::pose::Pose , core::scoring::motif::Xfres , protocols::backbone_moves::local_backbone_mover::FreePeptide , protocols::backbone_moves::local_backbone_mover::Residue , protocols::denovo_design::components::ResidueDihedrals , protocols::frag_picker::PhiPsiTalosIO
• Psi() : protocols::frag_picker::scores::Psi
• psi() : protocols::frag_picker::VallResidue , protocols::frags::RMSVallData , protocols::frags::VallData , protocols::kinematic_closure::ClosureProblem , protocols::loophash::BackboneSegment , protocols::match::upstream::ProteinBackboneBuildPoint , protocols::optimize_weights::PNatRotOptEPositionData , protocols::splice::BBDofs , protocols::stepwise::modeler::protein::MainChainTorsionSet
• psi_index() : core::scoring::OmegaTether
• psi_max() : core::sequence::ABEGO
• psi_min() : core::sequence::ABEGO
• PsiPredInterface() : core::io::external::PsiPredInterface
• PsiPredResult() : core::io::external::PsiPredResult
• PSSM2BfactorMover() : protocols::simple_moves::PSSM2BfactorMover
• pssm_() : protocols::protein_interface_design::ReportPSSMDifferences
• pssm_energy_at_frame_seqpos() : core::scoring::methods::NMerPSSMEnergy
• PSSMOptEPositionData() : protocols::optimize_weights::PSSMOptEPositionData
• ptask() : protocols::multistate_design::PackingState
• public_array_to_private_data() : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• pucker() : protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler
• pucker_state() : protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler
• pull_coords() : core::scoring::epr_deer::DEERIO
• pull_out_global_block() : protocols::helical_bundle_predict::HBPHelixAssignments
• pull_out_helix_blocks() : protocols::helical_bundle_predict::HBPHelixAssignments
• pulldomain() : protocols::hybridization::DDomainParse
• push() : protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering > , protocols::frag_picker::quota::ABEGO_SS_Pool , protocols::frag_picker::quota::QuotaPool , protocols::frag_picker::quota::SecondaryStructurePool , protocols::ligand_docking::ga_ligand_dock::OutputStructureStore , protocols::loop_grower::LoopComparator , protocols::loop_grower::LoopPartialSolutionStore
• push_back() : core::conformation::PseudoBondCollection , core::id::SequenceMapping , core::io::silent::SilentFileData , core::pack::task::TaskFactory , core::pose::copydofs::CopyDofsInfo , core::scoring::dssp::StrandPairingSet , core::scoring::motif::MotifHits , core::scoring::rna::RNA_Motifs , protocols::cluster::Cluster , protocols::cluster::GatherPosesMover , protocols::fldsgn::topology::BetaAlphaBetaMotifSet , protocols::fldsgn::topology::HelixPairingSet , protocols::fldsgn::topology::HSSTripletSet , protocols::fldsgn::topology::SheetSet , protocols::fldsgn::topology::StrandPairingSet , protocols::frag_picker::VallChunk , protocols::frag_picker::VallProvider , protocols::jd2::JobsContainer , protocols::loops::Loops , protocols::loops::LoopsFileData , protocols::moves::MonteCarlo , protocols::peptide_deriver::PeptideDeriverOutputterContainer , protocols::rna::denovo::coarse::SourcePositions , protocols::splice::ResidueBBDofs , protocols::toolbox::DecoySetEvaluation , protocols::wum::WorkUnitQueue
• push_back_and_finalize() : protocols::fldsgn::topology::StrandPairingSet
• push_back_backbone() : protocols::loop_grower::LoopPartialSolution
• push_back_CA_xyz() : protocols::toolbox::DecoySetEvaluation
• push_back_CA_xyz_from_silent_file() : protocols::toolbox::DecoySetEvaluation
• push_back_raw() : core::scoring::motif::MotifHits
• push_back_restorsions() : protocols::loop_grower::LoopPartialSolution
• push_back_rotamer() : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• push_back_rotamers() : core::pack::rotamer_set::RotamerSet_
• push_back_sheet() : protocols::loop_grower::LoopPartialSolution
• push_chain_residue_indices() : protocols::peptide_deriver::PeptideDeriverFilter
• push_front() : protocols::cluster::Cluster , protocols::wum::WorkUnitQueue
• push_job_to_front_of_queue() : protocols::jd3::job_distributors::JobExtractor
• push_passport() : core::conformation::Conformation , protocols::environment::ClientMover , protocols::environment::ProtectedConformation
• push_the_limits() : protocols::frag_picker::quota::QuotaSelector
• push_the_limits_to_the_winner() : protocols::frag_picker::quota::QuotaSelector
• put_constraints_on_base_step() : core::import_pose::RNA_HelixAssembler
• put_in_cutpoints() : protocols::stepwise::monte_carlo::mover::TransientCutpointHandler
• put_intra_into_total() : core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::hbonds::HBondOptions , core::scoring::methods::EnergyMethodOptions
• put_jump_stubs_intra_residue() : core::kinematics::FoldTree
• put_lock_on_silent_file() : protocols::rna::setup::RNA_CSA_JobDistributor
• PValuedFragmentScoreManager() : protocols::frag_picker::scores::PValuedFragmentScoreManager
• PyEnergyMethodRegistrator() : core::scoring::methods::PyEnergyMethodRegistrator
• pymol() : protocols::moves::PyMOLObserver
• pymol_color_change() : protocols::docking::DockingLowRes
• pymol_name() : protocols::moves::PyMOLMover
• PyMOLMover() : protocols::moves::PyMOLMover
• PyMOLObserver() : protocols::moves::PyMOLObserver
• pyrimidine_flip_trial() : protocols::rna::movers::ErraserMinimizerMover
• pythag() : core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl