Here is a list of all class members with links to the classes they belong to:

- c -

• C() : core::io::CrystInfo , core::scoring::BB_Pos , core::scoring::electron_density::OneGaussianScattering , core::scoring::fiber_diffraction::OneGaussianScattering
• c : core::scoring::saxs::FastSAXSEnergy
• C() : protocols::cryst::Spacegroup , protocols::fldsgn::topology::BB_Pos , protocols::indexed_structure_store::ResidueOrientEntry
• c : protocols::sic_dock::Vec3
• c0() : core::scoring::FACTSRsdTypeInfo
• C0_ : core::scoring::constraints::BigBinConstraint , core::scoring::etable::coulomb::Coulomb
• c0_ : core::scoring::FACTSRsdTypeInfo
• c1() : core::scoring::FACTSRsdTypeInfo
• C1_ : core::scoring::constraints::BigBinConstraint , core::scoring::etable::coulomb::Coulomb
• c1_ : core::scoring::FACTSRsdTypeInfo
• c1prime_atom_index() : core::chemical::rna::RNA_Info
• c1prime_index_ : core::chemical::rna::RNA_Info
• c2() : core::scoring::FACTSRsdTypeInfo
• c21 : protocols::normalmode::ContactStruct
• C2_ : core::scoring::etable::coulomb::Coulomb
• c2_ : core::scoring::FACTSRsdTypeInfo
• c2f : core::scoring::electron_density::ElectronDensity , core::scoring::electron_density_atomwise::ElectronDensityAtomwise , protocols::cryst::Spacegroup , protocols::cryst::WallpaperGroup
• c2f_ : protocols::cryst::Spacegroup , protocols::cryst::WallpaperGroup
• c2i : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• c2i_ : core::scoring::PoissonBoltzmannPotential
• c2prime_atom_index() : core::chemical::rna::RNA_Info
• c2prime_c3prime_bond_length_ : core::scoring::dna::DNATorsionPotential
• c2prime_c3prime_dist_harm_func_ : core::scoring::dna::DNATorsionPotential
• c2prime_c3prime_sd_ : core::scoring::dna::DNATorsionPotential
• c2prime_index_ : core::chemical::rna::RNA_Info
• c3() : core::scoring::FACTSRsdTypeInfo
• c3_ : core::scoring::FACTSRsdTypeInfo
• c3prime_atom_index() : core::chemical::rna::RNA_Info
• c3prime_c2prime_c1prime_angle_harm_func_ : core::scoring::dna::DNATorsionPotential
• c3prime_c2prime_c1prime_bond_angle_ : core::scoring::dna::DNATorsionPotential
• c3prime_index_ : core::chemical::rna::RNA_Info
• c4prime_atom_index() : core::chemical::rna::RNA_Info
• c4prime_c3prime_c2prime_angle_harm_func_ : core::scoring::dna::DNATorsionPotential
• c4prime_c3prime_c2prime_bond_angle_ : core::scoring::dna::DNATorsionPotential
• c4prime_index_ : core::chemical::rna::RNA_Info
• c4prime_o4prime_c1prime_angle_harm_func_ : core::scoring::rna::RNA_SugarCloseEnergy
• c4prime_o4prime_c1prime_angle_north_ : core::scoring::rna::RNA_SugarCloseEnergy
• c4prime_o4prime_c1prime_angle_south_ : core::scoring::rna::RNA_SugarCloseEnergy
• c4prime_o4prime_c1prime_bond_angle_ : core::scoring::rna::RNA_SugarCloseEnergy
• c5prime_atom_index() : core::chemical::rna::RNA_Info
• c5prime_index_ : core::chemical::rna::RNA_Info
• C_ : core::io::CrystInfo , core::scoring::BB_Pos
• c_ : core::scoring::carbohydrates::CHIEnergyFunction , core::scoring::electron_density::KromerMann , core::scoring::fiber_diffraction::FiberDiffraction , core::scoring::fiber_diffraction::FiberDiffractionEnergy , core::scoring::fiber_diffraction::FiberDiffractionEnergyDens , core::scoring::fiber_diffraction::KromerMann
• C_ : core::scoring::func::KarplusFunc , core::scoring::func::PeriodicFunc
• c_ : protocols::cryst::Spacegroup
• C_ : protocols::fldsgn::topology::BB_Pos , protocols::frag_picker::JCouplingIO , protocols::frag_picker::scores::JCoupling
• c_alpha_index() : core::scoring::disulfides::DisulfideAtomIndices
• c_alpha_index_ : core::scoring::disulfides::DisulfideAtomIndices
• c_anchor() : protocols::sic_dock::Rose
• C_atom_id() : protocols::match::upstream::UpstreamResTypeGeometry
• C_atom_id_ : core::scoring::constraints::BackboneStubLinearConstraint , protocols::match::upstream::UpstreamResTypeGeometry
• c_axis_ : protocols::docking::EllipsoidalRandomizationMover
• c_beta_index() : core::scoring::disulfides::DisulfideAtomIndices
• c_beta_index_ : core::scoring::disulfides::DisulfideAtomIndices
• C_bins : core::scoring::dna::DirectReadoutPotential
• c_clusters_ : protocols::pockets::PocketGrid
• c_cyd_seqpos_ : protocols::simple_moves::DisulfideInsertionMover
• c_flex : protocols::fold_from_loops::utils::NubSegment
• C_gbest_ : core::optimization::ParticleSwarmMinimizer
• c_grid_ : protocols::pockets::PocketGrid
• C_index_ : core::scoring::BB_Pos , protocols::fldsgn::topology::BB_Pos
• C_inertia_end_ : core::optimization::ParticleSwarmMinimizer
• C_inertia_start_ : core::optimization::ParticleSwarmMinimizer
• C_lbest_ : core::optimization::ParticleSwarmMinimizer
• c_n() : protocols::kinematic_closure::ClosureProblem
• c_n_bond() : protocols::backbone_moves::local_backbone_mover::FreePeptide , protocols::backbone_moves::local_backbone_mover::Residue
• c_n_bond_ : protocols::backbone_moves::local_backbone_mover::Residue
• c_n_ca() : protocols::kinematic_closure::ClosureProblem
• c_n_ca_angle() : protocols::backbone_moves::local_backbone_mover::FreePeptide , protocols::backbone_moves::local_backbone_mover::Residue
• c_n_ca_angle_ : protocols::backbone_moves::local_backbone_mover::Residue
• C_N_target_ : core::scoring::constraints::BackboneStubLinearConstraint
• C_pbest_ : core::optimization::ParticleSwarmMinimizer
• c_pdb_ : protocols::constel::ChainTerm
• c_per_entry : protocols::indexed_structure_store::search::StructureData , protocols::indexed_structure_store::search::StructurePairQuery , protocols::indexed_structure_store::search::StructureSingleQuery
• C_pi_sp2 : core::scoring::orbitals::OrbitalsStatistics
• C_pos() : protocols::match::upstream::ProteinBackboneBuildPoint
• C_pos_ : protocols::match::upstream::ProteinBackboneBuildPoint
• c_ps_ : protocols::constel::ChainTerm
• c_segment() : protocols::legacy_sewing::SegmentGraph
• c_str : protocols::environment::claims::DOFElement
• c_str_ : protocols::environment::claims::JumpClaim , protocols::environment::claims::TorsionClaim , protocols::environment::claims::XYZClaim
• C_target_ : core::scoring::constraints::BackboneStubLinearConstraint
• c_ter_stem_ : protocols::antibody_legacy::CDRH3Modeler
• c_term_pose : protocols::pose_creation::MakeJunctionsMover::Design
• c_term_stack : protocols::pose_creation::MakeJunctionsMover::Design
• c_terminal_constraint_strength() : protocols::aa_composition::AddHelixSequenceConstraintsMover
• c_terminal_constraint_strength_ : protocols::aa_composition::AddHelixSequenceConstraintsMover
• c_terminal_neighbor_ : protocols::sewing::data_storage::SmartSegment
• c_terminal_parent_ : protocols::sewing::data_storage::SmartSegment
• c_terminal_segment_ : protocols::sewing::data_storage::SmartAssembly
• c_terminal_segments_ : protocols::sewing::data_storage::SmartAssembly
• c_terminus_size() : protocols::aa_composition::AddHelixSequenceConstraintsMover
• c_terminus_size_ : protocols::aa_composition::AddHelixSequenceConstraintsMover
• c_xyz() : protocols::backbone_moves::local_backbone_mover::FreePeptide , protocols::backbone_moves::local_backbone_mover::Residue
• c_xyz_ : protocols::backbone_moves::local_backbone_mover::Residue
• CA() : core::scoring::BB_Pos , protocols::fldsgn::topology::BB_Pos , protocols::indexed_structure_store::ResidueOrientEntry , protocols::ub_e2c::ubi_e2c_modeler
• CA1_ : core::scoring::constraints::BigBinConstraint
• CA2_ : core::scoring::constraints::BigBinConstraint
• CA_ : core::scoring::BB_Pos , protocols::fldsgn::topology::BB_Pos
• CA_atom_id() : protocols::match::upstream::UpstreamResTypeGeometry
• CA_atom_id_ : core::scoring::constraints::BackboneStubLinearConstraint , protocols::match::upstream::UpstreamResTypeGeometry
• ca_c() : protocols::kinematic_closure::ClosureProblem
• ca_c_bond() : protocols::backbone_moves::local_backbone_mover::FreePeptide , protocols::backbone_moves::local_backbone_mover::Residue
• ca_c_bond_ : protocols::backbone_moves::local_backbone_mover::Residue
• ca_c_n() : protocols::kinematic_closure::ClosureProblem
• ca_c_n_angle() : protocols::backbone_moves::local_backbone_mover::FreePeptide , protocols::backbone_moves::local_backbone_mover::Residue
• ca_c_n_angle_ : protocols::backbone_moves::local_backbone_mover::Residue
• ca_ca_distance_ : protocols::protein_interface_design::movers::LoopFinder
• ca_cav_dist_sd_ : core::scoring::methods::ProClosureEnergy
• ca_cb_orient() : protocols::fldsgn::topology::Sheet
• ca_cb_orients() : protocols::fldsgn::topology::Sheet
• ca_cb_orients_ : protocols::fldsgn::topology::Sheet
• ca_coord_ : protocols::membrane::MPLipidAccessibility
• ca_cprev_n_h_interres_improper_params() : core::scoring::methods::ResidueCartBondedParameters
• ca_cprev_n_h_interres_improper_params_ : core::scoring::methods::ResidueCartBondedParameters
• ca_cst_ : protocols::seeded_abinitio::CAcstGenerator
• ca_dist_squared_ : protocols::frag_picker::nonlocal::NonlocalFrags
• CA_index_ : core::scoring::BB_Pos , protocols::fldsgn::topology::BB_Pos
• CA_MASK : core::scoring::electron_density::ElectronDensity
• ca_nnext_c_o_interres_improper_params() : core::scoring::methods::ResidueCartBondedParameters
• ca_nnext_c_o_interres_improper_params_ : core::scoring::methods::ResidueCartBondedParameters
• CA_only() : protocols::constraint_movers::AddConstraintsToCurrentConformationMover
• ca_only : protocols::fold_from_loops::constraint_generator::ConstraintConditions
• CA_only() : protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter
• ca_only_ : protocols::constraint_generator::AtomPairConstraintGenerator , protocols::constraint_generator::CoordinateConstraintGenerator
• CA_only_ : protocols::constraint_movers::AddConstraintsToCurrentConformationMover , protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter , protocols::protein_interface_design::filters::RmsdFilter , protocols::simple_moves::SuperimposeMover
• CA_pos() : protocols::match::upstream::ProteinBackboneBuildPoint
• CA_pos_ : protocols::match::upstream::ProteinBackboneBuildPoint
• CA_rmsd() : core::io::silent::BinarySilentStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RNA_SilentStruct
• CA_search_scores_and_tensors() : protocols::scoring::methods::pcs2::PcsEnergy
• CA_search_scores_and_tensors_with_svd() : protocols::scoring::methods::pcs2::PcsEnergy
• CA_target_ : core::scoring::constraints::BackboneStubLinearConstraint
• ca_xyz() : protocols::backbone_moves::local_backbone_mover::FreePeptide , protocols::backbone_moves::local_backbone_mover::Residue
• ca_xyz_ : protocols::backbone_moves::local_backbone_mover::Residue
• cacb_dihedral_tolerance_ : protocols::fldsgn::SheetConstraintGenerator
• CaCbCb_Angle_Func() : core::scoring::disulfides::CaCbCb_Angle_Func
• cacbcb_angle_func_ : core::scoring::disulfides::CentroidDisulfidePotential
• CaCbCb_angle_scores_ : core::scoring::disulfides::CaCbCb_Angle_Func
• CaCbCbCa_Dihedral_Func() : core::scoring::disulfides::CaCbCbCa_Dihedral_Func
• cacbcbca_dihedral_func_ : core::scoring::disulfides::CentroidDisulfidePotential
• CaCbCbCa_dihedral_scores_ : core::scoring::disulfides::CaCbCbCa_Dihedral_Func
• cache() : core::fragment::CacheWrapper< T, XCacheUnit > , core::fragment::Frame
• cache_ : core::chemical::ResidueTypeSet , core::fragment::Frame , core::pack::rotamers::SingleResidueRotamerLibraryFactory , protocols::frag_picker::scores::ProfileScoreL1 , protocols::frag_picker::scores::ProfileScoreStructL1 , protocols::frag_picker::scores::SecondarySimilarity , protocols::frag_picker::scores::TalosSSSimilarity
• cache_all_types_with_variants_aa() : core::chemical::ResidueTypeSetCache
• cache_all_types_with_variants_residuetypecops() : core::chemical::ResidueTypeSetCache
• cache_fragments() : protocols::forge::components::VarLengthBuild
• cache_fragments_ : protocols::forge::components::VarLengthBuild
• cache_limit() : protocols::canonical_sampling::TrajectoryRecorder
• cache_limit_ : protocols::canonical_sampling::TrajectoryRecorder , protocols::trajectory::DbTrajectoryWriter
• cache_mutex : protocols::indexed_structure_store::FragmentStoreManager , protocols::indexed_structure_store::StructureStoreManager
• cache_object() : core::chemical::ResidueTypeSet
• cache_pose() : protocols::frag_picker::VallProvider
• cache_prefix_ : core::simple_metrics::metrics::ResidueSummaryMetric , protocols::simple_filters::SimpleMetricFilter
• cache_profile() : protocols::frag_picker::VallProvider
• cache_remarks_ : core::io::silent::SilentStruct
• cache_resfile() : core::pack::task::operation::ReadResfile
• cache_selection_ : core::select::residue_selector::LayerSelector , core::select::util::SelectResiduesByLayer
• cache_size_ : protocols::features::ReportToDB
• cache_suffix_ : core::simple_metrics::metrics::ResidueSummaryMetric , protocols::simple_filters::SimpleMetricFilter
• cache_tag() : core::chemical::rotamers::BasicRotamerLibrarySpecification , core::chemical::rotamers::CenrotRotamerLibrarySpecification , core::chemical::rotamers::DunbrackRotamerLibrarySpecification , core::chemical::rotamers::NCAARotamerLibrarySpecification , core::chemical::rotamers::PDBRotamerLibrarySpecification , core::chemical::rotamers::RotamerLibrarySpecification
• cache_task() : protocols::evolution::NucleotideMutation , protocols::protein_interface_design::movers::RandomMutation
• cache_task_ : protocols::evolution::NucleotideMutation , protocols::protein_interface_design::movers::RandomMutation
• cache_up_to_date_ : core::chemical::ResidueTypeSetCache
• CacheableAtomID_MapVector() : core::id::CacheableAtomID_MapVector
• CacheableData : core::scoring::ResPairMinimizationData , core::scoring::ResSingleMinimizationData
• CacheableDataCOP : core::scoring::constraints::CstMinimizationData , core::scoring::ResidueNblistData , core::scoring::ResiduePairNeighborList , core::scoring::ResPairMinimizationData , core::scoring::ResSingleMinimizationData
• CacheableDataOP : core::scoring::constraints::CstMinimizationData , core::scoring::disulfides::DisulfMinData , core::scoring::ResidueNblistData , core::scoring::ResiduePairNeighborList , core::scoring::ResPairMinimizationData , core::scoring::ResSingleMinimizationData , protocols::denovo_design::components::StructureData
• CacheableObserver() : core::pose::datacache::CacheableObserver
• CacheablePoseRawPtr() : core::pose::datacache::CacheablePoseRawPtr
• CacheableResidueTypeSets() : core::chemical::CacheableResidueTypeSets
• cached_ : protocols::rosetta_scripts::MultiplePoseMover
• cached_aa_variants_map_ : core::chemical::ResidueTypeSetCache
• cached_atom_derivs_ : core::scoring::MultipoleElecPotential
• cached_calculate() : core::simple_metrics::CompositeRealMetric , core::simple_metrics::CompositeStringMetric , core::simple_metrics::PerResidueRealMetric , core::simple_metrics::PerResidueStringMetric , core::simple_metrics::RealMetric , core::simple_metrics::StringMetric
• cached_data : protocols::environment::EnvClaimBroker::BrokerResult
• cached_lookup_result_ : protocols::indexed_structure_store::filters::FragmentLookupFilter
• cached_pose_ : protocols::frag_picker::VallProvider
• cached_pose_by_state_ : core::scoring::methods::PoissonBoltzmannEnergy
• cached_pose_id_ : protocols::frag_picker::VallProvider
• cached_profile_ : protocols::frag_picker::VallProvider
• cached_profile_id_ : protocols::frag_picker::VallProvider
• cached_restype_variants_map_ : core::chemical::ResidueTypeSetCache
• cached_score() : protocols::frag_picker::scores::ABEGO_SS_Score , protocols::frag_picker::scores::AmbigCSScore , protocols::frag_picker::scores::AtomPairConstraintsScore , protocols::frag_picker::scores::CachingScoringMethod , protocols::frag_picker::scores::CSScore , protocols::frag_picker::scores::DihedralConstraintsScore , protocols::frag_picker::scores::DisulfideDistance , protocols::frag_picker::scores::FragmentCrmsd , protocols::frag_picker::scores::FragmentCrmsdResDepth , protocols::frag_picker::scores::FragmentDME , protocols::frag_picker::scores::GunnCostScore , protocols::frag_picker::scores::HydrophobicityProfileSimilarity , protocols::frag_picker::scores::HydrophobicitySimilarity , protocols::frag_picker::scores::InterbondAngleScore , protocols::frag_picker::scores::JCoupling , protocols::frag_picker::scores::LAMBEGO_Similarity , protocols::frag_picker::scores::MidPhiOut , protocols::frag_picker::scores::MidPsiOut , protocols::frag_picker::scores::PartialSecondarySimilarity , protocols::frag_picker::scores::PCS_FragDistance , protocols::frag_picker::scores::Phi , protocols::frag_picker::scores::PhiPsiRmsd , protocols::frag_picker::scores::PhiPsiSquareWell , protocols::frag_picker::scores::ProfileScore , protocols::frag_picker::scores::ProfileScoreBlosum62 , protocols::frag_picker::scores::ProfileScoreDistWeight , protocols::frag_picker::scores::ProfileScoreL1 , protocols::frag_picker::scores::ProfileScoreStructL1 , protocols::frag_picker::scores::ProfileScoreSubMatrix , protocols::frag_picker::scores::Psi , protocols::frag_picker::scores::RamaScore , protocols::frag_picker::scores::RDCScore , protocols::frag_picker::scores::SecondarySimilarity , protocols::frag_picker::scores::SolventAccessibility , protocols::frag_picker::scores::TalosSSSimilarity , protocols::frag_picker::scores::TorsionBinSimilarity
• cached_score_ : protocols::moves::SimulatedTempering
• cached_scores_id_ : protocols::frag_picker::scores::ABEGO_SS_Score , protocols::frag_picker::scores::AmbigCSScore , protocols::frag_picker::scores::CSScore , protocols::frag_picker::scores::DisulfideDistance , protocols::frag_picker::scores::FragmentAllAtomCrmsd , protocols::frag_picker::scores::FragmentChunkCrms , protocols::frag_picker::scores::FragmentCrmsd , protocols::frag_picker::scores::FragmentCrmsdResDepth , protocols::frag_picker::scores::FragmentDME , protocols::frag_picker::scores::HydrophobicityProfileSimilarity , protocols::frag_picker::scores::HydrophobicitySimilarity , protocols::frag_picker::scores::LAMBEGO_Similarity , protocols::frag_picker::scores::MidPhiOut , protocols::frag_picker::scores::MidPsiOut , protocols::frag_picker::scores::PartialSecondarySimilarity , protocols::frag_picker::scores::PCS_FragDistance , protocols::frag_picker::scores::Phi , protocols::frag_picker::scores::PhiPsiRmsd , protocols::frag_picker::scores::PhiPsiSquareWell , protocols::frag_picker::scores::ProfileScore , protocols::frag_picker::scores::ProfileScoreBlosum62 , protocols::frag_picker::scores::ProfileScoreDistWeight , protocols::frag_picker::scores::ProfileScoreL1 , protocols::frag_picker::scores::ProfileScoreStructL1 , protocols::frag_picker::scores::ProfileScoreSubMatrix , protocols::frag_picker::scores::Psi , protocols::frag_picker::scores::RamaScore , protocols::frag_picker::scores::SecondarySimilarity , protocols::frag_picker::scores::SolventAccessibility , protocols::frag_picker::scores::TalosSSSimilarity , protocols::frag_picker::scores::TorsionBinSimilarity
• cached_tries_ : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• CachedResidueSubset() : core::select::residue_selector::CachedResidueSubset
• CacheMap : core::fragment::Frame
• cacher_ : protocols::match::output::MatchCollisionFilter
• CacheWrapper() : core::fragment::CacheWrapper< T, XCacheUnit >
• CachingScoringMethod() : protocols::frag_picker::scores::CachingScoringMethod
• CAcrd : protocols::simple_filters::ResidueDepthData
• CAcstGenerator() : protocols::seeded_abinitio::CAcstGenerator
• cal_delta_internal_coordinates() : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• cal_delta_internal_coordinates_squared() : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• cal_distance() : core::pack::dunbrack::cenrot::CentroidRotamerSampleData , protocols::pockets::SmallMol
• cal_distance_squared() : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• cal_min_dist() : protocols::pockets::SmallMol
• cal_perrsd_score() : protocols::hybridization::FragmentBiasAssigner
• Calc() : core::scoring::sc::ElectrostaticComplementarityCalculator , core::scoring::sc::MolecularSurfaceCalculator , core::scoring::sc::ShapeComplementarityCalculator
• calc_ : core::simple_metrics::metrics::CalculatorMetric
• calc_4pdeer() : core::scoring::epr_deer::Simulated4PDEERTrace
• calc_accept_rate() : protocols::docking::DockingLowRes
• calc_all_dist() : protocols::make_rot_lib::MakeRotLibMover
• calc_alt_rot_matrix() : protocols::mean_field::MeanField
• calc_ang_score() : core::scoring::membrane::MPSpanAngleEnergy
• calc_angle() : protocols::rigid::RotateJumpAxisMover , protocols::simple_moves::TorsionDOFMover
• calc_atom_masks() : core::scoring::sasa::LeGrandSasa
• calc_bb_boltz_probs() : protocols::mean_field::FlexBBDesignMeanField , protocols::mean_field::FlexBBMeanField
• calc_bin_and_pos() : protocols::match::VoxelSetIterator
• calc_bin_index() : protocols::match::OccupiedSpaceHash
• calc_boltz_score() : protocols::monte_carlo::GenericSimulatedAnnealer
• calc_calcn : protocols::task_operations::RestrictByCalculatorsOperation
• calc_CAPRI_rank() : protocols::symmetric_docking::SymDockProtocol
• calc_cenlist() : protocols::simple_moves::StructProfileMover
• calc_centroid_dG() : protocols::analysis::InterfaceAnalyzerMover
• calc_centroids() : protocols::make_rot_lib::MakeRotLibMover
• calc_chain_endings() : protocols::denovo_design::components::ExtendedPoseBuilder
• calc_cosineang() : core::scoring::methods::GoapEnergy
• calc_curr_hbond_weights() : core::pack::interaction_graph::NPDHBSimpleNode
• calc_dE_ : protocols::enzdes::RepackWithoutLigandFilter
• calc_deltaEpd() : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode
• calc_dipscore() : core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl
• calc_dist() : protocols::energy_based_clustering::EnergyBasedClusteringProtocol , protocols::make_rot_lib::MakeRotLibMover
• calc_dotscore() : protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential
• calc_dr6_dS2_dXYZ() : core::scoring::nmr::pre::PREMultiSet
• calc_ElectricField() : protocols::sparta::PDB
• calc_energies_matrix() : protocols::mean_field::MeanField
• calc_energy() : core::scoring::membrane::FaMPEnvSmoothEnergy , core::scoring::membrane::MPHelicalityEnergy , core::scoring::membrane::MPResidueLipophilicityEnergy , core::scoring::methods::EnvSmoothEnergy , core::scoring::methods::MembraneEnvSmoothEnergy
• calc_ensemble_accept_rate_() : protocols::docking::DockingLowResEnsemble
• calc_etable_value() : core::scoring::etable::Etable , core::scoring::etable::MembEtable
• calc_exp_value_aa_matrix() : protocols::mean_field::FlexBBDesignMeanField
• calc_exp_value_rot_matrix() : protocols::mean_field::FlexBBMeanField
• calc_final_rotamer_probs() : protocols::make_rot_lib::MakeRotLibMover
• calc_final_rotamers() : protocols::make_rot_lib::MakeRotLibMover
• calc_fit_R() : protocols::evaluation::PCA
• calc_fnat() : protocols::symmetric_docking::SymDockProtocol
• calc_frac_atoms_kA_to_native() : protocols::flexpep_docking::FlexPepDockingPoseMetrics
• calc_frac_native_contacts() : protocols::flexpep_docking::FlexPepDockingPoseMetrics
• calc_freq_temp : core::pack::annealer::SimAnnealerBase
• calc_gamma_I() : core::scoring::nmr::pre::PRESingleSet
• calc_gdt() : protocols::comparative_modeling::Align_RmsdEvaluator
• calc_gdt_ : protocols::comparative_modeling::Align_RmsdEvaluator
• calc_geometry() : protocols::fldsgn::topology::BetaAlphaBetaMotif , protocols::fldsgn::topology::BetaAlphaBetaMotifSet , protocols::fldsgn::topology::Helix , protocols::fldsgn::topology::HelixPairing , protocols::fldsgn::topology::HelixPairingSet , protocols::fldsgn::topology::HSSTriplet , protocols::fldsgn::topology::Sheet , protocols::fldsgn::topology::SheetSet , protocols::fldsgn::topology::Strand
• calc_gJ() : core::io::nmr::ParaIon
• calc_hbond_sasaE() : protocols::analysis::InterfaceAnalyzerMover
• calc_hbond_sasaE_ : protocols::analysis::InterfaceAnalyzerMover
• calc_helices_ : protocols::denovo_design::filters::SSShapeComplementarityFilter
• calc_helix_cycle() : protocols::fldsgn::topology::BetaAlphaBetaMotif
• calc_HN_S2() : protocols::sparta::PDB
• calc_in_hours_ : core::simple_metrics::metrics::TimingProfileMetric
• calc_inertia_tensor() : protocols::normalmode::NormalMode
• calc_inout() : protocols::fldsgn::topology::BetaAlphaBetaMotif
• calc_inter_group_ : protocols::pose_metric_calculators::InterGroupNeighborsCalculator
• calc_interaction_energy() : protocols::symmetric_docking::SymDockProtocol , protocols::ub_e2c::ubi_e2c_modeler
• calc_interface_metrics() : protocols::flexpep_docking::FlexPepDockingPoseMetrics
• calc_interface_to_surface_fraction() : protocols::analysis::InterfaceAnalyzerMover
• calc_Irms() : protocols::symmetric_docking::SymDockProtocol
• calc_jacobian_cartesians() : protocols::simple_moves::BBConRotMover
• calc_kl_divergence() : core::scoring::func::MixtureFunc
• calc_long_range() : core::pack::interaction_graph::SimpleEdge
• calc_long_range_ : core::pack::interaction_graph::SimpleEdge
• calc_loops_ : protocols::denovo_design::filters::SSShapeComplementarityFilter
• calc_Lrmsd() : protocols::ub_e2c::ubi_e2c_modeler
• calc_mean_field() : protocols::mean_field::GenMeanFieldMover
• calc_medoids() : protocols::make_rot_lib::MakeRotLibMover
• calc_omega_E() : core::scoring::nmr::pre::PREMultiSet
• calc_omega_I() : core::scoring::nmr::pre::PRESingleSet
• calc_ordermatrix() : core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl
• calc_orderparam() : core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl
• calc_penalty_vec() : core::scoring::constraints::FabConstraint
• calc_pep_scores() : protocols::flexpep_docking::FlexPepDockingPoseMetrics
• calc_per_res_sasas() : core::scoring::sasa::SasaCalc
• calc_per_residue_and_regional_data() : protocols::analysis::InterfaceAnalyzerMover
• calc_per_residue_dG() : protocols::analysis::InterfaceAnalyzerMover
• calc_per_residue_dSASA() : protocols::analysis::InterfaceAnalyzerMover
• calc_per_residue_dSASA_general() : protocols::analysis::InterfaceAnalyzerMover
• calc_pfront_poses_filter_ranks() : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• calc_phi() : core::scoring::methods::GoapEnergy
• calc_phipsi_RMSD() : protocols::flexpep_docking::FlexPepDockingPoseMetrics
• calc_phithetascore() : protocols::fldsgn::potentials::sspot::HSPairPotential , protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential
• calc_point_mut_filters() : protocols::design_opt::PointMutationCalculator , protocols::matdes::MatDesPointMutationCalculator
• calc_product() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser
• calc_r6_S2() : core::scoring::nmr::pre::PREMultiSet
• calc_res_contact() : protocols::symmetric_docking::SymDockProtocol
• calc_residue_burial() : core::scoring::membrane::MPHelicalityEnergy , core::scoring::membrane::MPResidueLipophilicityEnergy
• calc_rms() : protocols::symmetric_docking::SymDockProtocol
• calc_rms_ : protocols::enzdes::RepackWithoutLigandFilter
• calc_rms_atom_id_map_ : protocols::stepwise::modeler::align::StepWisePoseAligner
• calc_rms_res() : core::pose::full_model_info::FullModelInfo , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• calc_rms_res_ : core::import_pose::FullModelPoseBuilder , protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer , protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::screener::SimpleRMSD_Screener , protocols::stepwise::modeler::align::StepWiseClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• calc_rmsd_to_native() : protocols::loop_modeling::utilities::TrajectoryLogger
• calc_rmsds() : protocols::rna::denovo::RNA_DeNovoProtocol
• calc_rnp_pair_dist_score() : core::scoring::rna::RNP_LowResPairDistPotential
• calc_rot_freq() : core::pack::annealer::SimAnnealerBase
• calc_rot_freq_ : core::pack::annealer::SimAnnealerBase
• calc_rotamer_clusters() : protocols::make_rot_lib::MakeRotLibMover
• calc_rsd_sasa() : core::select::util::SelectResiduesByLayer
• calc_rsigmascore() : protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential
• calc_running_avg() : protocols::make_rot_lib::MakeRotLibMover
• calc_sasa_bothsides() : protocols::fldsgn::topology::Sheet
• calc_sc_neighbors() : core::select::util::SelectResiduesByLayer
• calc_score() : core::scoring::constraints::MembraneSpanConstraint , core::scoring::constraints::MembraneSpanTermZConstraint , protocols::loop_modeling::utilities::TrajectoryLogger
• calc_secondary_struct() : protocols::surface_docking::FullatomRelaxMover
• calc_secondary_structure() : protocols::surface_docking::SurfaceDockingProtocol
• calc_secondary_structure_with_surface() : protocols::surface_docking::SurfaceDockingProtocol
• calc_short_range() : core::pack::interaction_graph::SimpleEdge
• calc_short_range_ : core::pack::interaction_graph::SimpleEdge
• calc_shortest_dist_by_atoms() : protocols::simple_filters::HelixHelixAngleFilter
• calc_span_score() : core::scoring::membrane::MPSpanInsertionEnergy
• calc_standard_deviations() : protocols::make_rot_lib::MakeRotLibMover
• calc_tau_c() : core::scoring::nmr::pre::PREMultiSet
• calc_temp_factor() : protocols::monte_carlo::GenericSimulatedAnnealer
• calc_theoretical_tau_r() : core::scoring::nmr::pre::PREMultiSet
• calc_time() : core::simple_metrics::metrics::TimingProfileMetric
• CalcContactArea() : core::scoring::sc::ContactMolecularSurfaceCalculator
• CalcContactMolecularSurface() : core::scoring::sc::ContactMolecularSurfaceCalculator
• calcdepth() : core::scoring::atomic_depth::AtomicDepth
• CalcDotsForAllAtoms() : core::scoring::sc::MolecularSurfaceCalculator
• CalcDotsForAtoms() : core::scoring::sc::MolecularSurfaceCalculator
• calcenergy : core::scoring::APBSConfig , core::scoring::APBSConfig::I_PARAM
• calcenergy_ : core::scoring::PoissonBoltzmannPotential
• calcforce : core::scoring::APBSConfig::I_PARAM
• CalcInterNeighborGroup() : protocols::toolbox::CalcInterNeighborGroup
• calcKineticEnergy() : protocols::cartesian::MolecularDynamics
• calcLevel1() : protocols::sparta::ANN
• calcLevel2() : protocols::sparta::ANN
• calcMetrics() : protocols::flexpep_docking::FlexPepDockingProtocol
• CalcNeighborDistance() : core::scoring::sc::ShapeComplementarityCalculator
• CalcNeighborDistanceFindClosestNeighbor() : core::scoring::sc::ContactMolecularSurfaceCalculator , core::scoring::sc::ShapeComplementarityCalculator
• calcPlane() : protocols::sparta::PDB
• calcRhoC() : core::scoring::electron_density::ElectronDensity
• calcs_and_calcns_ : protocols::task_operations::RestrictByCalculatorsOperation
• calcs_ready_ : protocols::analysis::InterfaceAnalyzerMover
• CalcSc() : core::scoring::sc::ShapeComplementarityCalculator
• calcSurface() : protocols::sparta::PDB
• calcTriangles() : protocols::sparta::PDB
• calcualate_total_score_and_tensors() : protocols::nmr::pcs::PCSEnergy , protocols::nmr::rdc::RDCEnergy
• calculate() : core::scoring::sasa::LeGrandSasa , core::scoring::sasa::SasaCalc , core::scoring::sasa::SasaMethod , 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::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::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric , protocols::analysis::simple_metrics::SequenceRecoveryMetric , protocols::cyclic_peptide::PeptideInternalHbondsMetric , protocols::dna::DNAParameters , protocols::filters::FilterValueMetric , protocols::filters::StochasticFilter , protocols::pack_daemon::NPDPropCalculator , protocols::protein_interface_design::ReportPSSMDifferences , protocols::protein_interface_design::ReportSequenceDifferences , protocols::quantum_annealing::InteractionGraphSummaryMetric , protocols::scoring::Interface , protocols::scoring::InterfaceInfo , protocols::simple_ddg::ddG , protocols::simple_ddg::DdGScan , protocols::vardist_solaccess::VarSolDistSasaCalculator
• calculate_all_chainbreaks() : protocols::analysis::LoopAnalyzerMover
• calculate_alt_state_hpatch_score() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• calculate_alt_state_npd_hbond_score() : core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >
• calculate_amount_total_hydrophobic_ASA() : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G >
• calculate_and_store_all_derivs() : core::scoring::MultipoleElecPotential
• calculate_angles() : protocols::features::SmotifFeatures
• calculate_atom_id_domain_map() : core::pose::toolbox::AtomLevelDomainMap
• calculate_atom_id_map() : core::pose::toolbox::AtomID_Mapper
• calculate_axes() : protocols::docking::EllipsoidalRandomizationMover
• calculate_background_energies() : protocols::pack_daemon::PackDaemon
• calculate_ccd_angle() : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• calculate_cdr_aromatic_nres() : protocols::antibody::AntibodyFeatures
• calculate_cdr_cluster() : protocols::antibody::clusters::CDRClusterSet
• calculate_cdr_contacts_nres() : protocols::antibody::AntibodyFeatures
• calculate_cdr_contacts_total() : protocols::antibody::AntibodyFeatures
• calculate_cdr_dpSASA() : protocols::antibody::AntibodyFeatures
• calculate_cdr_totals() : protocols::antibody::AntibodyFeatures
• calculate_center_xyz() : protocols::pockets::EggshellGrid
• calculate_contact_order() : core::scoring::methods::ContactOrderEnergy
• calculate_cost_only_with_svd() : protocols::scoring::methods::pcs2::PcsDataLanthanide
• calculate_current_temperature() : protocols::helical_bundle_predict::HBP_SigmoidalTemperatureScheduleGenerator , protocols::helical_bundle_predict::HBP_TemperatureScheduleGenerator
• calculate_decay_2_spin() : core::scoring::epr_deer::DEERDecayData
• calculate_derivatives_for_atoms_and_pseudo_base_atoms() : core::scoring::methods::LK_hack
• calculate_derivatives_for_residue_pair() : core::scoring::methods::LK_hack
• calculate_dipoles() : core::scoring::methods::GoapEnergy
• calculate_distance_matrix() : protocols::cluster::ClusterBase
• calculate_energy() : core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty , core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy , core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyEnergy , core::scoring::aa_composition_energy::AACompositionEnergy , core::scoring::aa_repeat_energy::AARepeatEnergy , core::scoring::annealing::ResidueArrayAnnealableEnergy , core::scoring::mhc_epitope_energy::MHCEpitopeEnergy , core::scoring::netcharge_energy::NetChargeEnergy , core::scoring::rna::data::RNA_ChemicalMappingEnergy , core::scoring::rna::RNA_PartitionEnergy , core::scoring::util_methods::DumpTrajectoryEnergy
• calculate_error_twist() : protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover
• calculate_feature_vector() : core::scoring::methods::ProQ_Energy
• calculate_feature_vector_proq2() : core::scoring::methods::ProQ_Energy
• calculate_fitness() : protocols::recon_design::FitnessFilter
• calculate_fitness_mpi() : protocols::recon_design::FitnessFilter
• calculate_fixed_fields_for_polarization() : core::scoring::MultipoleElecPotential
• calculate_free_ligand_score() : protocols::ligand_docking::ga_ligand_dock::GALigandDock
• calculate_free_receptor_score() : protocols::ligand_docking::ga_ligand_dock::GALigandDock
• calculate_GBpair_exact() : core::scoring::FACTSPotential
• calculate_GBpair_fast() : core::scoring::FACTSPotential
• calculate_GBpair_v1trunk() : core::scoring::FACTSPotential
• calculate_geometry() : protocols::docking::EllipsoidalRandomizationMover
• calculate_grid() : protocols::ligand_docking::ga_ligand_dock::GridScorer
• calculate_helical_parameters() : protocols::simple_filters::RepeatParameterFilter
• calculate_helical_parameters_helper() : protocols::simple_filters::RepeatParameterFilter
• calculate_highres_ref_energy() : protocols::docking::DockingEnsemble
• calculate_hpatch_deltaE() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• calculate_hydrogen_atom_reach() : core::scoring::etable::Etable
• calculate_hydrogen_interaction_cutoff() : core::scoring::vdwaals::VDW_Energy
• calculate_index2cart() : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• calculate_induced_fields_for_polarization() : core::scoring::MultipoleElecPotential
• calculate_interface_SASA() : protocols::docking::membrane::MPFindInterfaceMover
• calculate_interface_score() : protocols::peptide_deriver::PeptideDeriverFilter
• calculate_interface_unbound_energy() : protocols::ddg::ddGMover
• calculate_interres() : core::scoring::etable::BaseEtableEnergy< Derived >
• calculate_intra_xover4() : core::scoring::etable::BaseEtableEnergy< Derived >
• calculate_intrares() : core::scoring::etable::BaseEtableEnergy< Derived >
• calculate_iterations() : protocols::abinitio::abscript::AbscriptMover
• calculate_Jacobi_correction() : protocols::normalmode::NormalMode
• calculate_jacobians() : protocols::stepwise::sampler::rna::RNA_KinematicCloser
• calculate_jacobians_ : protocols::stepwise::sampler::rna::RNA_KinematicCloser
• calculate_jump() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler
• calculate_jump_sample() : protocols::abinitio::abscript::FragmentJumpCM
• calculate_ligand_CoM() : protocols::pockets::PlaidFingerprint
• calculate_ligand_resnums() : protocols::residue_selectors::LigandMetalContactSelector
• calculate_lk_ball_atom_energies() : core::scoring::lkball::LK_BallEnergy
• calculate_lk_ball_atom_energies_cp() : core::scoring::lkball::LK_BallEnergy
• calculate_lk_desolvation_of_single_atom_by_residue() : core::scoring::lkball::LK_BallEnergy
• calculate_lk_desolvation_of_single_atom_by_residue_no_count_pair() : core::scoring::lkball::LK_BallEnergy
• calculate_lowres_ref_energy() : protocols::docking::DockingEnsemble
• calculate_map() : core::sequence::AnnotatedSequence
• calculate_nblist_distance_thresholds() : core::scoring::etable::Etable
• calculate_neighbor_table() : protocols::pmut_scan::PointMutScanDriver
• calculate_normal_disbins() : core::scoring::etable::Etable
• calculate_npd_hbond_deltaE() : core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >
• calculate_num_rotamers_in_subtree() : core::scoring::trie::RotamerTrie< AT, CPDATA >
• calculate_offset() : core::scoring::GenTorsionParams
• calculate_orbital_icoor() : core::chemical::orbitals::AssignOrbitals
• calculate_orientation_vectors_and_pseudo_base_atoms() : core::scoring::methods::LK_hack
• calculate_pcs_score() : 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
• calculate_pcs_score_on_PCS_data_center_CA() : protocols::scoring::methods::pcs2::PcsEnergy
• calculate_PD_deltaE_for_substitution() : core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::NPDHBondNode< V, E, G >
• calculate_penalty_once_almost_from_scratch_using_reference_graph() : core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty
• calculate_penalty_once_from_scratch() : core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty
• calculate_per_position_scores() : core::sequence::SequenceAlignment
• calculate_per_residue_interface_score() : protocols::peptide_deriver::PeptideDeriverFilter
• calculate_plane_axes() : protocols::docking::EllipsoidalRandomizationMover
• calculate_pool_diversity() : protocols::mpi_refinement::MultiObjective
• calculate_protein_CoM() : protocols::pockets::NonPlaidFingerprint
• calculate_recenter_vector() : protocols::surface_docking::SurfaceOrientMover
• calculate_reflect() : protocols::cyclic_peptide::FlipChiralityMover
• calculate_res_res_fixed_fields_for_polarization() : core::scoring::MultipoleElecPotential
• calculate_res_res_induced_fields_for_polarization() : core::scoring::MultipoleElecPotential
• calculate_residue_atomic_contacts() : protocols::antibody::AntibodyFeatures
• calculate_residue_emap() : core::scoring::SplitUnfoldedTwoBodyPotential
• calculate_rg_score() : core::scoring::methods::RG_Energy_Fast , core::scoring::methods::RG_LocalEnergy
• calculate_rho_fast2() : core::scoring::fiber_diffraction::FiberDiffractionEnergyDens
• calculate_rmsd() : protocols::anchored_design::AnchoredDesignMover
• calculate_rotamer_set_design_targets_partition_sum() : protocols::enzdes::EnzdesFlexibleRegion
• calculate_rt() : core::scoring::constraints::RTConstraint
• calculate_sasa() : protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator
• calculate_score() : protocols::monte_carlo::MonteCarloInterface
• calculate_score_and_tensors_by_nls() : protocols::nmr::pcs::PCSEnergy
• calculate_score_and_tensors_by_svd() : protocols::nmr::pcs::PCSEnergy
• calculate_score_and_tensors_with_gridsearch() : protocols::nmr::pcs::PCSEnergy
• calculate_score_and_tensors_with_spinlabel() : protocols::nmr::pcs::PCSEnergy
• calculate_score_sum_of_pairs() : core::sequence::SequenceAlignment
• calculate_scores_and_tensors_from_pose_and_PCS_data() : 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
• calculate_silent_Es_ : protocols::enzdes::RepackLigandSiteWithoutLigandMover
• calculate_specificity() : protocols::dna::DnaInterfacePacker
• calculate_stability_metric() : core::chemical::gasteiger::GasteigerAtomTypeData
• calculate_standardized_scores() : protocols::monte_carlo::GenericSimulatedAnnealer
• calculate_structure_diversity() : protocols::mpi_refinement::MultiObjective
• calculate_subtree_containing_radii() : core::scoring::trie::RotamerTrie< AT, CPDATA >
• calculate_suiteness_bonus_ : core::scoring::rna::RNA_SuitePotential
• calculate_temps() : protocols::monte_carlo::GenericSimulatedAnnealer
• calculate_tensor_and_cost_with_svd() : protocols::scoring::methods::pcs2::PcsDataLanthanide , protocols::scoring::methods::pcs::PCS_data_per_lanthanides , protocols::scoring::methods::pcsTs1::PCS_data_per_lanthanides_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_per_lanthanides_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_per_lanthanides_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_per_lanthanides_Ts4
• calculate_tensor_only_with_svd() : protocols::scoring::methods::pcs2::PcsDataLanthanide
• calculate_total_cst_score() : core::scoring::constraints::AmbiguousConstraint , core::scoring::constraints::KofNConstraint
• calculate_total_samples() : protocols::helical_bundle::BackboneGridSampler , protocols::helical_bundle::BundleGridSampler
• calculate_total_score() : protocols::nmr::pre::PREEnergy
• calculate_variations() : protocols::mpi_refinement::StructAvrgMover
• calculate_weighted_energy() : core::pack::interaction_graph::ResidueArrayAnnealingEvaluator
• calculated() : core::pose::rna::RNA_FilteredBaseBaseInfo , core::pose::rna::RNA_RawBaseBaseInfo , core::scoring::CenListInfo , core::scoring::Membrane_FAEmbed , core::scoring::MembraneEmbed , core::scoring::rna::RNA_CentroidInfo , core::scoring::rna::RNA_ScoringInfo , core::scoring::SigmoidWeightedCenList< T > , protocols::scoring::InterfaceInfo
• calculated_ : core::pose::rna::RNA_FilteredBaseBaseInfo , core::pose::rna::RNA_RawBaseBaseInfo , core::scoring::CenListInfo , core::scoring::Membrane_FAEmbed , core::scoring::MembraneEmbed , core::scoring::rna::RNA_CentroidInfo , core::scoring::SigmoidWeightedCenList< T > , protocols::scoring::InterfaceInfo
• calculated_hpatch_deltaE_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• calculated_npd_hbond_deltaE_ : core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >
• calculated_surface_deltaE_ : core::pack::interaction_graph::SurfaceNode< V, E, G >
• calculateDensityMap() : core::scoring::cryst::PhenixInterface
• calculateZ() : core::scoring::methods::ProQ_Energy
• calculator() : protocols::pose_metric_calculators::MetricValueGetter
• calculator_ : protocols::calc_taskop_filters::RotamerBoltzmannWeight2 , protocols::helical_bundle::MakeBundleHelix , protocols::pose_metric_calculators::MetricValueGetter
• calculator_cop() : protocols::helical_bundle::MakeBundleHelix
• calculator_id() : protocols::calc_taskop_filters::RotamerBoltzmannWeight2
• calculator_id_ : protocols::calc_taskop_filters::RotamerBoltzmannWeight2
• calculator_name() : protocols::pack_daemon::NPDPropCalculatorCreator
• calculator_name_ : protocols::multistate_design::MetricCalculatorFitnessFunction , protocols::task_operations::RestrictToInterfaceOperation , protocols::task_operations::RestrictToNeighborhoodOperation
• calculator_op() : protocols::helical_bundle::MakeBundleHelix
• CalculatorFactory() : core::pose::metrics::CalculatorFactory
• CalculatorFilter() : protocols::filters::CalculatorFilter
• CalculatorMetric() : core::simple_metrics::metrics::CalculatorMetric
• calculators_ : core::pose::metrics::CalculatorFactory
• calibrate() : protocols::noesy_assign::CrossPeak , protocols::noesy_assign::CrossPeakList
• calibration_atom_type() : protocols::noesy_assign::PeakAssignment , protocols::noesy_assign::Resonance
• calibration_atom_type_ : protocols::noesy_assign::Resonance
• calibration_constant() : protocols::noesy_assign::PeakCalibrator
• calibration_constant_ : protocols::noesy_assign::PeakCalibrator
• calibration_constant_highs_ : protocols::noesy_assign::PeakCalibrator
• calibration_constant_lows_ : protocols::noesy_assign::PeakCalibrator
• calibration_convergence_ : protocols::noesy_assign::PeakAssignmentParameters
• calibration_cycles_ : protocols::noesy_assign::PeakAssignmentParameters
• calibration_eliminate_ : protocols::noesy_assign::PeakAssignmentParameters
• calibration_ignore_eliminated_peaks_ : protocols::noesy_assign::PeakAssignmentParameters
• calibration_max_noe_dist_ : protocols::noesy_assign::PeakAssignmentParameters
• calibration_max_nudging_ : protocols::noesy_assign::PeakAssignmentParameters
• calibration_start_nudging_ : protocols::noesy_assign::PeakAssignmentParameters
• calibration_stop_nudging_ : protocols::noesy_assign::PeakAssignmentParameters
• calibration_target_ : protocols::noesy_assign::PeakAssignmentParameters
• calibration_use_median_ : protocols::noesy_assign::PeakAssignmentParameters
• CalibratorMap : protocols::noesy_assign::PeakCalibratorMap
• calibrators_ : protocols::noesy_assign::PeakCalibratorMap
• call_count_ : core::scoring::util_methods::DumpTrajectoryEnergy
• call_mover : protocols::splice::SpliceOut
• call_mover_tail_ : protocols::splice::SpliceOut
• call_mover_tmp : protocols::splice::SpliceOutAntibody
• call_order() : protocols::rosetta_scripts::ParsedProtocol
• call_order_ : protocols::rosetta_scripts::ParsedProtocol
• call_output_observers() : protocols::jd2::Job , protocols::jd2::JobOutputter
• call_setup() : protocols::minimization_packing::PackRotamersMoverLazy
• Calpha_restraints_ : protocols::ligand_docking::LigandArea
• calpha_vector_ : protocols::cluster::calibur::SimPDB , protocols::cluster::calibur::Stru
• calphas_ : protocols::loop_grower::LoopPartialSolution
• calRMSD() : protocols::pockets::SmallMol
• came_from() : core::sequence::Cell
• camelid_ : protocols::antibody::Ab_TemplateInfo , protocols::antibody::GraftCDRLoopsProtocol , protocols::antibody_legacy::Antibody , protocols::antibody_legacy::AntibodyModeler , protocols::antibody_legacy::GraftMover
• camelid_constraints_ : protocols::antibody::GraftCDRLoopsProtocol , protocols::antibody_legacy::AntibodyModeler
• CamShiftEvaluator() : protocols::simple_filters::CamShiftEvaluator
• CamShiftEvaluatorCreator() : protocols::simple_filters::CamShiftEvaluatorCreator
• can_be_added_to() : protocols::legacy_sewing::sampling::requirements::LegacyGlobalRequirement , protocols::legacy_sewing::sampling::requirements::LegacyRequirementSet
• can_be_copied() : core::conformation::parametric::Parameter , core::conformation::parametric::ParameterizationCalculatorProperties
• can_be_copied_ : core::conformation::parametric::Parameter
• can_be_deleted() : protocols::jd2::Job , protocols::jd2::JobsContainer
• can_be_deleted_ : protocols::jd2::Job
• can_be_perturbed() : core::conformation::parametric::Parameter , core::conformation::parametric::ParameterizationCalculatorProperties
• can_be_perturbed_ : core::conformation::parametric::Parameter
• can_be_sampled() : core::conformation::parametric::Parameter , core::conformation::parametric::ParameterizationCalculatorProperties
• can_be_sampled_ : core::conformation::parametric::Parameter
• can_be_set() : core::conformation::parametric::Parameter , core::conformation::parametric::ParameterizationCalculatorProperties
• can_be_set_ : core::conformation::parametric::Parameter
• CAN_CONTROL : protocols::environment::claims::ClaimStrength
• can_delete() : protocols::sewing::data_storage::SmartAssembly
• can_hash() : protocols::sewing::hashing::Hasher
• CAN_INIT : protocols::topology_broker::claims::DofClaim
• can_load() : protocols::indexed_structure_store::DirStructureStoreBackend , protocols::indexed_structure_store::JSONStructureStoreBackend , protocols::indexed_structure_store::SilentStructureStoreBackend , protocols::indexed_structure_store::StructureStoreProvider
• can_pair() : core::chemical::AutomorphismIterator
• can_write() : protocols::indexed_structure_store::DirStructureStoreBackend , protocols::indexed_structure_store::JSONStructureStoreBackend , protocols::indexed_structure_store::SilentStructureStoreBackend , protocols::indexed_structure_store::StructureStoreProvider
• cancel_batch() : protocols::jd2::archive::ArchiveManager , protocols::jd2::archive::BaseArchiveManager
• cancel_batches_previous_to() : protocols::jd2::archive::BaseArchiveManager
• cancel_passports() : protocols::environment::Environment
• Candidate() : protocols::nonlocal::SmoothPolicy::Candidate
• candidate_address_ : protocols::canonical_sampling::mc_convergence_checks::DataBuffer
• candidate_best_rmsd_ : protocols::canonical_sampling::mc_convergence_checks::DataBuffer
• candidate_best_rmsds_ : protocols::canonical_sampling::mc_convergence_checks::DataBuffer
• candidate_coords_ : protocols::canonical_sampling::mc_convergence_checks::DataBuffer
• candidate_for : protocols::cluster::DataPoint
• candidate_helix_assignments_ : protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator
• candidate_i_ : protocols::frag_picker::nonlocal::NonlocalPair
• candidate_i_rank_ : protocols::frag_picker::nonlocal::NonlocalPair
• candidate_j_ : protocols::frag_picker::nonlocal::NonlocalPair
• candidate_j_rank_ : protocols::frag_picker::nonlocal::NonlocalPair
• candidate_nbr_index_ : protocols::canonical_sampling::mc_convergence_checks::DataBuffer
• candidate_res_atoms_reqd_near_target_atom() : protocols::match::downstream::AtomDistanceSecMatchRPE , protocols::match::downstream::GeometrySecMatchRPE , protocols::match::downstream::SecMatchResiduePairEvaluator
• candidates : protocols::cluster::DataPoint
• candidates_sink_ : protocols::frag_picker::FragmentPicker
• candidates_sinks_ : protocols::frag_picker::FragmentPicker
• canonical() : core::import_pose::libraries::BasePairStepLibrary
• canonical_ : core::import_pose::libraries::BasePairStepLibrary
• canonical_aa_ : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >
• canonical_aas_to_keep_ : core::pack::task::operation::RestrictAbsentCanonicalAASExceptNativeRLT , core::pack::task::operation::RestrictAbsentCanonicalAASRLT
• canonical_atom_alias() : core::chemical::ResidueTypeBase
• canonical_atom_aliases() : core::chemical::ResidueTypeBase
• canonical_atom_aliases_ : core::chemical::ResidueTypeBase
• canonical_base_pair_step_library() : core::import_pose::libraries::RNA_LibraryManager
• canonical_base_pair_step_library_ : core::import_pose::libraries::RNA_LibraryManager
• canonical_prepro_score_tables_ : core::scoring::RamaPrePro
• canonical_score_tables_ : core::scoring::RamaPrePro
• canonicals_use_voronoi_ : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >
• CanonicalSamplingMover() : protocols::canonical_sampling::CanonicalSamplingMover
• CAonly_ : protocols::simple_filters::LoopRmsdEvaluator , protocols::simple_filters::SelectRmsdEvaluator
• CAP : protocols::genetic_algorithm::Entity
• cap_ends() : protocols::helical_bundle::BackboneGridSampler
• cap_ends_ : protocols::helical_bundle::BackboneGridSampler
• cap_espGrid() : protocols::pockets::ElectrostaticpotentialGrid
• capping_residues_ : core::import_pose::RNA_HelixAssembler
• CAPs : protocols::genetic_algorithm::Entity
• capture_tracer_ : protocols::rpc::JSON_RPC
• carbohydrate_info() : core::chemical::ResidueType , core::conformation::Residue
• carbohydrate_info_ : core::chemical::ResidueType
• carbohydrate_omega_preferences_function_ : core::scoring::ScoringManager
• CarbohydrateInfo() : core::chemical::carbohydrates::CarbohydrateInfo
• CarbohydrateInfoManager() : core::chemical::carbohydrates::CarbohydrateInfoManager
• carbon_atom : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• carbon_donors_ : core::scoring::carbon_hbonds::CarbonHBondPotential
• carbon_hbond_parameter_ : core::scoring::carbon_hbonds::CarbonHBondPotential
• carbon_hbond_potential_ : core::scoring::carbon_hbonds::CarbonHBondEnergy , core::scoring::ScoringManager
• carbon_types_ : core::scoring::etable::Etable
• CarbonHBondEnergy() : core::scoring::carbon_hbonds::CarbonHBondEnergy
• CarbonHBondPotential() : core::scoring::carbon_hbonds::CarbonHBondPotential
• carboxyl_wants_2 : core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::UnsatCorrectionOptions
• careful_base_pair_classifier() : core::scoring::rna::data::RNA_DMS_LowResolutionPotential
• careful_base_pair_classifier_ : core::scoring::rna::data::RNA_DMS_LowResolutionPotential
• carry_out_filtering() : core::pose::rna::RNA_FilteredBaseBaseInfo
• cart2idx() : core::scoring::electron_density::ElectronDensity , core::scoring::PoissonBoltzmannPotential
• cart_ : protocols::ncbb::SecStructFinder
• cart_bonded_cutoff_ : protocols::score_filters::GeometryFilter
• cart_min() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• cart_min_ : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• cart_min_graft_ : protocols::antibody::design::AntibodyDesignMover
• cart_product() : protocols::fldsgn::MatchResidues
• cart_resl_ : core::scoring::motif::MotifHash , core::scoring::motif::XformScore , core::scoring::motif::XfragSet
• cart_size() : core::scoring::motif::MotifHash , core::scoring::motif::XformScore
• cart_size_ : core::scoring::motif::MotifHash , core::scoring::motif::XformScore
• cartbonded_ : protocols::ligand_docking::ga_ligand_dock::GridScorer
• cartbonded_ang_ : core::scoring::methods::EnergyMethodOptions
• cartbonded_improper_ : core::scoring::methods::EnergyMethodOptions
• cartbonded_len_ : core::scoring::methods::EnergyMethodOptions
• cartbonded_linear_ : core::scoring::methods::EnergyMethodOptions
• cartbonded_proton_ : core::scoring::methods::EnergyMethodOptions
• cartbonded_skip_cutpoints_ : core::scoring::methods::EnergyMethodOptions
• cartbonded_tors_ : core::scoring::methods::EnergyMethodOptions
• cartesian() : core::select::movemap::MoveMapFactory , protocols::minimization_packing::MinMover , protocols::minimization_packing::SaneMinMover , protocols::relax::RelaxProtocolBase
• cartesian_ : core::pack::RTMin , protocols::cryst::SetCrystWeightMover , protocols::minimization_packing::MinMover , protocols::minimization_packing::MinPackMover , protocols::minimization_packing::RotamerTrialsMinMover , protocols::minimization_packing::SaneMinMover , protocols::normalmode::NormalModeRelaxMover , protocols::relax::RelaxProtocolBase , protocols::relax::RepeatProteinRelax , protocols::rotamer_recovery::RRProtocolRelax , protocols::rotamer_recovery::RRProtocolRTMin , protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer
• cartesian_crossover_ : protocols::simple_moves::CombinePoseMover
• cartesian_minimize_ : protocols::normalmode::NormalModeRelaxMover
• cartesian_minimizer_ : protocols::stepwise::modeler::StepWiseMinimizer
• cartesian_relax_rounds() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• cartesian_relax_rounds_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• cartesian_specific_ : core::select::movemap::MoveMapFactory
• CartesianBondedEnergy() : core::scoring::methods::CartesianBondedEnergy
• CartesianHybridize() : protocols::hybridization::CartesianHybridize
• CartesianMD() : protocols::md::CartesianMD
• CartesianMinimizer() : core::optimization::CartesianMinimizer
• CartesianMinimizerMap() : core::optimization::CartesianMinimizerMap
• CartesianMultifunc() : core::optimization::CartesianMultifunc
• CartesianSampler() : protocols::hybridization::CartesianSampler
• CartesianSearchPattern() : protocols::hotspot_hashing::CartesianSearchPattern
• cartfrag_overlap_ : protocols::hybridization::CartesianHybridize , protocols::hybridization::HybridizeProtocol , protocols::seeded_abinitio::SegmentHybridizer
• CartGrid() : core::grid::CartGrid< T >
• cartmin_ : protocols::carbohydrates::GlycanSampler , protocols::carbohydrates::GlycanTreeModeler
• cartmin_lig_ : protocols::ligand_docking::ga_ligand_dock::GALigandDock
• cartom : protocols::cartesian::MolecularDynamics
• CartSCMinMinimizerMap() : core::pack::scmin::CartSCMinMinimizerMap
• CartSCMinMultifunc() : core::pack::scmin::CartSCMinMultifunc
• cas_chainA : protocols::simple_filters::SymmetricMotifFilter
• cas_chainB : protocols::simple_filters::SymmetricMotifFilter
• case_lines_ : core::chemical::Metapatch
• cases_ : core::chemical::Metapatch , core::chemical::Patch
• cast_flexbb_edge() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• cast_minimalist_flexbb_edge() : protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph
• cast_otfflexbb_edge() : protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
• cat_pi_total_ : protocols::pose_metric_calculators::CatPiCalculator
• catalog() : core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library > , core::fragment::picking_old::vall::VallLibrarian
• catalytic_atoms_ : protocols::match::downstream::SecondaryMatcherToDownstreamResidue
• catalytic_res() : protocols::enzdes::EnzdesBaseProtocol
• catalytic_res_part_of_interface_ : protocols::enzdes::DetectProteinLigandInterface
• catch_fragment() : protocols::loops::loop_closure::ccd::LoopClosure , protocols::loops::loop_closure::ccd::ShortLoopClosure
• catmin_movemap_ : protocols::enzdes::EnzdesFlexBBProtocol
• catmin_mover_ : protocols::enzdes::EnzdesFlexBBProtocol
• catmin_sfxn_ : protocols::enzdes::EnzdesFlexBBProtocol
• CatPiCalculator() : protocols::pose_metric_calculators::CatPiCalculator
• catres_only_ : protocols::enzdes::DetectProteinLigandInterface
• catres_packer_weight_ : protocols::enzdes::ProteinLigandInterfaceUpweighter
• CAvar_ : protocols::mpi_refinement::StructAvrgMover
• cavballs : core::scoring::packstat::CavityBallCluster , core::scoring::packstat::SasaResult
• cavity_balls : protocols::vip::VIP_Mover
• cavity_burial_probe_radius_ : protocols::analysis::PackStatMover
• cavity_pose : protocols::vip::VIP_Mover
• CavityBall() : core::scoring::packstat::CavityBall
• CavityCalculator() : protocols::denovo_design::calculators::CavityCalculator
• CavityVolumeFilter() : protocols::denovo_design::filters::CavityVolumeFilter
• CB() : core::scoring::BB_Pos , protocols::fldsgn::topology::BB_Pos
• CB_ : core::scoring::BB_Pos , protocols::fldsgn::topology::BB_Pos
• cb_ : protocols::sic_dock::scores::TrisBpyScore
• CB_Angle_Func() : core::scoring::disulfides::CB_Angle_Func
• cb_angle_func_ : core::scoring::disulfides::FullatomDisulfidePotential
• CB_atom_id() : protocols::match::upstream::UpstreamResTypeGeometry
• CB_atom_id_ : core::scoring::constraints::BackboneStubLinearConstraint , protocols::match::upstream::UpstreamResTypeGeometry
• CB_b_factor_cutoff_for_electrostatic_interactions_ : protocols::features::strand_assembly::SandwichFeatures
• cb_bias_ : protocols::rigid::RigidBodyMotionMover
• CB_CA_target_ : core::scoring::constraints::BackboneStubLinearConstraint
• cb_coord_ : protocols::membrane::MPLipidAccessibility
• cb_dist_cut() : core::select::residue_selector::InterGroupInterfaceByVectorSelector , protocols::simple_filters::DomainInterfaceFilter
• cb_dist_cut_ : core::select::residue_selector::InterGroupInterfaceByVectorSelector , protocols::simple_filters::DomainInterfaceFilter
• CB_dist_cutoff() : protocols::task_operations::RestrictInterGroupVectorOperation , protocols::task_operations::RestrictToInterfaceVectorOperation
• CB_dist_cutoff_ : protocols::task_operations::RestrictInterGroupVectorOperation , protocols::task_operations::RestrictToInterfaceVectorOperation
• Cb_Distance_Func() : core::scoring::disulfides::Cb_Distance_Func
• cb_distance_func_ : core::scoring::disulfides::CentroidDisulfidePotential
• cb_force() : protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::protein_interface_design::movers::PlacementMinimizationMover
• cb_force_ : protocols::protein_interface_design::filters::StubScoreFilter , protocols::protein_interface_design::filters::StubScoreLoopsFilter , protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::protein_interface_design::movers::PlacementMinimizationMover
• CB_force_constant_ : core::scoring::constraints::BackboneStubLinearConstraint
• cb_force_constant_ : protocols::protein_interface_design::movers::BestHotspotCstMover
• CB_force_constant_ : protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover , protocols::protein_interface_design::movers::SetupHotspotConstraintsMover
• CB_index_ : core::scoring::BB_Pos , protocols::fldsgn::topology::BB_Pos
• CB_target_ : core::scoring::constraints::BackboneStubLinearConstraint
• cbeta12_ : core::scoring::CenRotEnvPairPotential , core::scoring::SmoothEnvPairPotential
• cbeta6_ : core::scoring::CenRotEnvPairPotential , core::scoring::SmoothEnvPairPotential
• cbeta_den12_ : core::scoring::EnvPairPotential
• cbeta_den6_ : core::scoring::EnvPairPotential
• cbreaks_ : protocols::loop_grower::FragmentExtension
• CBScore() : protocols::sic_dock::CBScore
• CBScoreVisitor() : protocols::sic_dock::CBScoreVisitor
• CBSG_Dihedral_Func() : core::scoring::disulfides::CBSG_Dihedral_Func
• cbsg_dihedral_func_ : core::scoring::disulfides::FullatomDisulfidePotential
• cbx() : protocols::frag_picker::VallResidue
• cbx_ : protocols::frag_picker::VallResidue
• cby() : protocols::frag_picker::VallResidue
• cby_ : protocols::frag_picker::VallResidue
• cbz() : protocols::frag_picker::VallResidue
• cbz_ : protocols::frag_picker::VallResidue
• cc_ : protocols::cryst::Spacegroup , protocols::cryst::WallpaperGroup , protocols::sic_dock::scores::TrisBpyScore
• CC_aacen : core::scoring::electron_density::ElectronDensity
• CC_cen : core::scoring::electron_density::ElectronDensity
• ccd() : protocols::dna::DesignProteinBackboneAroundDNA , protocols::splice::Splice
• ccd_ : protocols::seeded_abinitio::CloseFold , protocols::splice::SampleRotamersFromPDB , protocols::splice::SampleRotamersFromPDB_RotamerSetOperation , protocols::splice::Splice
• ccd_close() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• ccd_close_ : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• ccd_close_res_ : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_MultiPoseCloser
• ccd_closer_ : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_MultiPoseCloser , protocols::stepwise::screener::ProteinCCD_ClosureScreener
• ccd_closure() : protocols::simple_moves::WobbleMover
• ccd_cutoff_ : protocols::forge::remodel::RemodelMover::instruction_flags
• CCD_loop_close() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer
• CCD_loop_close_sample_omega_recursively() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer
• ccd_loop_closure_mover_ : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer
• ccd_mover() : protocols::splice::SpliceOut
• ccd_mover_ : protocols::loops::loop_closure::ccd::LoopClosure
• ccd_threshold_ : protocols::antibody::H3PerturbCCD
• ccd_tolerance_ : protocols::rna::movers::RNA_LoopCloser
• CCDEndsGraftMover() : protocols::grafting::CCDEndsGraftMover
• CCDLoopClosureMover() : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• CCDMoveWrapper() : protocols::rbsegment_relax::CCDMoveWrapper
• ccenter : core::scoring::APBSConfig
• CCluster() : protocols::pockets::CCluster
• CClusterSet : protocols::pockets::CCluster , protocols::pockets::CClusterSet
• CCs : core::scoring::electron_density::ElectronDensity
• ccw : core::scoring::packstat::Event , core::scoring::packstat::trace
• ccw_angle : core::scoring::packstat::Event
• CD_1B_Methods : core::scoring::ScoreFunction
• cd_1b_methods_ : core::scoring::ScoreFunction
• cd_1b_types() : core::scoring::ScoreFunction
• cd_2b_begin() : core::scoring::ScoreFunction
• cd_2b_end() : core::scoring::ScoreFunction
• cd_2b_intrares_ : core::scoring::ScoreFunction
• cd_2b_intrares_begin() : core::scoring::ScoreFunction
• cd_2b_intrares_end() : core::scoring::ScoreFunction
• CD_2B_Methods : core::scoring::ScoreFunction
• cd_2b_methods_ : core::scoring::ScoreFunction
• cd_2b_pose_ : protocols::match::downstream::ScoringSecMatchRPE
• cd_2b_types() : core::scoring::ScoreFunction
• CD_LR_2B_MethodIterator : core::scoring::ScoreFunction
• CD_LR_2B_Methods : core::scoring::ScoreFunction
• cd_lr_2b_methods_ : core::scoring::ScoreFunction
• cd_lr_2b_methods_begin() : core::scoring::ScoreFunction
• cd_lr_2b_methods_end() : core::scoring::ScoreFunction
• cd_lr_2b_types() : core::scoring::ScoreFunction
• cd_sfxn_ : protocols::minimization_packing::GreenPacker
• cdf_ : core::chemical::mainchain_potential::MainchainScoreTable , core::scoring::Ramachandran , protocols::nonlocal::BiasedFragmentMover
• cdf_by_torsion_bin_ : core::scoring::Ramachandran
• cdf_for_aa() : core::scoring::Ramachandran
• cdf_for_aa_for_torsion_bin() : core::scoring::Ramachandran
• cdr() : protocols::antibody::CDRSetOptions , protocols::antibody::clusters::CDRCluster , protocols::antibody::clusters::ClusterData , protocols::antibody::design::CDRSeqDesignOptions , protocols::antibody::ParatopeMetric< T >
• cdr1 : protocols::tcr::TCRmodel::tcrtmplts
• cdr2hv4 : protocols::tcr::TCRmodel::tcrtmplts
• cdr3 : protocols::tcr::TCRmodel::tcrtmplts
• cdr_ : protocols::antibody::CDRSetOptions , protocols::antibody::clusters::CDRCluster , protocols::antibody::constraints::CDRDihedralConstraintMover , protocols::antibody::design::CDRGraftDesignOptions , protocols::antibody::design::CDRSeqDesignOptions
• cdr_cache_limit_ : protocols::antibody::AntibodyDatabaseManager
• cdr_cluster_enum_to_string() : protocols::antibody::clusters::CDRClusterEnumManager
• CDR_CLUSTER_INFO : core::pose::datacache::CacheableDataType
• cdr_cluster_is_present() : protocols::antibody::clusters::CDRClusterEnumManager
• cdr_cluster_manager_ : protocols::antibody::AntibodyInfo
• cdr_cluster_set_ : protocols::antibody::AntibodyInfo
• cdr_cluster_string_to_enum() : protocols::antibody::clusters::CDRClusterEnumManager
• cdr_constraint_ : protocols::antibody::AntibodyModelerProtocol
• cdr_definition : protocols::antibody::AntibodyNumbering
• cdr_definition_ : protocols::antibody::AntibodyCDRGrafter , protocols::antibody::residue_selector::AntibodyRegionSelector , protocols::antibody::residue_selector::CDRResidueSelector , protocols::antibody::task_operations::DisableAntibodyRegionOperation , protocols::antibody::task_operations::DisableCDRsOperation , protocols::antibody::task_operations::RestrictToCDRsAndNeighbors
• cdr_definition_enum_to_string() : protocols::antibody::AntibodyEnumManager
• cdr_definition_file_ : protocols::antibody::AntibodyNumberingParser
• cdr_definition_is_present() : protocols::antibody::AntibodyEnumManager
• cdr_definition_string_to_enum() : protocols::antibody::AntibodyEnumManager
• cdr_definition_to_enum_ : protocols::antibody::AntibodyEnumManager
• cdr_definition_to_string_ : protocols::antibody::AntibodyEnumManager
• cdr_definition_transform : protocols::antibody::AntibodyNumbering
• cdr_definition_transform_present() : protocols::antibody::AntibodyInfo
• cdr_definitions_defined_ : protocols::antibody::AntibodyNumberingParser
• cdr_definitions_defined_using_ : protocols::antibody::AntibodyNumberingParser
• cdr_design_options_ : protocols::antibody::design::AntibodySeqDesignTFCreator
• cdr_dihedral_cst_mover_ : protocols::antibody::design::AntibodyDesignMover
• cdr_dock_map_ : protocols::antibody::LHRepulsiveRampLegacy , protocols::antibody::RefineBetaBarrel
• cdr_graft_design_options_ : protocols::antibody::design::AntibodyDesignMover
• cdr_h3_cut_ : protocols::antibody_legacy::Antibody
• CDR_H3_filter() : protocols::antibody_legacy::CDRH3Modeler
• cdr_h3_frags_ : protocols::antibody::H3PerturbCCD , protocols::antibody_legacy::CDRH3Modeler
• cdr_is_set_ : protocols::antibody::constraints::CDRDihedralConstraintMover
• cdr_landmark_enum_to_string() : protocols::antibody::AntibodyEnumManager
• cdr_landmark_is_present() : protocols::antibody::AntibodyEnumManager
• cdr_landmark_string_to_enum() : protocols::antibody::AntibodyEnumManager
• cdr_landmark_to_enum_ : protocols::antibody::AntibodyEnumManager
• cdr_landmark_to_string_ : protocols::antibody::AntibodyEnumManager
• cdr_loop_ : protocols::antibody::GraftedStemOptimizer
• cdr_loop_end_ : protocols::antibody::CloseOneCDRLoop
• cdr_loop_start_ : protocols::antibody::CloseOneCDRLoop
• CDR_loops_ : protocols::antibody::snugdock::SnugDock , protocols::antibody::snugdock::SnugDockProtocol
• cdr_name_ : protocols::antibody::GraftedStemOptimizer , protocols::antibody::GraftOneCDRLoop
• cdr_name_enum_to_string() : protocols::antibody::AntibodyEnumManager
• cdr_name_is_present() : protocols::antibody::AntibodyEnumManager
• cdr_name_string_to_enum() : protocols::antibody::AntibodyEnumManager
• cdr_name_to_enum_ : protocols::antibody::AntibodyEnumManager
• cdr_name_to_string_ : protocols::antibody::AntibodyEnumManager
• cdr_numbering : protocols::antibody::AntibodyNumbering
• cdr_options_ : protocols::antibody::CDRSetOptionsParser , protocols::antibody::design::CDRGraftDesignOptionsParser , protocols::antibody::design::CDRSeqDesignOptionsParser
• cdr_overhang() : protocols::antibody::design::GeneralAntibodyModeler
• cdr_pdb_numbered_ : protocols::antibody::AntibodyInfo
• cdr_seq_ : protocols::antibody::design::NativeAntibodySeq
• cdr_seq_design_options_ : protocols::antibody::design::AntibodyDesignMover
• cdr_sequence_move_ : protocols::antibody::CDRsMinPackMin
• cdr_set_ : protocols::antibody::design::AntibodyDesignMover
• cdr_set_options_ : protocols::antibody::design::AntibodyDesignMover
• cdr_weight_ : protocols::antibody::design::CDRGraftDesignOptions
• CDRCluster() : protocols::antibody::clusters::CDRCluster
• CDRClusterEnumManager() : protocols::antibody::clusters::CDRClusterEnumManager
• CDRClusterFeatures() : protocols::antibody::clusters::CDRClusterFeatures
• CDRClusterMatcher() : protocols::antibody::clusters::CDRClusterMatcher
• CDRClusterSet() : protocols::antibody::clusters::CDRClusterSet
• CDRDBPose() : protocols::antibody::CDRDBPose
• CDRDBSequence() : protocols::antibody::CDRDBSequence
• CDRDihedralConstraintMover() : protocols::antibody::constraints::CDRDihedralConstraintMover
• CDRGraftDesignOptions() : protocols::antibody::design::CDRGraftDesignOptions
• CDRGraftDesignOptionsParser() : protocols::antibody::design::CDRGraftDesignOptionsParser
• cdrh3_map_ : protocols::antibody::H3RefineCCD
• CDRH3Modeler() : protocols::antibody_legacy::CDRH3Modeler
• cdrh_ : protocols::antibody_legacy::Antibody
• cdrl_ : protocols::antibody_legacy::Antibody
• CDRResidueSelector() : protocols::antibody::residue_selector::CDRResidueSelector
• cdrs_ : protocols::antibody::clusters::CDRClusterFeatures , protocols::antibody::design::MutateFrameworkForCluster , protocols::antibody::residue_selector::CDRResidueSelector , protocols::antibody::task_operations::AddCDRProfileSetsOperation , protocols::antibody::task_operations::DisableCDRsOperation , protocols::antibody::task_operations::RestrictToCDRsAndNeighbors
• cdrs_min_pack_min_ : protocols::antibody::GraftCDRLoopsProtocol
• cdrs_to_apply_ : protocols::antibody::constraints::ParatopeSiteConstraintMover
• cdrs_to_design_ : protocols::antibody::design::AntibodyDesignMover
• cdrs_to_graft_ : protocols::antibody::AntibodyCDRGrafter
• CDRSeqDesignOptions() : protocols::antibody::design::CDRSeqDesignOptions
• CDRSeqDesignOptionsParser() : protocols::antibody::design::CDRSeqDesignOptionsParser
• CDRSetOptions() : protocols::antibody::CDRSetOptions
• CDRSetOptionsParser() : protocols::antibody::CDRSetOptionsParser
• CDRsMinPackMin() : protocols::antibody::CDRsMinPackMin
• Cell() : core::sequence::Cell
• cell_angles : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• cell_dimensions : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• cell_index() : protocols::canonical_sampling::BiasEnergy::Histogram< T >
• cell_vertices_ : core::scoring::PDatom , core::scoring::power_diagram::PDsphere
• cell_volume : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• cellAngles : core::scoring::electron_density::ElectronDensity
• cellDimensions : core::scoring::electron_density::ElectronDensity
• CellOP : core::sequence::DP_Matrix
• cen : protocols::kinmatch::KRSQuery , protocols::pockets::SmallMol
• cen1_scorefxn_ : protocols::hybridization::MRMover
• cen2_scorefxn_ : protocols::hybridization::MRMover
• CEN2FULLATOM : protocols::abinitio::IterativeBase
• cen_cfg_file_ : core::scoring::saxs::SAXSEnergy
• cen_constraint_ : protocols::ub_e2c::ubi_e2c_modeler
• cen_cst_ : protocols::antibody::AntibodyModelerProtocol , protocols::antibody::H3PerturbCCD , protocols::antibody_legacy::CDRH3Modeler
• cen_cst_in_ : protocols::hybridization::HybridizeProtocol
• cen_dist10_pad : core::scoring::EnvPairPotential , core::scoring::membrane::MembraneData , core::scoring::MembranePotential
• cen_dist10_pad_ : core::scoring::membrane::MembraneData
• cen_dist10_pad_hinv : core::scoring::EnvPairPotential , core::scoring::membrane::MembraneData , core::scoring::MembranePotential
• cen_dist10_pad_hinv_ : core::scoring::membrane::MembraneData
• cen_dist10_pad_minus : core::scoring::EnvPairPotential , core::scoring::membrane::MembraneData , core::scoring::MembranePotential
• cen_dist10_pad_minus_ : core::scoring::membrane::MembraneData
• cen_dist10_pad_plus : core::scoring::EnvPairPotential , core::scoring::membrane::MembraneData , core::scoring::MembranePotential
• cen_dist10_pad_plus_ : core::scoring::membrane::MembraneData
• cen_dist12_pad : core::scoring::EnvPairPotential , core::scoring::membrane::MembraneData , core::scoring::MembranePotential
• cen_dist12_pad_ : core::scoring::membrane::MembraneData
• cen_dist12_pad_hinv : core::scoring::EnvPairPotential , core::scoring::membrane::MembraneData , core::scoring::MembranePotential
• cen_dist12_pad_hinv_ : core::scoring::membrane::MembraneData
• cen_dist12_pad_minus : core::scoring::EnvPairPotential , core::scoring::membrane::MembraneData , core::scoring::MembranePotential
• cen_dist12_pad_minus_ : core::scoring::membrane::MembraneData
• cen_dist12_pad_plus : core::scoring::EnvPairPotential , core::scoring::membrane::MembraneData
• cen_dist12_pad_plus_ : core::scoring::membrane::MembraneData
• cen_dist5_pad : core::scoring::EnvPairPotential , core::scoring::membrane::MembraneData , core::scoring::MembranePotential
• cen_dist5_pad_ : core::scoring::membrane::MembraneData
• cen_dist5_pad_hinv : core::scoring::EnvPairPotential , core::scoring::membrane::MembraneData , core::scoring::MembranePotential
• cen_dist5_pad_hinv_ : core::scoring::membrane::MembraneData
• cen_dist5_pad_minus : core::scoring::EnvPairPotential , core::scoring::membrane::MembraneData , core::scoring::MembranePotential
• cen_dist5_pad_minus_ : core::scoring::membrane::MembraneData
• cen_dist5_pad_plus : core::scoring::EnvPairPotential , core::scoring::membrane::MembraneData , core::scoring::MembranePotential
• cen_dist5_pad_plus_ : core::scoring::membrane::MembraneData
• cen_dist6_pad : core::scoring::EnvPairPotential , core::scoring::membrane::MembraneData
• cen_dist6_pad_ : core::scoring::membrane::MembraneData
• cen_dist6_pad_hinv : core::scoring::EnvPairPotential , core::scoring::membrane::MembraneData
• cen_dist6_pad_hinv_ : core::scoring::membrane::MembraneData
• cen_dist6_pad_plus : core::scoring::EnvPairPotential , core::scoring::membrane::MembraneData
• cen_dist6_pad_plus_ : core::scoring::membrane::MembraneData
• cen_dist7_pad : core::scoring::EnvPairPotential , core::scoring::membrane::MembraneData , core::scoring::MembranePotential
• cen_dist7_pad_ : core::scoring::membrane::MembraneData
• cen_dist7_pad_hinv : core::scoring::EnvPairPotential , core::scoring::membrane::MembraneData , core::scoring::MembranePotential
• cen_dist7_pad_hinv_ : core::scoring::membrane::MembraneData
• cen_dist7_pad_minus : core::scoring::EnvPairPotential , core::scoring::membrane::MembraneData , core::scoring::MembranePotential
• cen_dist7_pad_minus_ : core::scoring::membrane::MembraneData
• cen_dist7_pad_plus : core::scoring::EnvPairPotential , core::scoring::membrane::MembraneData , core::scoring::MembranePotential
• cen_dist7_pad_plus_ : core::scoring::membrane::MembraneData
• cen_dist_cutoff2 : core::scoring::EnvPairPotential
• cen_dist_cutoff_12_pad : core::scoring::CenRotEnvPairPotential , core::scoring::EnvPairPotential , core::scoring::SmoothEnvPairPotential
• Cen_Distance_Func() : core::scoring::disulfides::Cen_Distance_Func
• cen_distance_func_ : core::scoring::disulfides::CentroidDisulfidePotential
• cen_disulfide_potential_ : core::scoring::ScoringManager
• cen_dst_ : protocols::make_rot_lib::RotData
• cen_hb_potential_ : core::scoring::ScoringManager
• CEN_LIST_INFO : core::pose::datacache::CacheableDataType
• cen_res_polynom_map_ : core::scoring::membrane::MPResidueLipophilicityEnergy
• cen_res_spline_map_ : core::scoring::membrane::MPResidueLipophilicityEnergy
• cen_rot_pair_potential_ : core::scoring::ScoringManager
• cen_score() : protocols::abinitio::IterativeBase
• cen_score_ : protocols::abinitio::IterativeBase
• cen_score_patch() : protocols::abinitio::IterativeBase
• cen_score_patch_ : protocols::abinitio::IterativeBase
• cen_scorefxn() : protocols::comparative_modeling::LoopRelaxMover , protocols::grafting::AnchoredGraftMover
• cen_scorefxn_ : protocols::comparative_modeling::LoopRelaxMover , protocols::grafting::AnchoredGraftMover , protocols::legacy_sewing::LegacyAssemblyMover , protocols::relax::CentroidRelax , protocols::seeded_abinitio::CloseFold
• cen_seqpose_ : protocols::loop_grower::LoopGrower
• cen_sf_ : protocols::loop_grower::FragmentExtension , protocols::loop_grower::LoopGrower
• cen_vdw_ : protocols::ub_e2c::ubi_e2c_modeler
• CENcrd : protocols::simple_filters::ResidueDepthData
• cend : protocols::simple_moves::Hit
• cend_norm : protocols::simple_moves::Hit
• Cend_orient() : protocols::fldsgn::topology::SS_Base
• Cend_orient_ : protocols::fldsgn::topology::SS_Base
• Cend_pos() : protocols::fldsgn::topology::SS_Base
• Cend_pos_ : protocols::fldsgn::topology::SS_Base
• cenfilter() : protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashMoverWrapper
• cenfilter_ : protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashMoverWrapper
• CenHBEnergy() : core::scoring::methods::CenHBEnergy
• CenHBPotential() : core::scoring::CenHBPotential
• cenlist_from_pose() : core::scoring::CenRotEnvPairPotential , core::scoring::EnvPairPotential , core::scoring::SmoothEnvPairPotential
• CenListInfo() : core::scoring::CenListInfo
• cenpack_ : core::scoring::CenRotEnvPairPotential , core::scoring::SmoothEnvPairPotential
• cenpack_log_ : core::scoring::EnvPairPotential
• CenPairEnergy() : core::scoring::methods::CenPairEnergy
• CenPairMotifDegreeEnergy() : core::scoring::methods::CenPairMotifDegreeEnergy
• CenPairMotifEnergy() : core::scoring::methods::CenPairMotifEnergy
• cenrot_ : protocols::hybridization::CartesianHybridize , protocols::hybridization::HybridizeProtocol , protocols::loop_grower::FragmentExtension , protocols::loop_grower::LoopGrower
• cenrot_libraries_ : core::pack::dunbrack::cenrot::CenrotLibrary
• cenrot_repack_scorefxn_ : protocols::hybridization::CartesianHybridize
• cenrot_sf_ : protocols::loop_grower::FragmentExtension , protocols::loop_grower::LoopGrower
• CenRotDunEnergy() : core::pack::dunbrack::cenrot::CenRotDunEnergy
• CenRotEnvEnergy() : core::scoring::methods::CenRotEnvEnergy
• CenRotEnvPairPotential() : core::scoring::CenRotEnvPairPotential
• cenrotfilter_ : protocols::loop_grower::LoopGrower
• CenrotLibrary() : core::pack::dunbrack::cenrot::CenrotLibrary
• CenRotPairEnergy() : core::scoring::methods::CenRotPairEnergy
• CenrotRotamerLibrarySpecification() : core::chemical::rotamers::CenrotRotamerLibrarySpecification
• censcale_ : protocols::hybridization::MRMover
• censtartingscore_ : protocols::loop_grower::LoopGrower
• center : core::chemical::rna::GaussianParameter , core::conformation::membrane::Span , core::conformation::UltraLightResidue , core::id::NamedStubID , core::id::StubID , core::kinematics::Stub , core::pose::Pose , core::scoring::APBSConfig , core::scoring::MembraneEmbed , core::scoring::packstat::CavityBallCluster , core::scoring::packstat::PackingScore , protocols::electron_density::RefinementResult , protocols::membrane::geometry::EmbeddingDef , protocols::scoring::Interface , protocols::sparta::RingData
• center_ : core::conformation::UltraLightResidue , core::id::NamedStubID , core::id::StubID , core::scoring::hbonds::HBondEnergy , core::scoring::MembraneEmbed , core::scoring::nmr::NMRGridSearch , protocols::cyclic_peptide::FlipChiralityMover , protocols::docking::membrane::MPDockingMover , protocols::membrane::AddMembraneMover , protocols::membrane::geometry::EmbeddingDef , protocols::membrane::SetMembraneCenterMover , protocols::membrane::SetMembranePositionMover , protocols::qsar::scoring_grid::SingleGrid , protocols::rigid::WholeBodyRotationMover , protocols::viewer::triangle
• center_all() : protocols::toolbox::DecoySetEvaluation
• center_assigned_ : protocols::cyclic_peptide::FlipChiralityMover
• center_at_interface_ : protocols::docking::DockingInitialPerturbation
• center_cluster_db_path_ : protocols::antibody::clusters::CDRClusterMatcher
• center_is_set_ : core::scoring::nmr::NMRGridSearch
• center_jumps_in_single_stranded() : core::import_pose::options::RNA_FragmentMonteCarloOptions
• center_jumps_in_single_stranded_ : core::import_pose::options::RNA_FragmentMonteCarloOptions , protocols::rna::denovo::RNA_DeNovoPoseInitializer
• center_mass() : protocols::cyclic_peptide::FlipChiralityMover
• center_ndx_ : protocols::toolbox::KClusterElement
• center_of_mass() : core::scoring::epr_deer::EPRSpinLabel , protocols::hybridization::FoldTreeHybridize , protocols::loops::Loops , protocols::pose_length_moves::InsertResMover , protocols::simple_moves::Tumble
• center_of_mass_ : core::scoring::rna::RG_Energy_RNA
• center_on_middle_ca_ : protocols::electron_density::DockIntoDensityMover
• center_resnumber_ : protocols::relax::membrane::MPRangeRelaxMover , protocols::relax::RangeRelaxMover
• center_structure() : protocols::toolbox::DecoySetEvaluation
• centerofmass_ : protocols::loop_grower::LoopPartialSolution
• centers : core::scoring::packstat::PosePackData
• centers_ : core::scoring::packstat::PackingScore , core::scoring::rna::RNA_SuitePotential , core::scoring::rna::TNA_SuitePotential , protocols::qsar::scoring_grid::GridManager
• central_atoms_to_score() : core::scoring::mm::MMBondAngleResidueTypeParamSet
• central_atoms_to_score_ : core::scoring::methods::MMBondAngleEnergy , core::scoring::mm::MMBondAngleResidueTypeParamSet
• central_molecule_pdb_ : protocols::simple_moves::PeriodicBoxMover
• central_residue() : protocols::pose_metric_calculators::NeighborsByDistanceCalculator
• central_residue_ : protocols::pose_metric_calculators::NeighborsByDistanceCalculator
• central_residue_group_selector() : core::select::residue_selector::CloseContactResidueSelector
• central_residues() : protocols::pose_metric_calculators::NeighborhoodByDistanceCalculator
• central_residues_ : protocols::pose_metric_calculators::NeighborhoodByDistanceCalculator
• central_residues_selector_ : core::select::residue_selector::CloseContactResidueSelector
• central_resno_ : protocols::simple_moves::PeriodicBoxMover
• centralE : protocols::simple_moves::ThermodynamicData
• centroid() : core::import_pose::ImportPoseOptions , protocols::fold_from_loops::movers::NubInitioLoopClosureMover
• centroid_ : core::import_pose::ImportPoseOptions , protocols::fold_from_loops::movers::NubInitioLoopClosureMover , protocols::normalmode::NormalModeRelaxMover
• centroid_allowed_CSP_fraction_ : protocols::ub_e2c::ubi_e2c_modeler
• centroid_archive_ : protocols::abinitio::IterativeAbrelax
• centroid_axis() : protocols::rigid::RigidBodyTransMover
• centroid_bin_max() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• centroid_bin_max_ : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• centroid_bin_min() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• centroid_bin_min_ : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• centroid_bin_size() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• centroid_bin_size_ : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• centroid_build() : protocols::fldsgn::BluePrintBDR , protocols::forge::components::BDR , protocols::forge::components::VarLengthBuild , protocols::forge::remodel::RemodelMover
• centroid_CSP_weight_ : protocols::ub_e2c::ubi_e2c_modeler
• centroid_data_ : protocols::make_rot_lib::MakeRotLibOptionsData
• centroid_dG : protocols::analysis::InterfaceData
• centroid_dist_scores_ : core::scoring::disulfides::Cen_Distance_Func
• centroid_filter() : protocols::ub_e2c::ubi_e2c_modeler
• centroid_input_pose_ : protocols::topology_broker::RigidChunkClaimer
• centroid_loop_mover_str() : protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover
• centroid_loop_mover_str_ : protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover
• centroid_mapping_distance_padding_ : protocols::noesy_assign::PeakAssignmentParameters
• centroid_max_temperature() : protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions
• centroid_max_temperature_ : protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions
• centroid_min_temperature() : protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions
• centroid_min_temperature_ : protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions
• centroid_mode_perturbation() : protocols::ub_e2c::ubi_e2c_modeler
• centroid_move_generator_ : protocols::helical_bundle_predict::HelicalBundlePredictApplication
• centroid_neighbors() : core::scoring::membrane::MPHelicalityEnergy , core::scoring::membrane::MPResidueLipophilicityEnergy
• centroid_non_CSP_weight_ : protocols::ub_e2c::ubi_e2c_modeler
• centroid_output() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• centroid_output_ : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• centroid_relax_ : protocols::surface_docking::SurfaceDockingProtocol
• centroid_score_diff_cut() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• centroid_score_diff_cut_ : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions , protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• centroid_score_ref_ : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• centroid_scorefunction() : protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover
• centroid_scorefunction_ : protocols::anchored_design::AnchorMoversData , protocols::floppy_tail::FloppyTailMover , protocols::metal_interface::ZincHeterodimerMover , protocols::splice::TailSegmentMover
• centroid_scorefunction_min_ : protocols::anchored_design::AnchorMoversData
• centroid_scorefxn() : protocols::abinitio::Protocol , protocols::fold_from_loops::movers::NubInitioLoopClosureMover
• centroid_scorefxn_ : protocols::fold_from_loops::movers::NubInitioLoopClosureMover , protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• centroid_scores_ : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• centroid_screen() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• centroid_screen_ : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions , protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• centroid_sfx_ : protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover
• centroid_sfxn_ : protocols::helical_bundle_predict::HelicalBundlePredictApplication
• centroid_stage() : protocols::loop_modeler::LoopModeler
• centroid_stage_ : protocols::loop_modeler::LoopModeler
• centroid_temperature_generator_ : protocols::helical_bundle_predict::HelicalBundlePredictApplication
• centroid_vdw_ref_ : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• centroid_weights() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• centroid_weights_ : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• centroid_x : protocols::stepwise::modeler::rna::rigid_body::BaseBin
• centroid_xyz() : core::scoring::dna::DNA_EnvPairPotential
• centroid_y : protocols::stepwise::modeler::rna::rigid_body::BaseBin
• centroid_z : protocols::stepwise::modeler::rna::rigid_body::BaseBin
• CentroidDistanceScreener() : protocols::stepwise::screener::CentroidDistanceScreener
• CentroidDisulfideEnergy() : core::scoring::disulfides::CentroidDisulfideEnergy
• CentroidDisulfideEnergyComponents() : core::scoring::disulfides::CentroidDisulfideEnergyComponents
• CentroidDisulfideEnergyContainer() : core::scoring::disulfides::CentroidDisulfideEnergyContainer
• CentroidDisulfideNeighborConstIterator() : core::scoring::disulfides::CentroidDisulfideNeighborConstIterator
• CentroidDisulfideNeighborIterator() : core::scoring::disulfides::CentroidDisulfideNeighborIterator
• CentroidDisulfidePotential() : core::scoring::disulfides::CentroidDisulfidePotential
• CentroidRelax() : protocols::relax::CentroidRelax
• CentroidRelaxMover() : protocols::surface_docking::CentroidRelaxMover
• CentroidRotamerSampleData() : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• centroids_ : protocols::make_rot_lib::MakeRotLibMover
• CentroidScatter() : core::scoring::fiber_diffraction::CentroidScatter
• centroidscore_filter_ : protocols::protein_interface_design::movers::DockWithHotspotMover
• cenType_ : protocols::simple_moves::StructProfileMover
• cenx() : protocols::frag_picker::VallResidue
• cenx_ : protocols::frag_picker::VallResidue
• ceny() : protocols::frag_picker::VallResidue
• ceny_ : protocols::frag_picker::VallResidue
• cenz() : protocols::frag_picker::VallResidue
• cenz_ : protocols::frag_picker::VallResidue
• cfac : core::scoring::APBSConfig
• cg_ : protocols::fldsgn::SheetRemodelConstraintGenerator , protocols::forge::constraints::NtoCConstraintGenerator , protocols::forge::remodel::GenericRemodelConstraintGenerator
• CG_const_ : protocols::splice::Splice , protocols::splice::SpliceOut
• cglen : core::scoring::APBSConfig
• cgs_ : protocols::constraint_filters::ConstraintScoreFilter , protocols::denovo_design::movers::FastDesign
• ch1_ : protocols::protein_interface_design::movers::LoopFinder
• ch1_begin_num_ : core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator
• ch1_end_num_ : core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator
• ch2_ : protocols::protein_interface_design::movers::LoopFinder
• ch2_begin_num_ : core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator
• ch2_end_num_ : core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator
• chain() : core::conformation::Residue , core::fragment::AnnotatedFragData , core::fragment::FragData
• CHAIN : core::io::HeaderInformation
• chain : core::io::raw_data::DisulfideFile::ResNum , core::pack::task::operation::ChainIs , core::pose::PDBInfo , core::pose::Pose , core::pose::ResidueIndexDescriptionPDB , core::scoring::packstat::SimplePDB_Atom , protocols::antibody::clusters::CDRCluster , protocols::antibody::design::PDBNumbering , protocols::antibody::PDBLandmark , protocols::dna::DnaDesignDef , protocols::frags::VallData , protocols::ligand_docking::ligand_options::InterfaceInfo , protocols::ligand_docking::StartFrom , protocols::ligand_docking::Transform_info , protocols::pose_creation::ExtendedPoseMover
• Chain() : protocols::pose_length_moves::Chain
• chain() : protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots , protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover , protocols::protein_interface_design::movers::SetAtomTree , protocols::qsar::scoring_grid::GridSet , protocols::simple_filters::AngleToVector , protocols::splice::AlignEndsMover , protocols::task_operations::PreventChainFromRepackingOperation , protocols::task_operations::RestrictChainToRepackingOperation , protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation , protocols::task_operations::RestrictToAlignedSegmentsOperation , protocols::task_operations::SelectResiduesWithinChainOperation
• chain1() : protocols::simple_ddg::AlaScan
• chain1_ : core::scoring::motif::ResPairMotif , protocols::analysis::InterfaceAnalyzerMover , protocols::denovo_design::connection::ConnectionArchitect , protocols::simple_ddg::AlaScan
• chain1_interface_residues_ : core::pose::metrics::simple_calculators::InterfaceNeighborDefinitionCalculator , core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator
• chain1_letter_ : core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator
• chain1_number_ : core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator
• chain2() : protocols::simple_ddg::AlaScan
• chain2_ : core::scoring::motif::ResPairMotif , protocols::analysis::InterfaceAnalyzerMover , protocols::denovo_design::connection::ConnectionArchitect , protocols::simple_ddg::AlaScan
• chain2_interface_residues_ : core::pose::metrics::simple_calculators::InterfaceNeighborDefinitionCalculator , core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator
• chain2_letter_ : core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator
• chain2_number_ : core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator
• chain_ : core::conformation::Residue , core::fragment::AnnotatedFragData , core::io::nmr::AtomSelection , core::pack::task::operation::ChainIs , core::pack::task::operation::ResiduePDBIndexIs::ChainPos , core::pose::ResidueIndexDescriptionPDB , core::scoring::methods::D2H_SA_Energy , core::select::residue_selector::SSElementSelector , protocols::antibody::clusters::CDRCluster , protocols::antibody::PDBLandmark , protocols::denovo_design::movers::ExtendChainMover , protocols::features::ResidueGridScoresFeatures , protocols::features::ScreeningFeatures , protocols::frags::VallData , protocols::ligand_docking::AddHydrogens , protocols::ligand_docking::AtomCountFilter , protocols::ligand_docking::ChainExistsFilter , protocols::ligand_docking::CompleteConnectionsFilter , protocols::ligand_docking::GrowLigand , protocols::ligand_docking::HBondAcceptorFilter , protocols::ligand_docking::HBondDonorFilter , protocols::ligand_docking::HeavyAtomFilter , protocols::ligand_docking::LigandArea , protocols::ligand_docking::MinimizeLigand , protocols::ligand_docking::MolarMassFilter , protocols::ligand_docking::MolecularMassFilter , protocols::ligand_docking::RandomConformers , protocols::ligand_docking::TetherLigand , protocols::ligand_docking::WriteLigandMolFile , protocols::nmr::pcs::PCSLigandTransformMover , protocols::pmut_scan::MutationData , protocols::pose_creation::ExtendedPoseMover , protocols::pose_creation::MakeJunctionsMover , protocols::pose_creation::MergePDBMover , protocols::pose_length_moves::InsertResMover , protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots , protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover , protocols::qsar::qsarMover , protocols::qsar::scoring_grid::GridSet , protocols::qsar::scoring_grid::SingleGrid , protocols::simple_filters::AngleToVector , protocols::simple_filters::NetChargeFilter , protocols::simple_filters::PackStatFilter , protocols::simple_filters::ResidueSetChainEnergyFilter , protocols::simple_moves::FavorSequenceProfile , protocols::simple_moves::ReportXYZ , protocols::splice::AlignEndsMover , protocols::task_operations::JointSequenceOperation , protocols::task_operations::PreventChainFromRepackingOperation , protocols::task_operations::RestrictChainToRepackingOperation , protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation , protocols::task_operations::RestrictToAlignedSegmentsOperation , protocols::task_operations::RestrictToTerminiOperation , protocols::task_operations::SelectResiduesWithinChainOperation
• chain_B_resNum_ : protocols::features::strand_assembly::SandwichFragment
• chain_begin() : core::conformation::Conformation , core::pose::Pose
• chain_boundaries() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• chain_boundaries_ : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• chain_bounds_ : protocols::hbnet::HBNet
• chain_break_grid_index_screening : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• chain_break_res_ : protocols::topology_broker::AsymFoldandDockClaimer
• chain_break_scorefxn_ : protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker
• chain_break_screening_count : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• chain_break_screening_general() : protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker
• chain_break_screening_pose_ : protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker
• chain_closable_geometry_checker_ : protocols::stepwise::screener::RNA_ChainClosableGeometryResidueBasedScreener , protocols::stepwise::screener::RNA_ChainClosableGeometryScreener , protocols::stepwise::screener::RNA_ChainClosableGeometryStubBasedScreener
• chain_closable_geometry_count : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• chain_closable_geometry_count2 : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• chain_closable_geometry_count3 : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• chain_closable_geometry_screen : protocols::stepwise::modeler::rna::Filterer_Count
• chain_closable_geometry_to_anchor_checker_ : protocols::stepwise::screener::AnchorSugarScreener
• chain_closing_attempts_ : protocols::protein_interface_design::movers::PlaceOnLoop
• chain_closure_checker_ : protocols::stepwise::screener::RNA_ChainClosureScreener
• chain_connections() : core::import_pose::RNA_BasePairHandler , core::import_pose::RNA_DeNovoParameters
• chain_connections_ : core::import_pose::RNA_BasePairHandler , core::import_pose::RNA_DeNovoParameters , core::import_pose::RNA_JumpMover
• chain_cut() : protocols::simple_moves::CutChainMover
• chain_end() : core::conformation::Conformation , core::pose::Pose
• chain_ending : protocols::indexed_structure_store::ResidueEntry
• chain_endings() : core::conformation::Conformation , core::io::silent::BinarySilentStruct , core::io::silent::ProteinSilentStruct_Template< T > , protocols::environment::ProtectedConformation
• chain_endings_ : core::conformation::Conformation , core::io::silent::BinarySilentStruct , core::io::silent::ProteinSilentStruct_Template< T >
• chain_endings_str() : core::io::silent::BinarySilentStruct , core::io::silent::ProteinSilentStruct_Template< T >
• chain_endpoints : protocols::indexed_structure_store::search::StructureData
• chain_for_moltenres() : protocols::hbnet::HBNet
• chain_for_resid() : protocols::hbnet::HBNet
• chain_groups_ : protocols::analysis::InterfaceAnalyzerMover
• chain_id : protocols::ligand_docking::ligand_options::InterfaceInfo , protocols::ligand_docking::Rotate_info , protocols::ligand_docking::Translate_info , protocols::simple_moves::CutChainMover
• chain_id_ : protocols::simple_moves::CutChainMover
• chain_ids() : protocols::ligand_docking::TransformEnsemble_info , protocols::simple_ddg::ddG
• chain_ids_ : protocols::features::InterfaceDdGMover , protocols::simple_ddg::ddG , protocols::simple_ddg::DdgFilter , protocols::simple_moves::SwitchChainOrderMover
• chain_ids_to_exclude_ : protocols::ligand_docking::Translate
• chain_index : core::io::mmtf::sd_index
• chain_letter() : protocols::ligand_docking::Rotate_info , protocols::ligand_docking::Translate_info
• chain_letter_ : core::pose::ResidueIndexDescriptionChainEnd
• chain_letter_to_number() : core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator
• chain_letters() : protocols::pose_metric_calculators::ResidueDecompositionByChainCalculator
• chain_letters_ : protocols::pose_metric_calculators::ResidueDecompositionByChainCalculator
• chain_map_ : protocols::moves::StructureRestrictor
• chain_name : protocols::antibody::FrameWork
• chain_names_ : protocols::features::InterfaceDdGMover , protocols::simple_ddg::ddG
• chain_no_ : core::pose::ResidueIndexDescriptionChainEnd
• chain_num() : protocols::simple_filters::ChainBreak , protocols::simple_moves::DeleteChainMover , protocols::simple_moves::PSSM2BfactorMover , protocols::splice::Splice , protocols::splice::SpliceManager , protocols::task_operations::SeqprofConsensusOperation
• chain_num_ : protocols::simple_filters::ChainBreak , protocols::simple_moves::DeleteChainMover , protocols::simple_moves::PSSM2BfactorMover , protocols::splice::Splice , protocols::splice::SpliceManager , protocols::task_operations::SeqprofConsensusOperation
• chain_number_ : protocols::ligand_docking::Rotate_info , protocols::ligand_docking::Translate_info
• chain_numbers() : protocols::pose_metric_calculators::ResidueDecompositionByChainCalculator
• chain_numbers_ : protocols::pose_metric_calculators::ResidueDecompositionByChainCalculator
• chain_order() : protocols::simple_moves::SwitchChainOrderMover
• chain_pair_pose_prepared() : protocols::peptide_deriver::PeptideDeriverBasicStreamOutputter , protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter , protocols::peptide_deriver::PeptideDeriverOutputter , protocols::peptide_deriver::PeptideDeriverOutputterContainer , protocols::peptide_deriver::PeptideDeriverPoseOutputter
• CHAIN_RESID : core::pack::task::ResfileContents
• chain_sequence() : core::pose::Pose
• chain_sequences() : core::io::StructFileRep , core::pose::PDBInfo
• chain_sequences_ : core::io::StructFileRep , core::pose::PDBInfo
• chain_start_ : core::pose::ResidueIndexDescriptionChainEnd , protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockMoveRbJumpMover
• chain_string_ : protocols::ligand_docking::Rotate_info , protocols::ligand_docking::Translate_info
• chain_strings() : core::select::residue_selector::ChainSelector
• chain_strings_ : core::select::residue_selector::ChainSelector
• chain_to_cyclize_ : protocols::simple_moves::CyclizationMover
• chain_to_design_ : protocols::hotspot_hashing::HotspotStub , protocols::hotspot_hashing::HotspotStubSet , protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover , protocols::protein_interface_design::movers::SetupHotspotConstraintsMover
• chain_type() : core::conformation::membrane::ImplicitLipidInfo
• chain_type_ : core::conformation::membrane::ImplicitLipidInfo
• chainAfterLoop_ : protocols::pose_length_moves::NearNativeLoopCloser
• chainBeforeLoop_ : protocols::pose_length_moves::NearNativeLoopCloser
• chainbreak() : protocols::hybridization::FragmentBiasAssigner
• ChainBreak() : protocols::simple_filters::ChainBreak
• chainbreak_ : protocols::loop_grower::FragmentExtension , protocols::loop_grower::LoopGrower
• chainbreak_bias() : protocols::rigid::RigidBodyMotionMover
• CHAINBREAK_BOGUS_ATOM_ID() : core::id::AtomID
• CHAINBREAK_BOGUS_NAMED_ATOM_ID() : core::id::NamedAtomID
• chainbreak_check() : protocols::splice::Splice , protocols::splice::SpliceManager
• chainbreak_max_ : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• chainbreak_sfxn_ : protocols::rna::denovo::RNA_FragmentMonteCarlo
• chainbreak_suite_ : protocols::recces::sampler::rna::MC_RNA_KIC_Sampler , protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser , protocols::stepwise::sampler::rna::RNA_KIC_Sampler , protocols::stepwise::sampler::rna::RNA_KinematicCloser
• chainbreak_weight() : core::import_pose::options::RNA_FragmentMonteCarloOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• chainbreak_weight_ : core::import_pose::options::RNA_FragmentMonteCarloOptions , protocols::anchored_design::AnchorMoversData , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• ChainbreakDistFunc() : protocols::jumping::ChainbreakDistFunc
• ChainbreakEnergy() : core::scoring::methods::ChainbreakEnergy
• chainbreaks() : protocols::idealize::IdealizeMover
• chainbreaks_ : protocols::idealize::IdealizeMover
• chainbreakweights() : protocols::seeded_abinitio::CloseFold , protocols::seeded_abinitio::DefineMovableLoops
• chainbreakweights_ : protocols::seeded_abinitio::CloseFold , protocols::seeded_abinitio::DefineMovableLoops
• ChainCountFilter() : protocols::simple_filters::ChainCountFilter
• ChainExistsFilter() : protocols::ligand_docking::ChainExistsFilter
• chainID : core::io::AtomInformation , core::io::ModifiedResidueInformation , core::io::ResidueInformation , core::pose::PDBInfo::ResidueRecord , core::pose::PDBPoseMap::ResidueKey
• chainid : protocols::hbnet::HBondResStruct
• chainID1 : core::io::CisPeptideInformation , core::io::HELIXInformation , core::io::LinkInformation , core::io::SHEETInformation , core::io::SSBondInformation
• chainID2 : core::io::CisPeptideInformation , core::io::HELIXInformation , core::io::LinkInformation , core::io::SHEETInformation , core::io::SSBondInformation
• chainID_ : core::io::ResidueInformation
• ChainIs() : core::pack::task::operation::ChainIs
• ChainIsnt() : core::pack::task::operation::ChainIsnt
• chainName : protocols::sparta::PDB_Entry
• ChainPos() : core::pack::task::operation::ResiduePDBIndexIs::ChainPos
• chains() : core::io::StructFileRep , core::scoring::PQR , protocols::cluster::calibur::SimPDB , protocols::ligand_docking::InterfaceScoreCalculator , protocols::ligand_docking::TransformEnsemble_info , protocols::simple_moves::DeleteChainsMover
• chains_ : core::io::silent::SilentStruct , core::io::StructFileRep , protocols::constel::FilterByProxTerm , protocols::ligand_docking::HighResDocker , protocols::ligand_docking::HighResEnsemble , protocols::ligand_docking::InterfaceScoreCalculator , protocols::ligand_docking::Rotates , protocols::ligand_docking::SlideTogether , protocols::ligand_docking::StartFrom , protocols::pdbinfo_manipulations::SequenceSpecification , protocols::rbsegment_relax::OptimizeThreadingMover , protocols::seeded_abinitio::CloseFold , protocols::seeded_abinitio::DefineMovableLoops , protocols::simple_moves::DeleteChainsMover
• chains_exist_in_pose() : protocols::features::InterfaceFeatures
• chains_for_antigen_ : protocols::antibody::AntibodyInfo
• chains_for_cdrs_ : protocols::antibody::AntibodyInfo
• chains_from_termini() : core::conformation::Conformation , protocols::environment::ProtectedConformation
• chains_in_full_model() : core::pose::full_model_info::FullModelInfo , core::pose::full_model_info::FullModelParameters
• chains_to_ignore_ : protocols::energy_based_clustering::EnergyBasedClusteringOptions
• chains_to_ignore_loops_ : protocols::pack_interface::ProteinProteinInterfaceUpweighter , protocols::toolbox::IGInterfaceEdgeUpweighter
• chains_whose_residues_are_separate_chemical_entities() : core::io::StructFileRepOptions
• chains_whose_residues_are_separate_chemical_entities_ : core::io::StructFileRepOptions
• ChainSelector() : core::select::residue_selector::ChainSelector
• ChainSplitMover() : protocols::simple_moves::ChainSplitMover
• ChainTerm() : protocols::constel::ChainTerm
• chance_of_being_canonical_sw : protocols::features::strand_assembly::SandwichFeatures
• change_bond_type() : core::chemical::MutableResidueType
• change_chi_without_replacing_residue() : protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• change_chi_without_replacing_residue_ : protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• change_CoM_to_ligandCoM() : protocols::pockets::NonPlaidFingerprint
• change_conformation() : protocols::protein_interface_design::movers::AddChainBreak
• change_conformation_ : protocols::protein_interface_design::movers::AddChainBreak
• change_conformer() : protocols::ligand_docking::Transform , protocols::ligand_docking::TransformEnsemble
• change_conformers() : protocols::ligand_docking::TransformEnsemble
• change_espGrid_for_darc() : protocols::pockets::ElectrostaticpotentialGrid
• change_foldtree() : protocols::protein_interface_design::movers::AddChainBreak
• change_foldtree_ : protocols::protein_interface_design::movers::AddChainBreak , protocols::stepwise::monte_carlo::mover::TransientCutpointHandler
• change_FT_to_flankloop_ : protocols::antibody::H3RefineCCD
• change_FT_to_simpleloop_ : protocols::antibody::H3RefineCCD
• change_in_water_density_ : core::conformation::membrane::ImplicitLipidInfo
• change_volume_move() : protocols::simple_moves::PeriodicBoxMover
• change_weight() : protocols::moves::MonteCarlo
• ChangeAncestory() : core::chemical::ChangeAncestory
• ChangeAndResetFoldTreeMover() : protocols::simple_moves::ChangeAndResetFoldTreeMover
• ChangeBondType() : core::chemical::ChangeBondType
• changed() : core::scoring::FACTSResidueInfo , protocols::denovo_design::components::StructureData
• changed_ : core::scoring::FACTSResidueInfo
• changed_frags_ : protocols::struct_fragment::StructFragmentMover
• changed_residues_ : core::kinematics::ResidueCoordinateChangeList
• ChangeFoldTreeMover() : protocols::moves::ChangeFoldTreeMover
• changes_connections_on() : core::chemical::AddConnect , core::chemical::AddConnectAndTrackingVirt , core::chemical::AddConnectDeleteChildProton , core::chemical::ConnectSulfurAndMakeVirtualProton , core::chemical::Patch , core::chemical::PatchCase , core::chemical::PatchOperation , core::chemical::SetPolymerConnectAtom
• changes_to_wrong_aa() : core::chemical::ResidueTypeFinder
• changing_baseline() : protocols::simple_filters::DeltaFilter
• changing_baseline_ : protocols::simple_filters::DeltaFilter
• changing_seqpos_ : protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
• char2ss_type() : protocols::comparative_modeling::features::SSFeature
• char_type() : protocols::rbsegment_relax::RBResidueRange
• charge() : core::chemical::Atom , core::scoring::elec::electrie::ElecAtom , core::scoring::PQR , protocols::qsar::scoring_grid::ChargeAtom
• CHARGE : protocols::simple_filters::InterfaceHbondsFilter
• charge_ : core::chemical::AddAtom , core::chemical::Atom , core::chemical::gasteiger::GasteigerAtomTypeData , core::chemical::SetAtomicCharge , core::chemical::SetFormalCharge , core::chemical::SetNetFormalCharge , core::io::nmr::ParaIon , core::scoring::elec::electrie::ElecAtom
• charge_atom_list_ : protocols::qsar::scoring_grid::ChargeGrid
• charge_charge_electrostatic() : protocols::qsar::scoring_grid::ChargeGrid
• charge_charge_rep_cutoff_ : protocols::hbnet::HBNet
• charge_penalties_range_ : core::scoring::netcharge_energy::NetChargeEnergySetup
• ChargeAtom() : protocols::qsar::scoring_grid::ChargeAtom
• ChargeCalculator() : protocols::pose_metric_calculators::ChargeCalculator
• ChargeChargeFeatures() : protocols::features::ChargeChargeFeatures
• charged() : core::scoring::FACTSRsdTypeInfo
• charged_ : core::pack::task::operation::ResidueTypeFilter , core::scoring::FACTSRsdTypeInfo
• charged_chains_ : core::scoring::methods::PoissonBoltzmannEnergy
• Charged_Group : protocols::simple_filters::InterfaceHbondsFilter
• charged_res_ : protocols::simple_filters::InterfaceHbondsFilter
• charged_residues_ : core::scoring::methods::PoissonBoltzmannEnergy
• charged_residues_map_ : core::scoring::methods::PBLifetimeCache
• ChargeGrid() : protocols::qsar::scoring_grid::ChargeGrid
• charges() : core::scoring::elec::electrie::ElecAtom
• CharmmPeriodicFunc() : core::scoring::func::CharmmPeriodicFunc
• chbreak_intcpt_ : protocols::abinitio::abscript::AbscriptStageMover
• chbreak_sf_ : protocols::analysis::LoopAnalyzerMover
• chbreak_slope_ : protocols::abinitio::abscript::AbscriptStageMover
• CHEAT_CoM() : protocols::pockets::FingerprintBase
• check() : protocols::toolbox::KClusterElement
• check2bsc() : protocols::match::downstream::ScoringSecMatchRPE
• check_alignment_tolerance_ : protocols::stepwise::modeler::align::StepWisePoseAligner
• check_all_junctions_good() : protocols::pose_creation::MakeJunctionsMover
• check_and_accept() : protocols::denovo_design::movers::BuildDeNovoBackboneMover
• check_and_create_fragments() : protocols::hybridization::HybridizeProtocol , protocols::seeded_abinitio::SegmentHybridizer
• check_and_initialize() : protocols::hotspot_hashing::movers::PlaceProbeMover
• check_angle_in_range() : protocols::recces::sampler::MC_OneTorsion
• check_angles_in_range() : protocols::recces::sampler::rna::MC_RNA_KIC_Sampler
• check_annotation() : core::io::rna::RDAT
• check_annotations() : core::io::rna::RDAT
• check_atom_bin_in_range() : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• check_atom_numbers_for_backbone_oxygens() : core::scoring::rna::RNA_LowResolutionPotential
• check_auto_stop() : protocols::loop_grower::LoopGrower
• check_backbones_match() : protocols::energy_based_clustering::EnergyBasedClusteringProtocol
• check_balanced_secstruct() : core::pose::rna::RNA_SecStruct
• check_base_base_OK() : core::scoring::rna::RNA_FullAtomStackingEnergy , core::scoring::rna::StackElecEnergy
• check_base_pair() : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• check_base_pairs() : core::import_pose::RNA_BasePairHandler
• check_base_stack() : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• check_base_stack_in_partition() : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• check_basic_connectivity() : protocols::denovo_design::components::SolutionPredicate
• check_batch() : protocols::jd2::BatchJobInputter
• check_block_stack_res() : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• check_boltzmann() : protocols::moves::SimulatedTempering
• check_bounds() : core::scoring::func::SOGFunc , core::scoring::func::SOGFunc_Impl , core::scoring::motif::MotifHash
• check_calculator_exists() : core::pose::metrics::CalculatorFactory
• check_candidate_has_all_variant_sets() : core::chemical::ResidueTypeFinder
• check_canonicalness_cutoff_ : protocols::features::strand_assembly::SandwichFeatures
• check_cdr_quality() : protocols::antibody::AntibodyInfo
• check_centroid_interaction() : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• check_centroid_interaction_floating_base() : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• check_chain_closable_geometry() : protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker
• check_chain_closable_geometry_strict() : protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker
• check_chainbreak_variants() : protocols::topology_broker::TopologyBroker
• check_chains() : protocols::denovo_design::components::StructureData
• check_chbonded() : core::scoring::rna::data::RNA_DMS_Potential
• check_clash() : protocols::hbnet::HBNet
• check_clear_for_stacking() : core::scoring::rna::RNA_LowResolutionPotential
• check_close_chain_break() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• check_closure() : protocols::rna::movers::RNA_LoopCloser
• check_closure_criteria() : protocols::forge::remodel::RemodelLoopMover
• check_compatibility() : protocols::stepwise::modeler::rna::sugar::SugarModeling
• check_compatible_symmetry_type() : protocols::cyclic_peptide::crosslinker::Metal_HelperBase , protocols::cyclic_peptide::crosslinker::OctahedralMetal_Helper , protocols::cyclic_peptide::crosslinker::SquarePlanarMetal_Helper , protocols::cyclic_peptide::crosslinker::SquarePyramidalMetal_Helper , protocols::cyclic_peptide::crosslinker::TetrahedralMetal_Helper , protocols::cyclic_peptide::crosslinker::TrigonalPlanarMetal_Helper , protocols::cyclic_peptide::crosslinker::TrigonalPyramidalMetal_Helper
• check_compatible_with_sequence() : core::pose::rna::RNA_SecStruct
• check_conformers() : protocols::ligand_docking::Transform
• check_consistency() : core::conformation::signals::LengthEvent , protocols::denovo_design::components::StructureData
• check_coordinates() : protocols::loop_grower::LoopGrower
• check_correct_vector_lengths() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser
• check_data() : core::scoring::aa_composition_energy::AACompositionEnergySetup , core::scoring::netcharge_energy::NetChargeEnergySetup
• check_data_consistency() : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• check_default_full_repacker() : protocols::relax::ClassicRelax
• check_default_mc() : protocols::relax::ClassicRelax
• check_default_rottrial() : protocols::relax::ClassicRelax
• check_disjoint() : core::scoring::loop_graph::LoopGraph
• check_distance() : protocols::denovo_design::connection::AreConnectablePredicate
• check_disulfide_cb_distance() : protocols::denovo_design::DisulfidizeMover
• check_disulfide_match_rt() : protocols::denovo_design::DisulfidizeMover
• check_disulfide_score() : protocols::denovo_design::DisulfidizeMover
• check_disulfide_seqpos() : protocols::denovo_design::DisulfidizeMover
• check_domain_map() : core::pose::copydofs::CopyDofs , core::scoring::NeighborList
• check_downstream_hit_incompatibility() : protocols::match::Matcher
• check_duplicate() : protocols::pose_creation::MergePDBMover
• check_edges_for_atom_info() : core::kinematics::FoldTree
• check_elements() : protocols::fldsgn::filters::HSSTripletFilter
• check_ensemble_member_compatibility() : protocols::docking::DockingEnsemblePrepackProtocol
• check_entries() : protocols::indexed_structure_store::StructureStore
• check_equation() : core::simple_metrics::metrics::CalculatorMetric
• check_fa_dun() : protocols::match::upstream::BuildSet
• check_fa_dun_ : protocols::match::upstream::BuildSet
• check_features_reporter_dependencies() : protocols::features::ReportToDB
• check_file_size() : core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded
• check_filters() : protocols::abinitio::AbrelaxApplication , protocols::flexpep_docking::FlexPepDockingProtocol
• check_fold_tree() : core::kinematics::FoldTree
• check_fold_tree_cutpoints_ok() : protocols::rna::denovo::RNA_FragmentMonteCarlo
• check_fold_tree_OK() : core::import_pose::libraries::ChunkSet , core::import_pose::libraries::RNA_ChunkLibrary
• check_for_base_neighbor() : core::scoring::rna::RNA_LowResolutionPotential
• check_for_closeness() : protocols::rna::setup::RNA_CSA_JobDistributor , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::modeler::align::StepWiseClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• check_for_closeness_without_working_parameters() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• check_for_deprecated_commands() : core::pack::task::ResfileContents
• check_for_extra_column() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser
• check_for_graft_instruction_inconsistencies() : protocols::antibody::AntibodyDatabaseManager
• check_for_helix_merges() : protocols::helical_bundle_predict::HBPHelixAssignments
• check_for_input_domain_or_from_scratch() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• check_for_intramolecular_submotif_jump() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• check_for_loop_modeling_case() : protocols::rna::denovo::RNA_DeNovoProtocol , protocols::rna::denovo::RNA_FragmentMonteCarlo
• check_for_parse_error() : protocols::metal_interface::ZincSiteFinder
• check_for_parser_in_go_main() : protocols::jd2::JobDistributor
• check_for_precomputed_copy_dofs_info() : protocols::simple_moves::CopyDofMover
• check_for_symmetric_peaks() : protocols::noesy_assign::PeakAssignmentResidueMap
• check_for_top_designs() : protocols::antibody::design::AntibodyDesignMover
• check_for_unexpected_cutpoints() : core::scoring::loop_graph::LoopGraph
• check_for_unique_cutpoint() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer
• check_for_unique_cutpoint_flanked_by_bridge_res() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer
• check_for_unpaired_segments() : protocols::denovo_design::components::SolutionPredicate
• check_forming_base_pair() : core::scoring::rna::RNA_LowResolutionPotential
• check_forward_backward() : core::import_pose::libraries::RNA_JumpLibrary , core::import_pose::RNA_JumpMover
• check_frequency() : protocols::moves::MonteCarlo
• check_frequency_ : protocols::moves::MonteCarlo
• check_from_scratch() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• check_grid() : protocols::ligand_docking::Transform , protocols::ligand_docking::TransformEnsemble
• check_hairpin() : core::scoring::SS_Killhairpins_Info
• check_hbond_score() : protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker
• check_hbonded() : core::scoring::rna::data::RNA_DMS_Potential
• check_high_res_protocol() : protocols::docking::DockingProtocol
• check_if_connected_residues_belong_to_regions() : protocols::simple_filters::RegionalConnections
• check_if_really_connected() : protocols::simple_moves::ConstrainToIdealMover
• check_if_residues_are_Ctermini() : core::io::StructFileRepOptions
• check_if_residues_are_Ctermini_ : core::io::StructFileRepOptions
• check_if_residues_are_Ntermini() : core::io::StructFileRepOptions
• check_if_residues_are_Ntermini_ : core::io::StructFileRepOptions
• check_if_rna_from_sequence_line() : core::io::silent::SilentFileData
• check_ignore_residues_reasonable() : protocols::helical_bundle_predict::HelicalBundlePredictApplication
• check_improper_termini() : protocols::denovo_design::components::StructureData
• check_in_bond_angle_list() : protocols::simple_moves::ConstrainToIdealMover
• check_in_bonded_list() : protocols::simple_moves::ConstrainToIdealMover
• check_in_chain_connections() : core::import_pose::RNA_JumpMover
• check_in_pairing_sets() : core::import_pose::RNA_DeNovoParameters
• check_internals() : protocols::comparative_modeling::MultiThreadingMover
• check_internals_() : core::sequence::ChemicalShiftSequence , core::sequence::SequenceProfile
• check_intra_residue() : core::scoring::rna::RNA_TorsionPotential
• check_jump_in_range() : protocols::recces::sampler::rna::MC_RNA_OneJump
• check_lengths_sensible() : protocols::aa_composition::AddHelixSequenceConstraintsMover
• check_library_expiry_dates() : protocols::loophash::MPI_LoopHashRefine_Master , protocols::mpi_refinement::MPI_Refine_Master
• check_lig_code() : core::scoring::motif::ResPairMotif
• check_line_len() : protocols::antibody::CDRSetOptionsParser , protocols::antibody::design::CDRGraftDesignOptionsParser , protocols::antibody::design::CDRSeqDesignOptionsParser
• check_linestream() : core::chemical::mainchain_potential::MainchainScoreTable
• check_loop_abego() : protocols::pose_length_moves::PossibleLoop
• check_loop_closed() : protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker
• check_loop_cycles_are_disjoint() : core::scoring::loop_graph::LoopGraph
• check_loop_length() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• check_loop_residues_sensible() : protocols::generalized_kinematic_closure::GeneralizedKIC
• check_loops() : protocols::abinitio::FragmentSampler
• check_matching_atom_names() : protocols::stepwise::modeler::align::StepWisePoseAligner
• check_membrane_fold_tree() : core::conformation::membrane::MembraneInfo
• check_methods() : core::scoring::ScoreFunction
• check_methods_in_right_order() : core::scoring::ScoreFunction
• check_mmt() : protocols::simple_moves::TorsionDOFMover
• check_MMT_ : protocols::simple_moves::TorsionDOFMover
• check_movable_groups() : protocols::denovo_design::components::StructureData , protocols::denovo_design::connection::AreConnectablePredicate
• check_moved() : protocols::recces::sampler::rna::MC_RNA_KIC_Sampler , protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• check_moving_res_in_chain() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• check_moving_sugar() : protocols::stepwise::screener::SugarInstantiator
• check_N_to_C_direction_by_ : protocols::features::strand_assembly::SandwichFeatures
• check_next_pairing() : protocols::jumping::SheetBuilder
• check_non_upstream_only_hit_incompatibility() : protocols::match::Matcher
• check_nonideal_mintype() : protocols::relax::FastRelax
• check_nucleic_acid_virtual_phosphates() : core::chemical::ResidueTypeFinder
• check_nucleic_acid_virtual_phosphates_ : core::chemical::ResidueTypeFinder
• check_num_requested_atoms() : protocols::features::ProteinResidueConformationFeatures
• check_order() : core::kinematics::FoldTree
• check_other_partition_for_contact() : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• check_overlap() : protocols::hybridization::InsertChunkMover , protocols::kinematic_closure::ClosureSolution , protocols::kinematic_closure::solution_pickers::FilteredSolutions
• check_overlap_ : protocols::kinematic_closure::solution_pickers::FilteredSolutions
• check_pairing_intersect() : protocols::jumping::SheetBuilder
• check_path() : protocols::antibody::AntibodyNumberingParser , protocols::antibody::CDRSetOptionsParser , protocols::antibody::design::CDRGraftDesignOptionsParser , protocols::antibody::design::CDRSeqDesignOptionsParser
• check_path_distance() : core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• check_pdb_code() : core::scoring::motif::ResPairMotif
• check_pdb_for_mem() : protocols::membrane::AddMembraneMover , protocols::membrane::symmetry::SymmetricAddMembraneMover
• check_periodicity_ : protocols::match::downstream::AtomDihedralSecMatchRPE
• check_permutation() : protocols::denovo_design::architects::BetaSheetArchitect
• check_phosphate_contacts_donor() : protocols::stepwise::modeler::rna::phosphate::PhosphateMover
• check_pleat() : core::scoring::dssp::StrandPairing , core::scoring::dssp::StrandPairingSet
• check_pose() : protocols::denovo_design::components::StructureData , protocols::denovo_design::movers::BuildDeNovoBackboneMover , protocols::sparta::Sparta
• check_pose_consistency() : protocols::denovo_design::components::StructureData
• check_pose_list() : protocols::stepwise::modeler::StepWiseMinimizer
• check_pose_pssm_match() : protocols::splice::SpliceOut
• check_pose_tree_compatibility() : protocols::toolbox::match_enzdes_util::InvrotTree , protocols::toolbox::match_enzdes_util::TheozymeInvrotTree
• check_potential_dsbuilder_incompatibility_ : protocols::match::Matcher
• check_property_overlap() : core::scoring::bin_transitions::BinTransitionData
• check_rama() : core::sequence::ABEGO , core::sequence::ABEGOManager , protocols::kinematic_closure::ClosureSolution , protocols::kinematic_closure::solution_pickers::FilteredSolutions , protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::simple_moves::BackboneMover
• check_rama2() : core::sequence::ABEGO
• check_rama_ : protocols::kinematic_closure::solution_pickers::FilteredSolutions
• check_rama_scores() : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• check_rama_scores_ : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• check_range() : protocols::canonical_sampling::BiasEnergy::Histogram< T > , protocols::membrane::geometry::EmbeddingDef
• check_rdat() : core::io::rna::RDAT
• check_relevant_residues() : protocols::features::FeaturesReporter
• check_relevant_residues_range() : protocols::features::FeaturesReporter
• check_res_map() : core::import_pose::libraries::RNA_ChunkLibrary
• check_residentity_overlap() : core::scoring::bin_transitions::BinTransitionData
• check_residue_indices_valid() : protocols::cyclic_peptide::crosslinker::Metal_HelperBase , protocols::cyclic_peptide::crosslinker::OctahedralMetal_Helper , protocols::cyclic_peptide::crosslinker::SquarePlanarMetal_Helper , protocols::cyclic_peptide::crosslinker::SquarePyramidalMetal_Helper , protocols::cyclic_peptide::crosslinker::TetrahedralMetal_Helper , protocols::cyclic_peptide::crosslinker::TrigonalPlanarMetal_Helper , protocols::cyclic_peptide::crosslinker::TrigonalPyramidalMetal_Helper
• check_residue_records_size() : core::pose::PDBInfo
• check_residue_type() : protocols::denovo_design::DisulfidizeMover
• check_residues() : protocols::denovo_design::components::StructureData
• check_rmsd() : protocols::ligand_docking::Transform
• check_rmsd_ : protocols::ligand_docking::Transform
• check_rotamer_well_order() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser
• check_same_chain() : protocols::stepwise::monte_carlo::mover::AddMover
• check_score_filter() : protocols::rna::denovo::RNA_FragmentMonteCarlo
• check_screen() : protocols::stepwise::legacy::screener::ProteinAtrRepScreener , protocols::stepwise::legacy::screener::RNA_AtrRepScreener , protocols::stepwise::legacy::screener::SimplePoseSelection , protocols::stepwise::legacy::screener::SimpleRMSD_Screener , protocols::stepwise::modeler::protein::checker::ProteinAtrRepChecker , protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker , protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker , protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker , protocols::stepwise::screener::AlignRMSD_Screener , protocols::stepwise::screener::AnchorSugarScreener , protocols::stepwise::screener::BaseCentroidScreener , protocols::stepwise::screener::CentroidDistanceScreener , protocols::stepwise::screener::IntegrationTestBreaker , protocols::stepwise::screener::O2PrimeScreener , protocols::stepwise::screener::PackScreener , protocols::stepwise::screener::PartitionContactScreener , protocols::stepwise::screener::PhosphateScreener , protocols::stepwise::screener::PoseSelectionScreener , protocols::stepwise::screener::ProteinCCD_ClosureScreener , protocols::stepwise::screener::ResidueContactScreener , protocols::stepwise::screener::RNA_ChainClosableGeometryResidueBasedScreener , protocols::stepwise::screener::RNA_ChainClosableGeometryScreener , protocols::stepwise::screener::RNA_ChainClosableGeometryStubBasedScreener , protocols::stepwise::screener::RNA_ChainClosureScreener , protocols::stepwise::screener::SampleApplier , protocols::stepwise::screener::Scorer , protocols::stepwise::screener::StepWiseScreener , protocols::stepwise::screener::StubDistanceScreener , protocols::stepwise::screener::SugarInstantiator , protocols::stepwise::screener::TagDefinition , protocols::stepwise::screener::VDW_BinScreener
• check_screen_and_kick_out_displaced_model() : protocols::stepwise::modeler::align::StepWiseClusterer
• check_secstructs() : protocols::rna::denovo::movers::RNA_DeNovoProtocolMover
• check_sequence() : protocols::noesy_assign::FragsToAtomDist , protocols::stepwise::modeler::protein::InputStreamWithResidueInfo
• check_sequence_profile() : protocols::splice::SpliceManager
• check_sequence_seqpos() : core::io::rna::RDAT
• check_setup() : core::optimization::AtomTreeMinimizer
• check_sheet_pairings() : protocols::jumping::SheetBuilder
• check_single_format() : protocols::pdbinfo_manipulations::SequenceSpecification
• check_solution() : protocols::denovo_design::components::FoldGraph
• check_source_segment() : protocols::splice::SpliceOut
• check_spanning() : core::scoring::MembranePotential
• check_ss() : core::select::residue_selector::SecondaryStructureSelector , protocols::simple_moves::ClassicFragmentMover
• check_ss_ : protocols::simple_moves::ClassicFragmentMover
• check_ss_lengths() : protocols::frags::TorsionFragmentMover
• check_ss_lengths_ : protocols::frags::TorsionFragmentMover
• check_start_segment() : protocols::denovo_design::components::SolutionPredicate
• check_state() : protocols::forge::remodel::RemodelDesignMover
• check_status() : protocols::frag_picker::quota::ABEGO_SS_Map
• check_stop_segment() : protocols::denovo_design::components::SolutionPredicate
• check_strand_too_closeness() : protocols::features::strand_assembly::StrandBundleFeatures
• check_sugar_atom() : core::scoring::rna::data::RNA_DataBackboneEnergy
• check_superimpose_res() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• check_sw_by_dis() : protocols::features::strand_assembly::StrandBundleFeatures
• check_tag() : protocols::cluster::GatherPosesMover
• check_tail_residues_sensible() : protocols::generalized_kinematic_closure::GeneralizedKIC
• check_temp_consistency() : protocols::canonical_sampling::TemperingBase
• check_template_poses() : protocols::denovo_design::components::SolutionPredicate
• check_that_terminal_res_are_unstacked() : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• check_threads() : core::pack::task::PackerTask_
• check_tolerance_ : protocols::rna::movers::RNA_LoopCloser
• check_topology() : core::kinematics::FoldTree
• check_two_pairings() : protocols::jumping::SheetBuilder
• check_updated() : protocols::denovo_design::architects::StrandArchitect
• check_valid_membrane() : core::conformation::Conformation
• check_value() : protocols::match::downstream::AtomGeometrySecMatchRPE
• check_variant_sets_have_all_candidate_variants() : core::chemical::ResidueTypeFinder
• check_VDW_screen_bin_is_setup() : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• check_virial_pressure() : protocols::simple_moves::PeriodicBoxMover
• check_working_parameters() : protocols::stepwise::modeler::StepWiseConnectionSampler
• CheckAtomCollision2() : core::scoring::sc::MolecularSurfaceCalculator
• checkFormat() : protocols::sparta::GDB
• checkpoint() : protocols::abinitio::MembraneAbinitio , protocols::checkpoint::CheckPointer , protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication , protocols::splice::RBInMover , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• checkpoint_ : protocols::abinitio::MembraneAbinitio , protocols::forge::remodel::RemodelMover::instruction_flags , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• checkpoint_clear() : protocols::jd2::BOINCJobDistributor , protocols::jobdist::BaseJobDistributor
• checkpoint_completed() : protocols::boinc::Boinc
• checkpoint_count_ : protocols::boinc::Boinc , protocols::canonical_sampling::MetropolisHastingsMover
• checkpoint_exists() : protocols::monte_carlo::GenericSimulatedAnnealer
• checkpoint_file() : protocols::monte_carlo::GenericSimulatedAnnealer
• checkpoint_file_ : protocols::monte_carlo::GenericSimulatedAnnealer
• checkpoint_file_exists() : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• checkpoint_file_name() : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• checkpoint_file_name_low() : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• checkpoint_filename_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• checkpoint_gz_ : protocols::dna::DnaInterfaceMultiStateDesign , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• checkpoint_gzip_ : protocols::genetic_algorithm::GeneticAlgorithmBase
• checkpoint_ids_ : protocols::abinitio::MembraneAbinitio , protocols::canonical_sampling::MetropolisHastingsMover , protocols::checkpoint::CheckPointer
• checkpoint_interval_ : protocols::dna::DnaInterfaceMultiStateDesign , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• checkpoint_job_identifier_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• checkpoint_prefix_ : protocols::dna::DnaInterfaceMultiStateDesign , protocols::genetic_algorithm::GeneticAlgorithmBase , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• checkpoint_read() : protocols::jd2::BOINCJobDistributor , protocols::jobdist::BaseJobDistributor , protocols::simple_filters::ReportFilter
• checkpoint_recovery() : protocols::splice::RBInMover
• checkpoint_rename_ : protocols::dna::DnaInterfaceMultiStateDesign , protocols::genetic_algorithm::GeneticAlgorithmBase , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• checkpoint_write() : protocols::jd2::BOINCJobDistributor , protocols::jobdist::BaseJobDistributor , protocols::simple_filters::ReportFilter
• checkpoint_write_interval() : protocols::genetic_algorithm::GeneticAlgorithmBase
• checkpoint_write_interval_ : protocols::genetic_algorithm::GeneticAlgorithmBase
• CheckPointCollision() : core::scoring::sc::MolecularSurfaceCalculator
• checkpointed_cycle_block() : protocols::abinitio::FragmentSampler
• CheckPointer() : protocols::checkpoint::CheckPointer
• checkpointer_ : protocols::abinitio::abscript::AbscriptMover::StageTracker
• checkpointfile_ : protocols::frag_picker::nonlocal::NonlocalFrags
• checkpointing_file() : protocols::simple_filters::ReportFilter , protocols::splice::RBInMover , protocols::splice::Splice
• checkpointing_file_ : protocols::simple_filters::ReportFilter , protocols::splice::RBInMover , protocols::splice::Splice , protocols::splice::SpliceIn
• checkpointing_frequency() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• checkpointing_frequency_ : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• checkpoints_ : protocols::abinitio::FragmentSampler , protocols::abinitio::Protocol , protocols::loophash::Mover_LoopHashRefine , protocols::loops::loop_mover::LoopMover , protocols::multistage_rosetta_scripts::MRSJobQueen , protocols::relax::ClassicRelax , protocols::relax::FastRelax
• checkpoints_map_ : protocols::frag_picker::nonlocal::NonlocalFrags
• CheckProbeCollision() : core::scoring::sc::MolecularSurfaceCalculator
• checksymm_ : protocols::loop_grower::FragmentExtension , protocols::loop_grower::LoopGrower , protocols::loop_grower::LoopPartialSolutionStore
• chem_comp_type : core::io::AtomInformation
• chem_shift_scorefxn_ : protocols::rna::denovo::RNA_FragmentMonteCarlo
• CHEMICAL : core::kinematics::Edge
• chemical_edge_set_ : core::scoring::PolymerBondedEnergyContainer
• chemical_edges_ : core::scoring::PolymerBondedEnergyContainer
• chemical_name_ : core::chemical::Element
• CHEMICAL_SHIFT_ANISOTROPY_DATA : core::pose::datacache::CacheableDataType
• chemical_symbol_ : core::chemical::Element
• ChemicalManager() : core::chemical::ChemicalManager
• ChemicalShiftAnisotropy() : core::scoring::ChemicalShiftAnisotropy , core::scoring::CSA
• ChemicalShiftAnisotropyEnergy() : core::scoring::methods::ChemicalShiftAnisotropyEnergy
• ChemicalShiftData() : core::scoring::rna::chemical_shift::ChemicalShiftData
• ChemicalShiftEvaluator() : protocols::sparta::ChemicalShiftEvaluator
• ChemicalShiftEvaluatorCreator() : protocols::sparta::ChemicalShiftEvaluatorCreator
• ChemicalShiftScoringScheme() : core::sequence::ChemicalShiftScoringScheme
• ChemicalShiftSequence() : core::sequence::ChemicalShiftSequence
• ChemicalShiftSequenceCreator() : core::sequence::ChemicalShiftSequenceCreator
• chemshift_column() : protocols::abinitio::IterativeBase
• chemshift_column_ : protocols::abinitio::IterativeBase
• chemshift_compliance() : protocols::noesy_assign::PeakAssignment
• chemshift_overlap_ : protocols::noesy_assign::PeakAssignment
• chemshift_overlap_weight_ : protocols::noesy_assign::PeakAssignmentParameters
• cheshire_cell() : protocols::cryst::Spacegroup , protocols::cryst::WallpaperGroup
• CheshireCell() : protocols::cryst::CheshireCell
• chgm : core::scoring::APBSConfig::I_PARAM
• chi() : core::conformation::Residue , core::io::raw_data::DecoyStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RNA_SilentStruct , core::pack::dunbrack::ChiSet , core::pack::task::operation::RotamerExplosion , core::pose::Pose , protocols::dna::DNABase , protocols::dna::DnaInterfaceMinMover , protocols::minimization_packing::TaskAwareMinMover , protocols::optimize_weights::PNatRotOptERotamerData , protocols::symmetry::SetupNCSMover
• chi1() : core::scoring::motif::ResPairMotif , core::scoring::motif::Xfres , protocols::indexed_structure_store::ResidueSidechainEntry
• chi11() : core::scoring::motif::ResPairMotif
• chi12() : core::scoring::motif::ResPairMotif
• chi13() : core::scoring::motif::ResPairMotif
• chi14() : core::scoring::motif::ResPairMotif
• chi1_ : core::scoring::motif::ResPairMotif , protocols::loop_grower::ResTorsions
• chi2() : core::scoring::motif::ResPairMotif , core::scoring::motif::Xfres , core::scoring::saxs::FastSAXSEnergy , protocols::indexed_structure_store::ResidueSidechainEntry
• chi21() : core::scoring::motif::ResPairMotif
• chi22() : core::scoring::motif::ResPairMotif
• chi23() : core::scoring::motif::ResPairMotif
• chi24() : core::scoring::motif::ResPairMotif
• chi2_ : core::scoring::fiber_diffraction::FiberDiffractionEnergy , core::scoring::fiber_diffraction::FiberDiffractionEnergyDens , core::scoring::motif::ResPairMotif , protocols::loop_grower::ResTorsions
• CHI2_ANGLES : protocols::sparta::Sparta::SpartaLib
• chi2max() : protocols::task_operations::LimitAromaChi2_RotamerSetOperation , protocols::task_operations::LimitAromaChi2Operation
• chi2max_ : protocols::task_operations::LimitAromaChi2_RotamerSetOperation , protocols::task_operations::LimitAromaChi2Operation
• chi2min() : protocols::task_operations::LimitAromaChi2_RotamerSetOperation , protocols::task_operations::LimitAromaChi2Operation
• chi2min_ : protocols::task_operations::LimitAromaChi2_RotamerSetOperation , protocols::task_operations::LimitAromaChi2Operation
• chi3() : core::scoring::motif::Xfres , protocols::indexed_structure_store::ResidueSidechainEntry
• chi3_ : protocols::loop_grower::ResTorsions
• chi4() : core::scoring::motif::Xfres , protocols::indexed_structure_store::ResidueSidechainEntry
• chi4_ : protocols::loop_grower::ResTorsions
• chi4E() : core::scoring::methods::ProClosureEnergy
• chi_ : core::conformation::Residue , core::io::raw_data::DecoyStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::pack::task::operation::ExtraRotamers , core::pack::task::operation::RotamerExplosion , core::scoring::motif::Xfres , protocols::dna::DNABase , protocols::dna::DnaInterfaceMinMover , protocols::docking::DockingHighResLegacy , protocols::docking::DockingLowRes , protocols::minimization_packing::MinimalRotamer , protocols::minimization_packing::TaskAwareMinMover , protocols::optimize_weights::PNatRotOptERotamerData , protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockingLowRes , protocols::symmetry::SetupNCSMover
• chi_2_proton_chi() : core::chemical::ResidueType
• chi_2_proton_chi_ : core::chemical::ResidueType
• chi_actions_ : core::select::movemap::MoveMapFactory
• chi_angles_ : protocols::legacy_sewing::SewResidue
• chi_atom_vds() : core::chemical::MutableResidueType
• chi_atoms() : core::chemical::MutableChiRecord , core::chemical::ResidueType , core::conformation::Residue
• chi_atoms_ : core::chemical::MutableChiRecord , core::chemical::ResidueType
• chi_chain1_ : protocols::seeded_abinitio::SeedSetupMover
• chi_chain2_ : protocols::seeded_abinitio::SeedSetupMover
• chi_clones() : core::conformation::symmetry::SymmetryInfo
• chi_clones_ : core::conformation::symmetry::SymmetryInfo
• chi_dev() : protocols::comparative_modeling::Align_RotamerEvaluator
• chi_dev_ : protocols::comparative_modeling::Align_RotamerEvaluator
• chi_diff_threshold_ : protocols::dna::PDBOutput
• CHI_energy_function_ : core::scoring::ScoringManager
• chi_follows() : core::conformation::symmetry::SymmetryInfo
• chi_follows_ : core::conformation::symmetry::SymmetryInfo
• chi_is_independent() : core::conformation::symmetry::SymmetryInfo
• chi_is_nonrotameric() : core::pack::dunbrack::DunbrackRotamerSampleData
• chi_mag_ : protocols::cryst::DockLatticeMover
• chi_matches_coords() : protocols::minimization_packing::MinimalRotamer
• chi_mean() : core::pack::dunbrack::DunbrackRotamerMeanSD< S, N, P > , core::pack::dunbrack::DunbrackRotamerSampleData
• chi_mean_ : core::pack::dunbrack::DunbrackRotamerMeanSD< S, N, P > , core::pack::dunbrack::DunbrackRotamerSampleData
• chi_min_ : protocols::enzdes::EnzdesBaseProtocol
• chi_movable_selector() : protocols::fold_from_loops::NubInitioMover
• chi_no_ : core::chemical::ClearChiRotamers
• chi_north_anti() : core::chemical::rna::RNA_FittedTorsionInfo
• chi_north_potential_guanosine_ : core::scoring::rna::RNA_TorsionPotential
• chi_north_potential_others_ : core::scoring::rna::RNA_TorsionPotential
• chi_north_syn() : core::chemical::rna::RNA_FittedTorsionInfo
• chi_number_pseudoalpha() : core::chemical::rna::RNA_Info
• chi_number_pseudoalpha_ : core::chemical::rna::RNA_Info
• chi_number_pseudobeta() : core::chemical::rna::RNA_Info
• chi_number_pseudobeta_ : core::chemical::rna::RNA_Info
• chi_number_pseudoepsilon() : core::chemical::rna::RNA_Info
• chi_number_pseudoepsilon_ : core::chemical::rna::RNA_Info
• chi_number_pseudogamma() : core::chemical::rna::RNA_Info
• chi_number_pseudogamma_ : core::chemical::rna::RNA_Info
• chi_number_pseudozeta() : core::chemical::rna::RNA_Info
• chi_number_pseudozeta_ : core::chemical::rna::RNA_Info
• chi_poly_lookup() : core::scoring::hbonds::HBondDatabase
• chi_poly_lookup_ : core::scoring::hbonds::HBondDatabase
• chi_potential_syn_guanosine_bonus_ : core::scoring::rna::RNA_TorsionPotential
• chi_probability() : core::pack::dunbrack::DunbrackRotamerSampleData
• chi_purine_north_potential_ : core::scoring::rna::RNA_TorsionPotential
• chi_purine_south_potential_ : core::scoring::rna::RNA_TorsionPotential
• chi_pyrimidine_north_potential_ : core::scoring::rna::RNA_TorsionPotential
• chi_pyrimidine_south_potential_ : core::scoring::rna::RNA_TorsionPotential
• chi_ranges_ : protocols::make_rot_lib::MakeRotLibOptionsData
• chi_rmsd() : core::scoring::motif::MotifHit
• chi_rmsd_ : core::scoring::motif::MotifHit
• chi_rotamer_ : protocols::recces::sampler::rna::MC_RNA_KIC_Sampler , protocols::stepwise::sampler::rna::RNA_KIC_Sampler
• chi_rotamers() : core::chemical::MutableChiRecord , core::chemical::MutableResidueType , core::chemical::ResidueType , core::conformation::Residue
• chi_rotamers_ : core::chemical::MutableChiRecord , core::chemical::ResidueType
• chi_sample() : protocols::match::upstream::FullChiSampleSet
• chi_sample_level_ : core::pack::task::EX
• chi_samplers_ : protocols::recces::sampler::rna::MC_RNA_KIC_Sampler , protocols::recces::sampler::rna::MC_RNA_Suite
• chi_samples() : protocols::match::upstream::FullChiSampleSet
• chi_samples_ : protocols::match::upstream::FullChiSampleSet
• chi_sd() : core::pack::dunbrack::DunbrackRotamerMeanSD< S, N, P > , core::pack::dunbrack::DunbrackRotamerSampleData
• chi_sd_ : core::pack::dunbrack::DunbrackRotamerMeanSD< S, N, P > , core::pack::dunbrack::DunbrackRotamerSampleData
• chi_south_anti() : core::chemical::rna::RNA_FittedTorsionInfo
• chi_south_potential_guanosine_ : core::scoring::rna::RNA_TorsionPotential
• chi_south_potential_others_ : core::scoring::rna::RNA_TorsionPotential
• chi_south_syn() : core::chemical::rna::RNA_FittedTorsionInfo
• chi_start_for_active_residue_ : core::pack::scmin::AtomTreeSCMinMinimizerMap
• chi_std_devs_ : core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser
• chi_stdev() : protocols::recces::options::RECCES_Options
• chi_stdev_ : protocols::recces::options::RECCES_Options
• chi_step_ : protocols::ligand_docking::ga_ligand_dock::LigandAligner
• chi_tor_out_ : protocols::recces::RECCES_Mover
• chi_torsion_ids_ : protocols::recces::RECCES_Mover
• chi_torsions() : core::io::silent::RNA_SilentStruct
• chi_torsions_ : core::io::silent::RNA_SilentStruct
• chi_valid() : core::chemical::MutableResidueType
• chi_vec : protocols::splice::ROT
• chi_xx() : protocols::scoring::methods::pcs::PCS_tensor , protocols::scoring::methods::pcsTs1::PCS_tensor_Ts1 , protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2 , protocols::scoring::methods::pcsTs3::PCS_tensor_Ts3 , protocols::scoring::methods::pcsTs4::PCS_tensor_Ts4
• chi_xx_ : protocols::scoring::methods::pcs2::PcsTensor , protocols::scoring::methods::pcs::PCS_tensor , protocols::scoring::methods::pcsTs1::PCS_tensor_Ts1 , protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2 , protocols::scoring::methods::pcsTs3::PCS_tensor_Ts3 , protocols::scoring::methods::pcsTs4::PCS_tensor_Ts4
• chi_xy() : protocols::scoring::methods::pcs::PCS_tensor , protocols::scoring::methods::pcsTs1::PCS_tensor_Ts1 , protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2 , protocols::scoring::methods::pcsTs3::PCS_tensor_Ts3 , protocols::scoring::methods::pcsTs4::PCS_tensor_Ts4
• chi_xy_ : protocols::scoring::methods::pcs2::PcsTensor , protocols::scoring::methods::pcs::PCS_tensor , protocols::scoring::methods::pcsTs1::PCS_tensor_Ts1 , protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2 , protocols::scoring::methods::pcsTs3::PCS_tensor_Ts3 , protocols::scoring::methods::pcsTs4::PCS_tensor_Ts4
• chi_xz() : protocols::scoring::methods::pcs::PCS_tensor , protocols::scoring::methods::pcsTs1::PCS_tensor_Ts1 , protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2 , protocols::scoring::methods::pcsTs3::PCS_tensor_Ts3 , protocols::scoring::methods::pcsTs4::PCS_tensor_Ts4
• chi_xz_ : protocols::scoring::methods::pcs2::PcsTensor , protocols::scoring::methods::pcs::PCS_tensor , protocols::scoring::methods::pcsTs1::PCS_tensor_Ts1 , protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2 , protocols::scoring::methods::pcsTs3::PCS_tensor_Ts3 , protocols::scoring::methods::pcsTs4::PCS_tensor_Ts4
• chi_yy() : protocols::scoring::methods::pcs::PCS_tensor , protocols::scoring::methods::pcsTs1::PCS_tensor_Ts1 , protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2 , protocols::scoring::methods::pcsTs3::PCS_tensor_Ts3 , protocols::scoring::methods::pcsTs4::PCS_tensor_Ts4
• chi_yy_ : protocols::scoring::methods::pcs2::PcsTensor , protocols::scoring::methods::pcs::PCS_tensor , protocols::scoring::methods::pcsTs1::PCS_tensor_Ts1 , protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2 , protocols::scoring::methods::pcsTs3::PCS_tensor_Ts3 , protocols::scoring::methods::pcsTs4::PCS_tensor_Ts4
• chi_yz() : protocols::scoring::methods::pcs::PCS_tensor , protocols::scoring::methods::pcsTs1::PCS_tensor_Ts1 , protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2 , protocols::scoring::methods::pcsTs3::PCS_tensor_Ts3 , protocols::scoring::methods::pcsTs4::PCS_tensor_Ts4
• chi_yz_ : protocols::scoring::methods::pcs2::PcsTensor , protocols::scoring::methods::pcs::PCS_tensor , protocols::scoring::methods::pcsTs1::PCS_tensor_Ts1 , protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2 , protocols::scoring::methods::pcsTs3::PCS_tensor_Ts3 , protocols::scoring::methods::pcsTs4::PCS_tensor_Ts4
• ChiAngleNormalization() : protocols::qsar::scoring_grid::ChiAngleNormalization
• chibin_combo_indexer_ : protocols::match::output::SameChiBinComboGrouper
• ChiBinComboCountMap : protocols::match::output::SameChiBinComboGrouper
• chidev() : core::pack::dunbrack::RotamerLibraryScratchSpace
• chidev_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• chidevpen() : core::pack::dunbrack::RotamerLibraryScratchSpace
• chidevpen_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• CHIEnergyFunction() : core::scoring::carbohydrates::CHIEnergyFunction
• child() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• child_index() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• child_mover_ : protocols::ligand_docking::UnconstrainedTorsionsMover
• children : core::kinematics::Node , protocols::jd3::JGJobNode , protocols::jd3::JGResultNode
• children_ : core::conformation::carbohydrates::GlycanNode , protocols::jd3::JGJobNode , protocols::jd3::JGResultNode , protocols::loop_modeling::LoopMover
• chimean() : core::pack::dunbrack::RotamerLibraryScratchSpace
• chimean_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• chimeans_ : core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser
• chimera_ : protocols::legacy_sewing::SewSegment
• chimerize() : protocols::sewing::data_storage::SmartAssembly
• chino_ : core::chemical::AddChi , core::chemical::AddChiRotamer , core::chemical::AddProtonChi , core::chemical::RedefineChi
• chinum() : protocols::simple_moves::sidechain_moves::SetChiMover
• chinum_ : protocols::simple_moves::sidechain_moves::SetChiMover
• chiral_seq_pos_ : protocols::simple_moves::chiral::ChiralMover
• ChiralFlipAtoms() : core::chemical::ChiralFlipAtoms
• ChiralFlipNaming() : core::chemical::ChiralFlipNaming
• chirality_ : protocols::simple_moves::chiral::ChiralMover
• chirality_sign() : core::scoring::MultipoleParameter
• chirality_sign_ : core::scoring::MultipoleParameter
• ChiralMover() : protocols::simple_moves::chiral::ChiralMover
• chis : protocols::ligand_docking::ga_ligand_dock::PlaceableRotamer , protocols::sewing::hashing::LigandCoordInfo
• chis2rotid() : protocols::ligand_docking::ga_ligand_dock::EntropyEstimator
• chis_ : core::chemical::MutableResidueType , protocols::pose_creation::MakePolyXMover , protocols::sewing::data_storage::SmartSewingResidue
• chis_from_pose() : protocols::pose_metric_calculators::RotamerRecovery
• chisamples_for_rotamer_and_chi() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >
• chisd() : core::pack::dunbrack::RotamerLibraryScratchSpace
• chisd_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• ChiSet() : core::pack::dunbrack::ChiSet
• ChiSetOP : core::pack::rotamer_set::RotamerSet_
• chitip_atom() : protocols::match::upstream::UpstreamResTypeGeometry
• chitip_atoms() : protocols::match::upstream::UpstreamResTypeGeometry
• chitip_atoms_ : protocols::match::upstream::UpstreamResTypeGeometry
• ChiVector : protocols::simple_moves::sidechain_moves::SidechainMoverBase
• chiweights_ : protocols::ligand_docking::ga_ligand_dock::EntropyEstimator
• ChiWellRmsdEvaluator() : protocols::simple_filters::ChiWellRmsdEvaluator
• ChiWellRmsdEvaluatorCreator() : protocols::simple_filters::ChiWellRmsdEvaluatorCreator
• choices() : protocols::genetic_algorithm::DiscreteRandomizer , protocols::genetic_algorithm::PositionSpecificRandomizer
• choices_ : protocols::genetic_algorithm::DiscreteRandomizer , protocols::genetic_algorithm::PositionSpecificRandomizer
• cholesky_bw() : protocols::simple_moves::BBGaussianMover
• cholesky_fw() : protocols::simple_moves::BBGaussianMover
• choose() : protocols::nonlocal::Chunk , protocols::nonlocal::Policy , protocols::nonlocal::SmoothPolicy , protocols::nonlocal::UniformPolicy
• choose_anchor_position() : protocols::hybridization::HybridizeFoldtreeDynamic , protocols::nonlocal::StarTreeBuilder
• choose_anchors() : protocols::hybridization::HybridizeFoldtreeDynamic
• choose_atoms() : protocols::constraint_generator::HydrogenBondConstraintGenerator
• choose_best_metal_coordinator() : protocols::sewing::hashing::LigandBindingResPlacer
• choose_best_solution_ : protocols::rna::denovo::coarse::CoarseRNA_LoopCloser , protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser
• choose_best_solution_based_on_score_function() : protocols::rna::denovo::coarse::CoarseRNA_LoopCloser , protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser
• choose_cutpoint() : protocols::loops::Loop , protocols::star::Extender
• choose_cutpoints() : protocols::loops::Loops
• choose_database_filter() : protocols::features::ProteinSilentReport
• choose_desired_centroid() : protocols::ligand_docking::LigandBaseProtocol
• choose_effective_sequence_separation() : core::scoring::constraints::Constraint , core::scoring::constraints::MultiConstraint
• choose_fragment() : protocols::simple_moves::ClassicFragmentMover , protocols::simple_moves::SmoothFragmentMover , protocols::simple_moves::SmoothSymmetricFragmentMover
• choose_least_perturb_solution() : protocols::rna::denovo::coarse::CoarseRNA_LoopCloser , protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser
• choose_least_perturb_solution_ : protocols::rna::denovo::coarse::CoarseRNA_LoopCloser , protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser
• choose_motif() : protocols::denovo_design::connection::ConnectionArchitect
• choose_n_best() : protocols::enzdes::PackRotamersMoverPartGreedy
• choose_new_movable_group() : protocols::denovo_design::components::StructureData
• choose_next_pairing() : protocols::jumping::SheetBuilder
• choose_origin_with_lowest_eggshell_ruggedness() : protocols::pockets::NonPlaidFingerprint
• choose_random() : protocols::stepwise::modeler::options::StepWiseBasicModelerOptions , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_MultiPoseCloser , protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• choose_random_ : protocols::stepwise::modeler::options::StepWiseBasicModelerOptions , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_MultiPoseCloser , protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler , protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList , protocols::stepwise::monte_carlo::mover::AddOrDeleteMover , protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• choose_solution() : protocols::recces::sampler::rna::MC_RNA_KIC_Sampler
• choose_window_length() : protocols::simple_moves::ClassicFragmentMover
• choose_window_start() : protocols::simple_moves::ClassicFragmentMover
• Chunk() : protocols::nonlocal::Chunk , protocols::pose_creation::SliceToMiniProteinMover::Chunk
• chunk_ : protocols::frag_picker::FragmentCandidate
• chunk_atoms_xyz_ : protocols::frag_picker::scores::AtomBasedConstraintsScore
• chunk_ca_distances_ : protocols::frag_picker::scores::DisulfideDistance , protocols::frag_picker::scores::PCS_FragDistance
• chunk_coordinates_ : protocols::frag_picker::scores::FragmentAllAtomCrmsd , protocols::frag_picker::scores::FragmentChunkCrms , protocols::frag_picker::scores::FragmentCrmsd , protocols::frag_picker::scores::FragmentCrmsdResDepth , protocols::frag_picker::scores::FragmentDME
• chunk_coverage() : core::import_pose::libraries::RNA_ChunkLibrary
• chunk_coverage_ : core::import_pose::libraries::RNA_ChunkLibrary
• chunk_gunn_data_ : protocols::frag_picker::scores::GunnCostScore
• chunk_initialization_pdb_files() : core::import_pose::options::RNA_FragmentMonteCarloOptions
• chunk_initialization_pdb_files_ : core::import_pose::options::RNA_FragmentMonteCarloOptions
• chunk_insertion_weight_ : protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol
• chunk_key() : protocols::frag_picker::VallChunk
• chunk_key_ : protocols::frag_picker::VallChunk
• chunk_library_from_input_source() : protocols::jd3::chunk_library_inputters::ChunkLibraryInputter , protocols::jd3::chunk_library_inputters::PDBChunkLibraryInputter
• chunk_library_input_sources_from_command_line() : protocols::jd3::chunk_library_inputters::ChunkLibraryInputter , protocols::jd3::chunk_library_inputters::PDBChunkLibraryInputter
• chunk_library_input_sources_from_tag() : protocols::jd3::chunk_library_inputters::ChunkLibraryInputter , protocols::jd3::chunk_library_inputters::PDBChunkLibraryInputter
• chunk_library_inputs_from_command_line() : protocols::jd3::chunk_library_inputters::ChunkLibraryInputterFactory
• chunk_library_inputter : protocols::jd3::chunk_library::ChunkLibraryPreliminaryLarvalJob
• chunk_library_inputter_creator_map_ : protocols::jd3::chunk_library_inputters::ChunkLibraryInputterFactory
• chunk_library_inputter_creators() : protocols::jd3::chunk_library_inputters::ChunkLibraryInputterFactory
• chunk_library_inputter_for_job() : protocols::jd3::chunk_library::ChunkLibraryJobQueen
• chunk_library_inputter_xml_schema_group_name() : protocols::jd3::chunk_library_inputters::ChunkLibraryInputterFactory
• chunk_pdb_files() : core::import_pose::options::RNA_FragmentMonteCarloOptions
• chunk_pdb_files_ : core::import_pose::options::RNA_FragmentMonteCarloOptions
• chunk_phi_ : protocols::frag_picker::scores::MidPhiOut , protocols::frag_picker::scores::PhiPsiRmsd , protocols::frag_picker::scores::PhiPsiSquareWell
• chunk_psi_ : protocols::frag_picker::scores::MidPsiOut , protocols::frag_picker::scores::PhiPsiRmsd , protocols::frag_picker::scores::PhiPsiSquareWell
• chunk_set() : core::import_pose::libraries::RNA_ChunkLibrary
• chunk_sets() : core::import_pose::libraries::RNA_ChunkLibrary
• chunk_sets_ : core::import_pose::libraries::RNA_ChunkLibrary
• chunk_silent_files() : core::import_pose::options::RNA_FragmentMonteCarloOptions
• chunk_silent_files_ : core::import_pose::options::RNA_FragmentMonteCarloOptions
• ChunkLibraryInnerLarvalJob() : protocols::jd3::chunk_library::ChunkLibraryInnerLarvalJob
• ChunkLibraryInputSource() : protocols::jd3::chunk_library_inputters::ChunkLibraryInputSource
• ChunkLibraryInputSourcesAndInputters : protocols::jd3::chunk_library_inputters::ChunkLibraryInputterFactory
• ChunkLibraryInputter() : protocols::jd3::chunk_library_inputters::ChunkLibraryInputter
• ChunkLibraryInputterFactory() : protocols::jd3::chunk_library_inputters::ChunkLibraryInputterFactory
• ChunkLibraryInputterMap : protocols::jd3::chunk_library_inputters::ChunkLibraryInputterFactory
• ChunkLibraryInputterRegistrator() : protocols::jd3::chunk_library_inputters::ChunkLibraryInputterRegistrator< T >
• ChunkLibraryJobQueen() : protocols::jd3::chunk_library::ChunkLibraryJobQueen
• ChunkLibraryJobResult() : protocols::jd3::chunk_library::ChunkLibraryJobResult
• ChunkLibraryPreliminaryLarvalJob() : protocols::jd3::chunk_library::ChunkLibraryPreliminaryLarvalJob
• ChunkList : protocols::abinitio::abscript::ResidueChunkSelection
• Chunks : protocols::nonlocal::SingleFragmentMover
• chunks_ : protocols::frag_picker::FragmentPicker , protocols::frag_picker::VallProvider , protocols::hybridization::HybridizeFoldtreeDynamic , protocols::nonlocal::SingleFragmentMover , protocols::rigid::RigidBodyMotionMover , protocols::rna::movers::ErraserMinimizerMover
• ChunkSet() : core::import_pose::libraries::ChunkSet
• ChunkTrialMover() : protocols::hybridization::ChunkTrialMover
• Ci() : core::scoring::FACTSResidueInfo
• Ci_ : core::scoring::FACTSResidueInfo
• CI_1B_Methods : core::scoring::ScoreFunction
• ci_1b_methods_ : core::scoring::ScoreFunction
• ci_1b_types() : core::scoring::ScoreFunction
• ci_2b_begin() : core::scoring::ScoreFunction
• ci_2b_end() : core::scoring::ScoreFunction
• ci_2b_intrares_ : core::scoring::ScoreFunction
• ci_2b_intrares_begin() : core::scoring::ScoreFunction
• ci_2b_intrares_end() : core::scoring::ScoreFunction
• CI_2B_Methods : core::scoring::ScoreFunction
• ci_2b_methods_ : core::scoring::ScoreFunction
• ci_2b_types() : core::scoring::ScoreFunction
• CI_LR_2B_MethodIterator : core::scoring::ScoreFunction
• CI_LR_2B_Methods : core::scoring::ScoreFunction
• ci_lr_2b_methods_ : core::scoring::ScoreFunction
• ci_lr_2b_methods_begin() : core::scoring::ScoreFunction
• ci_lr_2b_methods_end() : core::scoring::ScoreFunction
• ci_lr_2b_types() : core::scoring::ScoreFunction
• ci_rpes_ : protocols::minimization_packing::GreenPacker
• ci_sfxn_ : protocols::minimization_packing::GreenPacker
• ciBR() : core::pack::annealer::FASTERAnnealer
• ciBR_only_ : core::pack::annealer::FASTERAnnealer , protocols::pack_daemon::FASTER_IG_Repacker
• cid : protocols::constel::ResMut
• cid_ : protocols::constel::ChainTerm
• cif_files_ : core::scoring::cryst::PhenixInterface , protocols::cryst::SetRefinementOptionsMover
• Circle() : core::scoring::packstat::Circle
• circle : core::scoring::packstat::Event , core::scoring::packstat::trace , core::scoring::PDinter , core::scoring::power_diagram::PDinter
• circle_ : core::scoring::PDinter , core::scoring::power_diagram::PDinter
• circles_ : core::scoring::packstat::LeeRichards , core::scoring::packstat::Slice
• CircularGeneral1D_Func() : core::scoring::func::CircularGeneral1D_Func
• CircularHarmonicFunc() : core::scoring::func::CircularHarmonicFunc
• CircularPermutation() : protocols::fldsgn::CircularPermutation
• CircularPermuteFreePeptideMover() : protocols::backbone_moves::local_backbone_mover::free_peptide_movers::CircularPermuteFreePeptideMover
• CircularPowerFunc() : core::scoring::func::CircularPowerFunc
• CircularSigmoidalFunc() : core::scoring::func::CircularSigmoidalFunc
• CircularSplineFunc() : core::scoring::func::CircularSplineFunc
• cis_chi4_mean_ : core::scoring::methods::ProClosureEnergy
• cis_chi4_sd_ : core::scoring::methods::ProClosureEnergy
• cis_omega() : core::sequence::ABEGO , protocols::idealize::IdealizeMover
• cis_omega_ : core::sequence::ABEGO , protocols::idealize::IdealizeMover
• cis_peptide_bonds() : protocols::cyclic_peptide_predict::HierarchicalHybridJD_JobResultsSummary
• cis_peptide_bonds_ : protocols::cyclic_peptide_predict::HierarchicalHybridJD_JobResultsSummary
• cis_trans_conf : protocols::antibody::clusters::ClusterData
• cis_trans_match() : protocols::antibody::clusters::CDRCluster
• cis_trans_match_ : protocols::antibody::clusters::CDRCluster
• cispep_map() : core::io::StructFileRep
• cispep_map_ : core::io::StructFileRep
• Cjump_ : protocols::cryst::DockLatticeMover
• cl_outputters_ : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::standard::StandardJobQueen
• claim_accepted() : protocols::topology_broker::TopologyClaimer
• claim_backbone() : protocols::environment::claims::TorsionClaim
• claim_backbone_ : protocols::environment::claims::TorsionClaim
• claim_list_ : protocols::environment::ScriptCM
• claim_right_ : protocols::topology_broker::FragmentClaimer
• claim_sidechain() : protocols::environment::claims::TorsionClaim
• claim_sidechain_ : protocols::environment::claims::TorsionClaim
• claim_source_ : protocols::environment::claims::EnvClaim , protocols::topology_broker::claims::DofClaim
• claimer() : protocols::topology_broker::TopologyBroker
• claimer_ : protocols::topology_broker::ConstraintEvaluatorWrapper , protocols::topology_broker::RigidBodyRandomTMHMover
• claimer_builds_own_fold_tree() : protocols::topology_broker::MembraneTopologyClaimer , protocols::topology_broker::TMHTopologySamplerClaimer , protocols::topology_broker::TopologyClaimer
• ClaimerMessage() : protocols::topology_broker::ClaimerMessage
• claimers_ : protocols::topology_broker::TopologyBroker , protocols::topology_broker::TopologyClaimerFactory
• ClaimRight : protocols::topology_broker::claims::DofClaim
• claims_ : protocols::abinitio::abscript::AbscriptMover , protocols::abinitio::abscript::RigidChunkCM , protocols::environment::EnvClaimBroker
• ClaimStrength() : protocols::environment::claims::ClaimStrength
• clash : protocols::kinmatch::KRSQuery
• clash_ : core::scoring::nmr::NMRDummySpinlabelConformer
• clash_atom_scale_ : protocols::scoring::methods::TargetClashEnergy
• clash_check() : core::scoring::motif::ResPairMotifQuery , core::scoring::nmr::NMRDummySpinlabelEnsemble , protocols::scoring::ImplicitFastClashCheck
• clash_check_ : core::scoring::motif::ResPairMotifQuery , protocols::protein_interface_design::movers::MapHotspot , protocols::protein_interface_design::movers::TryRotamers
• clash_check_resn_ : protocols::scoring::methods::TargetClashEnergy
• clash_check_test() : protocols::scoring::ImplicitFastClashCheck
• clash_check_trimer() : protocols::scoring::ImplicitFastClashCheck
• clash_count : protocols::legacy_sewing::HashResult , protocols::scoring::ImplicitFastClashCheck
• clash_dis : protocols::sic_dock::CBScoreVisitor
• clash_dis_ : protocols::sic_dock::CBScore
• clash_dis_sq : protocols::sic_dock::CorrectionVisitor
• clash_dist() : protocols::matdes::ClashCheckFilter
• clash_dist_ : protocols::matdes::ClashCheckFilter
• clash_dist_cutoff_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• clash_off() : core::scoring::nmr::NMRDummySpinlabelConformer
• clash_on() : core::scoring::nmr::NMRDummySpinlabelConformer
• clash_penalty_ : protocols::scoring::VDW_GridEnergy
• clash_radius_ : protocols::sewing::requirements::ClashRequirement , protocols::sewing::requirements::LigandClashRequirement
• clash_residues_ : protocols::protein_interface_design::filters::ClashWithTargetFilter
• clash_score() : core::scoring::nmr::NMRDummySpinlabelConformer , protocols::ligand_docking::ga_ligand_dock::GridScorer , protocols::motif_grafting::movers::motif2scaffold_data , protocols::motif_grafting::movers::MotifMatch
• clash_score_ : core::scoring::nmr::NMRDummySpinlabelConformer
• clash_score_cutoff_ : protocols::protein_interface_design::filters::ClashWithTargetFilter
• clash_scorefxn_ : protocols::legacy_sewing::LegacyRepeatAssemblyMover
• clash_thresh_ : protocols::simple_filters::SymmetricMotifFilter
• clash_threshold_ : core::pack::hbonds::HBondGraphInitializerIG , protocols::hbnet::HBNet , protocols::pose_creation::MergePDBMover , protocols::pose_metric_calculators::ClashCountCalculator
• clash_wt_ : protocols::simple_filters::SymmetricMotifFilter
• ClashBasedRepackShell() : core::pack::task::operation::ClashBasedRepackShell
• ClashBasedShellSelector() : core::pack::task::residue_selector::ClashBasedShellSelector
• ClashCheckerPtr : core::scoring::motif::MotifHash
• ClashCheckFilter() : protocols::matdes::ClashCheckFilter
• ClashCountCalculator() : protocols::pose_metric_calculators::ClashCountCalculator
• clashes() : core::scoring::hbonds::graph::HBondNode , protocols::sic_dock::Rose
• clashes_naive() : protocols::sic_dock::Rose
• ClashRequirement() : protocols::sewing::requirements::ClashRequirement
• ClashRequirementCreator() : protocols::sewing::requirements::ClashRequirementCreator
• clashtolerance_ : protocols::loop_grower::SheetSampler
• ClashWithTargetFilter() : protocols::protein_interface_design::filters::ClashWithTargetFilter
• class_key() : protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputter , protocols::jd3::pose_outputters::mmTFPoseOutputter , protocols::jd3::pose_outputters::PDBPoseOutputter , protocols::jd3::pose_outputters::PoseOutputter , protocols::jd3::pose_outputters::ScoreFileOutputter , protocols::jd3::pose_outputters::SilentFilePoseOutputter
• class_name() : core::pack::task::residue_selector::ClashBasedShellSelector , core::select::jump_selector::AndJumpSelector , core::select::jump_selector::InterchainJumpSelector , core::select::jump_selector::JumpIndexSelector , core::select::jump_selector::NotJumpSelector , core::select::jump_selector::OrJumpSelector , 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::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 , protocols::antibody::AntibodyFeatures , protocols::antibody::clusters::CDRClusterFeatures , protocols::antibody::design::ResnumFromStringsWithRangesSelector , protocols::antibody::residue_selector::AntibodyRegionSelector , protocols::antibody::residue_selector::CDRResidueSelector , 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::carbohydrates::GlycanTreeMinMover , protocols::constraint_filters::ConstraintScoreFilter , protocols::constraint_filters::SavePoseConstraintToFileFilter , protocols::constraint_filters::ShowConstraintsFilter , 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::cyclic_peptide::CrosslinkerMover , protocols::cyclic_peptide::CycpepSymmetryFilter , protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter , protocols::cyclic_peptide::PeptideInternalHbondsFilter , protocols::cyclic_peptide::RamaMutationSelector , protocols::denovo_design::architects::BetaSheetArchitect , protocols::denovo_design::architects::BlueprintArchitect , protocols::denovo_design::architects::CompoundArchitect , protocols::denovo_design::architects::HelixArchitect , protocols::denovo_design::architects::StrandArchitect , protocols::denovo_design::components::CompoundPerturber , protocols::denovo_design::components::ConnectionPerturber , protocols::denovo_design::components::HelixPairing , protocols::denovo_design::components::HelixPerturber , protocols::denovo_design::components::HelixSheetPairing , protocols::denovo_design::components::NullPoseFolder , protocols::denovo_design::components::RandomTorsionPoseFolder , protocols::denovo_design::components::RemodelLoopMoverPoseFolder , protocols::denovo_design::components::StrandPairing , protocols::denovo_design::components::StructureData , protocols::denovo_design::connection::ConnectionArchitect , protocols::denovo_design::constraints::FileConstraintGenerator , 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::FoldTreeFromFoldGraphMover , protocols::denovo_design::movers::RotateSegmentMover , protocols::denovo_design::movers::SealFoldTreeMover , protocols::denovo_design::movers::SetPoseSecstructFromStructureDataMover , protocols::denovo_design::residue_selectors::NamedSegmentSelector , protocols::denovo_design::residue_selectors::PairedSheetResidueSelector , protocols::denovo_design::task_operations::ConsensusLoopDesignOperation , protocols::environment::claims::CutBiasClaim , protocols::environment::claims::EnvLabelSelector , protocols::environment::claims::JumpClaim , protocols::environment::claims::TorsionClaim , protocols::environment::claims::VirtResClaim , protocols::environment::claims::XYZClaim , protocols::enzdes::DiffAtomSasaFilter , protocols::enzdes::EnzdesScorefileFilter , protocols::enzdes::EnzScoreFilter , protocols::enzdes::LigBurialFilter , protocols::enzdes::LigDSasaFilter , protocols::enzdes::LigInterfaceEnergyFilter , protocols::enzdes::RemoveLigandFilter , protocols::enzdes::RepackWithoutLigandFilter , protocols::enzdes::ResidueConformerFilter , protocols::evolution::AASynthesisFitnessCost , protocols::evolution::AlignmentAAFinder , protocols::evolution::AlignmentGapInserter , protocols::features::AtomAtomPairFeatures , protocols::features::AtomInResidueAtomInResiduePairFeatures , protocols::features::AtomTypesFeatures , protocols::features::BetaTurnDetectionFeatures , protocols::features::ChargeChargeFeatures , protocols::features::DdGFeatures , protocols::features::GeometricSolvationFeatures , protocols::features::HBondFeatures , protocols::features::HBondParameterFeatures , protocols::features::helixAssembly::ConcurrencyTest , protocols::features::helixAssembly::HelixBundleFeatures , protocols::features::HelixCapFeatures , protocols::features::InterfaceFeatures , protocols::features::JobDataFeatures , protocols::features::LoopAnchorFeatures , protocols::features::ModelFeatures , protocols::features::OrbitalsFeatures , protocols::features::PairFeatures , protocols::features::PdbDataFeatures , protocols::features::PoseCommentsFeatures , protocols::features::PoseConformationFeatures , protocols::features::ProteinBackboneAtomAtomPairFeatures , protocols::features::ProteinBackboneTorsionAngleFeatures , protocols::features::ProteinBondGeometryFeatures , protocols::features::ProteinResidueConformationFeatures , protocols::features::ProteinRMSDFeatures , protocols::features::ProteinRMSDNoSuperpositionFeatures , protocols::features::RadiusOfGyrationFeatures , protocols::features::ResidueBurialFeatures , protocols::features::ResidueConformationFeatures , protocols::features::ResidueFeatures , protocols::features::ResidueGridScoresFeatures , protocols::features::ResidueScoresFeatures , protocols::features::ResidueSecondaryStructureFeatures , protocols::features::ResidueTotalScoresFeatures , protocols::features::ResidueTypesFeatures , protocols::features::RotamerBoltzmannWeightFeatures , protocols::features::RotamerFeatures , protocols::features::RotamerRecoveryFeatures , protocols::features::RuntimeFeatures , protocols::features::SaltBridgeFeatures , protocols::features::ScoreFunctionFeatures , protocols::features::ScoreTypeFeatures , protocols::features::ScreeningFeatures , protocols::features::SecondaryStructureSegmentFeatures , protocols::features::SimpleMetricFeatures , protocols::features::SmotifFeatures , protocols::features::strand_assembly::SandwichFeatures , protocols::features::strand_assembly::StrandBundleFeatures , protocols::features::StructureFeatures , protocols::features::StructureScoresFeatures , protocols::features::TaskOperationFeatures , protocols::features::TotalScoreFeatures , protocols::features::TrajectoryMapFeatures , protocols::features::UnrecognizedAtomFeatures , protocols::features::WaterFeatures , protocols::filters::CalculatorFilter , protocols::filters::CombinedFilter , protocols::filters::CompoundFilter , protocols::filters::ContingentFilter , protocols::filters::FalseFilter , protocols::filters::IfThenFilter , protocols::filters::MoveBeforeFilter , protocols::filters::ReplicateFilter , protocols::filters::StochasticFilter , protocols::filters::TimeFilter , protocols::filters::TrueFilter , 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::SheetConstraintGenerator , protocols::fold_from_loops::constraint_generator::AutomaticSheetConstraintGenerator , protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator , protocols::fold_from_loops::filters::ConstraintFulfilmentFilter , protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter , protocols::fold_from_loops::filters::ScorePoseSegmentFromResidueSelectorFilter , protocols::fold_from_loops::selectors::ConstraintResidueSelector , protocols::fold_from_loops::selectors::CutpointResidueSelector , protocols::fold_from_loops::selectors::ProteinResidueSelector , protocols::frag_picker::FragmentScoreFilter , protocols::hbnet::UnsatSelector , protocols::helical_bundle::BundleReporterFilter , protocols::indexed_structure_store::filters::FragmentLookupFilter , protocols::legacy_sewing::sampling::requirements::LegacyGlobalLengthRequirement , protocols::legacy_sewing::sampling::requirements::LegacyResidueRetentionRequirement , protocols::legacy_sewing::sampling::requirements::LegacySegmentDsspRequirement , protocols::legacy_sewing::sampling::requirements::LegacySegmentLengthRequirement , protocols::ligand_docking::AtomCountFilter , protocols::ligand_docking::ChainExistsFilter , protocols::ligand_docking::CompleteConnectionsFilter , protocols::ligand_docking::HBondAcceptorFilter , protocols::ligand_docking::HBondDonorFilter , protocols::ligand_docking::HeavyAtomFilter , protocols::ligand_docking::MolarMassFilter , protocols::ligand_docking::MolecularMassFilter , 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::loops::filters::LoopAnalyzerFilter , protocols::loops::loops_definers::LoopsDatabaseDefiner , protocols::loops::loops_definers::LoopsExplicitDefiner , protocols::loops::loops_definers::LoopsFileDefiner , protocols::loops::loops_definers::LoopsStringDefiner , protocols::matdes::ClashCheckFilter , protocols::matdes::GetRBDOFValues , protocols::matdes::InterfacePackingFilter , protocols::matdes::OligomericAverageDegreeFilter , protocols::matdes::SymUnsatHbondFilter , protocols::peptide_deriver::PeptideDeriverFilter , 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::residue_selectors::HBondSelector , protocols::residue_selectors::LigandMetalContactSelector , protocols::residue_selectors::NativeSelector , protocols::residue_selectors::StoredResidueSubsetSelector , protocols::residue_selectors::TaskSelector , protocols::rna::movers::RNAThreadAndMinimizeMover , protocols::score_filters::GeometryFilter , protocols::score_filters::ScoreCutoffFilter , protocols::score_filters::ScoreTypeFilter , protocols::sewing::hashing::AlignmentFileGeneratorMover , 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::simple_ddg::AlaScan , 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::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::LongestContinuousApolarSegmentFilter , 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
• class_name_ : protocols::constraint_generator::ConstraintGenerator
• classic_mcm_protocol() : protocols::symmetric_docking::SymDockProtocol
• classic_protocol() : protocols::ligand_docking::LigandDockProtocol
• ClassicAbinitio() : protocols::abinitio::ClassicAbinitio
• ClassicFragmentMover() : protocols::simple_moves::ClassicFragmentMover
• ClassicFragmentMoverOP : protocols::forge::remodel::RemodelLoopMover
• ClassicGrid() : protocols::qsar::scoring_grid::ClassicGrid
• ClassicMatchAlgorithm() : protocols::match::downstream::ClassicMatchAlgorithm
• ClassicRelax() : protocols::relax::ClassicRelax
• classification() : core::io::HeaderInformation
• classification_ : core::io::HeaderInformation
• classifier : core::pose::rna::RNA_SuiteInfo
• classify_onebody_enmeth() : core::scoring::MinimizationNode
• classify_twobody_enmeth() : core::scoring::MinimizationEdge , core::scoring::MinimizationNode
• classname() : core::conformation::symmetry::SymmDataLoader , core::fragment::FragmentSetLoader , core::import_pose::PoseResourceLoader , protocols::loophash::LoopHashLibraryLoader , protocols::loops::LoopsFileLoader , protocols::surface_docking::SurfaceVectorLoader
• ClassType : protocols::sparta::GDB
• CLD : protocols::sic_dock::SICFast
• CLD2 : protocols::sic_dock::SICFast
• clean_constraint_string() : protocols::denovo_design::constraints::FileConstraintGenerator
• clean_fasta_file_contents() : protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions
• clean_frag_cache() : core::fragment::FragmentIO
• clean_jumps() : protocols::abinitio::TemplateJumpSetup , protocols::jumping::BaseJumpSetup , protocols::jumping::JumpSelector , protocols::jumping::JumpSetup , protocols::jumping::ResiduePairJumpSetup , protocols::jumping::SheetBuilder
• clean_pose() : protocols::simple_ddg::ddG
• clean_pose_store() : protocols::cluster::ClusterBase
• clean_residue_task() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• clean_up() : protocols::frag_picker::scores::ABEGO_SS_Score , protocols::frag_picker::scores::AmbigCSScore , protocols::frag_picker::scores::AtomBasedConstraintsScore , protocols::frag_picker::scores::CachingScoringMethod , protocols::frag_picker::scores::CSScore , protocols::frag_picker::scores::DisulfideDistance , protocols::frag_picker::scores::FragmentCrmsd , protocols::frag_picker::scores::FragmentCrmsdResDepth , protocols::frag_picker::scores::FragmentDME , protocols::frag_picker::scores::FragmentScoreManager , protocols::frag_picker::scores::GunnCostScore , protocols::frag_picker::scores::HydrophobicityProfileSimilarity , protocols::frag_picker::scores::HydrophobicitySimilarity , protocols::frag_picker::scores::JCoupling , protocols::frag_picker::scores::LAMBEGO_Similarity , protocols::frag_picker::scores::MidPhiOut , protocols::frag_picker::scores::MidPsiOut , protocols::frag_picker::scores::PartialSecondarySimilarity , protocols::frag_picker::scores::PCS_FragDistance , protocols::frag_picker::scores::Phi , protocols::frag_picker::scores::PhiPsiRmsd , protocols::frag_picker::scores::PhiPsiSquareWell , protocols::frag_picker::scores::ProfileScore , protocols::frag_picker::scores::ProfileScoreBlosum62 , protocols::frag_picker::scores::ProfileScoreDistWeight , protocols::frag_picker::scores::ProfileScoreL1 , protocols::frag_picker::scores::ProfileScoreStructL1 , protocols::frag_picker::scores::ProfileScoreSubMatrix , protocols::frag_picker::scores::Psi , protocols::frag_picker::scores::RamaScore , protocols::frag_picker::scores::RDCScore , protocols::frag_picker::scores::ScoreEValuator , protocols::frag_picker::scores::SecondarySimilarity , protocols::frag_picker::scores::SolventAccessibility , protocols::frag_picker::scores::TalosSSSimilarity , protocols::frag_picker::scores::TorsionBinSimilarity
• clean_up_after_packing() : core::pack::interaction_graph::AnnealableGraphBase , core::pack::interaction_graph::MultiplexedAnnealableGraph , core::pack::interaction_graph::ResidueArrayAnnealingEvaluator
• clean_up_bgtfc_edges_marked_for_deletion() : core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >
• clean_up_edges_marked_for_deletion() : core::pack::interaction_graph::InteractionGraphBase
• clean_up_residuearrayannealableenergy_after_packing() : core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty , core::scoring::aa_composition_energy::AACompositionEnergy , core::scoring::annealing::ResidueArrayAnnealableEnergy , core::scoring::util_methods::DumpTrajectoryEnergy
• clean_up_rna_two_body_energy_tables() : core::scoring::rna::RNA_PairwiseLowResolutionEnergy
• cleaned_alignment_file() : protocols::evolution::AlignmentGapInserter
• cleaned_alignment_file_ : protocols::evolution::AlignmentGapInserter
• cleanup() : protocols::minimization_packing::GreenPacker , protocols::minimization_packing::PackRotamersMover
• cleanup_after_psipred() : core::io::external::PsiPredInterface
• cleanup_files() : core::scoring::PoissonBoltzmannPotential
• cleanup_pose() : protocols::stepwise::modeler::protein::InputStreamWithResidueInfo
• clear() : core::chemical::CacheableResidueTypeSets , core::chemical::mainchain_potential::MainchainScoreTable , core::chemical::ResidueTypeSelector , core::conformation::Conformation , core::fragment::Frame , core::fragment::picking_old::concepts::Book< Pages > , core::fragment::picking_old::concepts::Library< Books > , core::id::AtomID_Map< T > , core::id::DOF_ID_Map< T > , core::id::NamedAtomID_Map< T > , core::id::SequenceMapping , core::io::sequence_comparation::DesignContrast , core::io::silent::SilentFileData , core::kinematics::AtomTree , core::kinematics::FoldTree , core::kinematics::MoveMap , core::kinematics::ResidueCoordinateChangeList , core::pack::annealer::SimAnnealerBase , core::pack::rotamer_set::WaterPackingInfo , core::pack::task::operation::DisallowIfNonnative , core::pack::task::operation::DisallowIfNonnativeRLT , core::pack::task::operation::PreventRepacking , core::pack::task::operation::RestrictResidueToRepacking , core::pack::task::TaskFactory , core::pose::copydofs::CopyDofsInfo , core::pose::datacache::ObserverCache , core::pose::datacache::SpecialSegmentsObserver , core::pose::metrics::PoseMetricContainer , core::pose::PDBPoseMap , core::pose::Pose , core::scoring::CenHBPotential , core::scoring::constraints::Constraints , core::scoring::constraints::ConstraintSet , core::scoring::constraints::ResidueConstraints , core::scoring::EMapVector , core::scoring::Energies , core::scoring::Hairpins , core::scoring::hbonds::HBondSet , core::scoring::motif::XformScore , core::scoring::NeighborList , core::scoring::power_diagram::PowerDiagram , core::scoring::SmoothScoreTermCoeffs , core::scoring::Strands , core::scoring::TMscoreStore , core::select::residue_selector::AndResidueSelector , core::sequence::DP_Matrix , core::sequence::SequenceAlignment , core::simple_metrics::SimpleMetricData , protocols::abinitio::AbrelaxMover , protocols::antibody::clusters::CDRClusterSet , protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel , protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD , protocols::canonical_sampling::TemperingBase , protocols::cluster::Cluster , protocols::cluster::GatherPosesMover , protocols::denovo_design::components::Segment , protocols::dna::DnaChains , protocols::environment::ProtectedConformation , protocols::evaluation::MetaPoseEvaluator , protocols::filters::CompoundFilter , protocols::filters::Filter , protocols::filters::FilterCollection , protocols::fldsgn::topology::BB_Pos , protocols::fldsgn::topology::BetaAlphaBetaMotifSet , protocols::fldsgn::topology::HelixPairingSet , protocols::fldsgn::topology::HSSTripletSet , protocols::fldsgn::topology::SheetSet , protocols::fldsgn::topology::StrandPairingSet , protocols::forge::build::BuildManager , protocols::forge::remodel::RemodelAccumulator , protocols::frag_picker::BoundedCollector< StrictWeakOrdering > , protocols::frag_picker::CandidatesCollector , protocols::frag_picker::GrabAllCollector , protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering > , protocols::frag_picker::quota::ABEGO_SS_Pool , protocols::frag_picker::quota::QuotaCollector , protocols::frag_picker::quota::QuotaPool , protocols::frag_picker::quota::SecondaryStructurePool , protocols::frag_picker::scores::AdaptiveScoreHistogram , protocols::frag_picker::scores::ProfileScore , protocols::frag_picker::scores::ProfileScoreBlosum62 , protocols::frag_picker::scores::ProfileScoreDistWeight , protocols::frag_picker::scores::ProfileScoreL1 , protocols::frag_picker::scores::ProfileScoreStructL1 , protocols::frag_picker::scores::ProfileScoreSubMatrix , protocols::frags::FragLib , protocols::frags::SingleResidueTorsionFragmentLibrary , protocols::frags::TorsionFragmentLibrary , protocols::hbnet::HBNetScore , protocols::helical_bundle_predict::HBPHelixAssignments , protocols::hotspot_hashing::HotspotStubSet , protocols::jd2::JobsContainer , protocols::jd3::dag_node_managers::NodeManager , protocols::jd3::dag_node_managers::NodeManagerStorageMatrix , protocols::jumping::JumpSetup , protocols::jumping::ResiduePairJumpSetup , protocols::kinematic_closure::perturbers::PerturberSet , protocols::ligand_docking::ga_ligand_dock::OutputStructureStore , protocols::ligand_docking::ga_ligand_dock::RotamerPairEnergies , protocols::loop_grower::LoopPartialSolutionStore , protocols::loop_modeling::utilities::LoopMoverGroup , protocols::loops::Loops , protocols::match::Bool3DGrid , protocols::match::downstream::ActiveSiteGrid , protocols::moves::CompositionMover , protocols::moves::MoverContainer , protocols::moves::MoverStatistics , protocols::moves::PDBDumpMover , protocols::mpi_refinement::Scheduler , protocols::pack_daemon::TopEntitySet , protocols::peptide_deriver::PeptideDeriverOutputterContainer , protocols::pockets::CClusterSet , protocols::pockets::PClusterSet , protocols::pockets::PocketGrid , protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::qsar::qsarMap , protocols::recces::Histogram , protocols::rosetta_scripts::ParsedProtocol , protocols::simple_filters::NeighborTypeFilter , protocols::simple_moves::BackboneMover , protocols::simple_moves::LoggedFragmentMover , protocols::splice::ResidueBBDofs , protocols::toolbox::DecoySetEvaluation , protocols::toolbox::KClusterElement , protocols::toolbox::match_enzdes_util::EnzdesLoopsFile , protocols::wum::SilentStructStore , protocols::wum::WorkUnitQueue
• clear_() : core::scoring::func::SOGFunc , core::scoring::func::SOGFunc_Impl
• clear_active_dofs() : core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::SCMinMinimizerMap
• clear_active_pose_constraints() : protocols::toolbox::match_enzdes_util::EnzdesCstParamCache
• clear_active_pose_constraints_for_block() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• clear_all() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• clear_all_residues_ : protocols::flxbb::FlxbbDesign
• clear_at_inds() : protocols::match::downstream::AtomGeometrySecMatchRPE
• clear_atoms() : core::optimization::DOF_Node
• clear_authors() : core::io::HeaderInformation
• clear_blacklist() : protocols::wum::WorkUnitBase
• clear_bprots_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• clear_buffers() : protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter
• clear_cached_data() : protocols::denovo_design::components::StructureDataFactory , protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• clear_cached_maps() : core::chemical::ResidueTypeSetCache
• clear_cached_residuearrayannealableenergy_information() : core::pack::interaction_graph::InteractionGraphFactory
• clear_calculators() : core::pose::metrics::CalculatorFactory
• clear_cdr_set_exclude_options() : protocols::antibody::CDRSetOptionsParser
• clear_cdr_set_include_options() : protocols::antibody::CDRSetOptionsParser
• clear_channel_from_garbage_collector() : protocols::jd2::MpiFileBuffer
• clear_checkpoints() : protocols::abinitio::MembraneAbinitio , protocols::checkpoint::CheckPointer
• clear_chi_rotamers() : core::chemical::MutableChiRecord , core::chemical::MutableResidueType
• clear_children() : protocols::loop_modeling::LoopMover
• clear_combine_history() : protocols::simple_moves::CombinePoseMover
• clear_comments() : core::io::silent::SilentStruct
• clear_compounds() : core::io::HeaderInformation
• clear_connected_resonances() : protocols::noesy_assign::Resonance
• clear_connections() : protocols::legacy_sewing::SegmentGraph
• clear_consideration() : core::pack::interaction_graph::ResidueArrayAnnealingEvaluator
• clear_constraints() : protocols::forge::remodel::RemodelConstraintGenerator
• clear_current_job_output() : protocols::jd2::JobDistributor
• clear_data() : protocols::fldsgn::topology::SS_Info2 , protocols::motifs::BuildPosition , protocols::toolbox::KClusterElement
• clear_dCCdx_res_cache() : core::scoring::electron_density::ElectronDensity
• clear_dependencies() : protocols::forge::build::BuildInstruction , protocols::forge::build::BuildManager
• clear_design_taskset() : protocols::flxbb::FlxbbDesign
• clear_designable_residues_ : protocols::denovo_design::movers::FastDesign
• clear_dof_nodes() : core::optimization::MinimizerMap
• clear_downstream_orientation_atoms() : protocols::match::MatcherTask
• clear_edges() : protocols::toolbox::ResidueNetwork
• clear_energies() : core::io::silent::SilentStruct , core::scoring::Energies , protocols::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• clear_evaluators() : protocols::jd2::JobOutputter
• clear_events() : core::pose::datacache::LengthEventCollector
• clear_experimental_techniques() : core::io::HeaderInformation
• clear_extent_eval() : core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library >
• clear_extent_gen() : core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library >
• clear_external_geom_samplers() : protocols::match::downstream::ClassicMatchAlgorithm
• clear_filters() : protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::match::output::MatchProcessor
• clear_focus() : core::pack::task::residue_selector::ClashBasedShellSelector , core::select::residue_selector::NeighborhoodResidueSelector
• clear_fragment_eval() : core::fragment::picking_old::vall::VallLibrarian
• clear_fragment_gen() : core::fragment::picking_old::vall::VallLibrarian
• clear_fragments() : protocols::forge::components::VarLengthBuild , protocols::forge::remodel::RemodelLoopMover , protocols::loops::loop_mover::LoopMover
• clear_free_peptide_movers() : protocols::backbone_moves::local_backbone_mover::LocalBackboneMover
• clear_from_pose() : protocols::denovo_design::components::StructureDataFactory
• clear_glycan_trees() : core::conformation::Conformation
• clear_hash_map() : protocols::match::HitHasher
• clear_hbond_counts() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode
• clear_hbonds() : core::scoring::hbonds::HBondResPairMinData
• clear_history() : protocols::pack_daemon::MultistateFitnessFunction
• clear_icoor() : core::chemical::MutableResidueType
• clear_imporated_data() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser
• clear_induced_fields() : core::scoring::MultipoleElecPotential
• clear_info() : protocols::moves::Mover
• clear_initialization() : protocols::dna::DnaInterfacePacker
• clear_input_sources() : protocols::jd3::InnerLarvalJob
• clear_internals() : protocols::protein_interface_design::PatchdockReader
• clear_inverse_rotamers() : protocols::forge::constraints::InverseRotamersRCG
• clear_jumps() : protocols::rigid::RigidBodyPerturbNoCenterMover , protocols::scoring::InterfaceInfo
• clear_keywords() : core::io::HeaderInformation
• clear_lib() : protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD
• clear_loop_residues() : protocols::generalized_kinematic_closure::GeneralizedKIC
• clear_match_data() : protocols::match::output::CloudPDBWriter
• clear_motif_cst() : protocols::fold_from_loops::NubInitioMover
• clear_motif_cst_ : protocols::fold_from_loops::NubInitioMover
• clear_movers() : protocols::loop_modeling::LoopProtocol
• clear_movers_and_refiners() : protocols::loop_modeling::LoopProtocol
• clear_movesets() : protocols::rbsegment_relax::RBSegmentRelax
• clear_mutation_sets() : protocols::task_operations::MutationSetDesignOperation
• clear_observers() : core::conformation::Conformation
• clear_orbitals() : core::chemical::MutableResidueType
• clear_other_pose_list() : core::pose::full_model_info::FullModelInfo
• clear_output() : protocols::jd2::Job
• clear_overall_prob_set() : protocols::task_operations::ResidueProbDesignOperation
• clear_pairings() : protocols::denovo_design::components::StructureData
• clear_parameters_list() : core::conformation::parametric::ParametersSet
• clear_parameters_set_list() : core::conformation::Conformation
• clear_parents() : protocols::genetic_algorithm::GeneticAlgorithmBase
• clear_perturber_residue_list() : protocols::generalized_kinematic_closure::GeneralizedKIC
• clear_perturber_residue_lists() : protocols::generalized_kinematic_closure::GeneralizedKIC
• clear_perturbers() : protocols::kinematic_closure::KicMover
• clear_poses() : protocols::moves::MonteCarlo
• clear_positions() : protocols::task_operations::ConservativeDesignOperation
• clear_postfold_movers() : protocols::denovo_design::movers::BuildDeNovoBackboneMover
• clear_prefold_movers() : protocols::denovo_design::movers::BuildDeNovoBackboneMover
• clear_prob_set() : protocols::task_operations::ResidueProbDesignOperation
• clear_properties() : core::chemical::AtomType
• clear_rcgs() : protocols::forge::components::VarLengthBuild
• clear_refiners() : protocols::loop_modeling::LoopProtocol
• clear_res_list() : core::pose::full_model_info::FullModelInfo
• clear_reset_filters() : protocols::filters::CombinedFilter , protocols::filters::CompoundFilter
• clear_residue_connections() : core::conformation::Residue
• clear_residues() : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• clear_reslabel() : core::pose::PDBInfo
• clear_rnl_pose() : protocols::enzdes::EnzdesScorefileFilter
• clear_rotamer() : protocols::recces::sampler::MC_Comb , protocols::recces::sampler::rna::MC_RNA_MultiSuite , protocols::recces::sampler::rna::MC_RNA_Suite , protocols::stepwise::sampler::StepWiseSamplerComb , protocols::stepwise::sampler::StepWiseSamplerSizedAny , protocols::stepwise::sampler::StepWiseSamplerSizedComb
• clear_rotamer_bb_torsion_indices() : core::chemical::rotamers::NCAARotamerLibrarySpecification
• clear_rots() : protocols::motifs::BuildPosition
• clear_rv_infos() : protocols::forge::remodel::ResidueVicinityRCG
• clear_score() : protocols::moves::MoverStatistics
• clear_seeds_ : protocols::seeded_abinitio::CAcstGenerator
• clear_segments() : protocols::backrub::BackrubMover
• clear_sequence_constraints() : core::pose::Pose , core::scoring::constraints::ConstraintSet
• clear_serial_data() : protocols::wum::WorkUnitBase
• clear_setup_movers() : protocols::forge::components::VarLengthBuild
• clear_shared_silent_data() : core::io::silent::SilentFileData
• clear_stored_constraints() : protocols::forge::remodel::RemodelConstraintGenerator
• clear_stored_solutions() : protocols::generalized_kinematic_closure::GeneralizedKIC
• clear_structure_map() : core::io::raw_data::RawFileData , core::io::silent::SilentFileData
• clear_suckers() : protocols::simple_moves::AddCavitiesMover
• clear_sym_def() : protocols::symmetry::ExtractAsymmetricPoseMover
• clear_sym_def_ : protocols::symmetry::ExtractAsymmetricPoseMover
• clear_target_states() : protocols::toolbox::match_enzdes_util::InvrotTree
• clear_task() : protocols::calc_taskop_movers::DesignRepackMover
• clear_task_factory() : protocols::calc_taskop_movers::DesignRepackMover , protocols::seeded_abinitio::SeedSetupMover
• clear_title() : core::io::HeaderInformation
• clear_torsion_string_stack() : protocols::loops::loop_closure::kinematic_closure::BaseTabooPerturber , protocols::loops::loop_closure::kinematic_closure::KinematicPerturber
• clear_torsions_using() : protocols::normalmode::NormalMode
• clear_Tsymm() : core::conformation::symmetry::SymmetricConformation
• clear_two_body_energy() : core::pack::hbonds::BareMinimumPDEdge , core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::PrecomputedPairEnergiesEdge
• clear_two_body_energy_for_edge() : core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph
• clear_user_provided_movers() : protocols::forge::components::VarLengthBuild
• clear_Vall() : core::fragment::picking_old::FragmentLibraryManager
• ClearChiRotamers() : core::chemical::ClearChiRotamers
• ClearCompositionConstraintsMover() : protocols::aa_composition::ClearCompositionConstraintsMover
• ClearConstraintsMover() : protocols::constraint_movers::ClearConstraintsMover
• clearMask() : core::scoring::electron_density::ElectronDensity
• clearSmallPockets() : protocols::pockets::PocketGrid
• client() : protocols::environment::ScriptCM
• client_ : protocols::environment::ScriptCM
• ClientMover() : protocols::environment::ClientMover
• ClientMoverOP : protocols::abinitio::abscript::AbscriptMover , protocols::abinitio::abscript::AbscriptStageMover
• clip_to_nrchi_range() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >
• clique() : protocols::features::clique_saver
• clique_saver() : protocols::features::clique_saver
• cliques_ : protocols::features::clique_saver
• clone() : core::chemical::CacheableResidueTypeSets
• Clone() : core::chemical::Element , core::chemical::gasteiger::GasteigerAtomTypeData
• clone() : core::chemical::mainchain_potential::MainchainScoreTable , core::chemical::MutableResidueType , core::chemical::PoseResidueTypeSet , core::chemical::ResidueType , core::chemical::ResidueTypeSetCache , core::chemical::rotamers::BasicRotamerLibrarySpecification , core::chemical::rotamers::CenrotRotamerLibrarySpecification , core::chemical::rotamers::DunbrackRotamerLibrarySpecification , core::chemical::rotamers::NCAARotamerLibrarySpecification , core::chemical::rotamers::PDBRotamerLibrarySpecification , core::chemical::rotamers::RotamerLibrarySpecification , core::chemical::rotamers::StoredRotamerLibrarySpecification , core::conformation::carbohydrates::GlycanNode , core::conformation::carbohydrates::GlycanTree , core::conformation::carbohydrates::GlycanTreeSet , core::conformation::carbohydrates::GlycanTreeSetObserver , core::conformation::Conformation , core::conformation::membrane::AqueousPoreParameters , core::conformation::membrane::ImplicitLipidInfo , core::conformation::parametric::BooleanValuedParameter , core::conformation::parametric::Parameter , core::conformation::parametric::Parameters , core::conformation::parametric::ParametersSet , core::conformation::parametric::ParametrizationCalculator , core::conformation::parametric::RealValuedParameter , core::conformation::parametric::RealVectorValuedParameter , core::conformation::parametric::SizeValuedParameter , core::conformation::parametric::SizeVectorValuedParameter , core::conformation::Residue , core::conformation::symmetry::MirrorSymmetricConformation , core::conformation::symmetry::SymmData , core::conformation::symmetry::SymmetricConformation , core::conformation::symmetry::SymmetryInfo , core::conformation::symmetry::SymmetryTransform , core::energy_methods::DEEREnergy , core::fragment::AnnotatedFragData , core::fragment::BaseCacheUnit , core::fragment::BBTorsionAndAnglesSRFD , core::fragment::BBTorsionSRFD , core::fragment::ConstantLengthFragSet , core::fragment::DownJumpSRFD , core::fragment::FragData , core::fragment::FragSet , core::fragment::FragSetCollection , core::fragment::Frame , core::fragment::IndependentBBTorsionSRFD , core::fragment::JumpingFrame , core::fragment::MapCacheUnit< T > , core::fragment::MinimalFragSet , core::fragment::NonContinuousFrame , core::fragment::OrderedFragSet , 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 , core::fragment::picking_old::vall::gen::LengthGen , core::fragment::picking_old::vall::gen::SecStructGen , core::fragment::picking_old::vall::gen::VallFragmentGen , core::fragment::SecstructSRFD , core::fragment::SingleResidueFragData , core::fragment::UpJumpSRFD , core::fragment::VectorCacheUnit< T > , core::grid::CartGrid< T > , core::id::CacheableAtomID_MapVector , core::import_pose::libraries::RNA_ChunkLibrary , 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::import_pose::PDBSilentStruct , 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 , core::io::StructFileRep , core::io::StructFileRepOptions , core::kinematics::FoldTree , core::kinematics::jacobian::JacobianStructure , core::kinematics::jacobian::ModuleType1 , core::kinematics::jacobian::SeriesJacobians , core::kinematics::MoveMap , core::kinematics::tree::Atom , core::kinematics::tree::BondedAtom , core::kinematics::tree::JumpAtom , core::optimization::MinimizerOptions , core::pack::dunbrack::cenrot::CenRotDunEnergy , core::pack::dunbrack::DunbrackConstraint , core::pack::dunbrack::DunbrackEnergy , core::pack::dunbrack::RotamerConstraint , core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser , core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty , core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty , core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphContainer , core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphOptions , core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNodeData , core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy , core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyEnergy , core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid , core::pack::interaction_graph::HPatchEnergy , core::pack::interaction_graph::SurfaceEnergy , core::pack::palette::CustomBaseTypePackerPalette , core::pack::palette::DefaultPackerPalette , core::pack::palette::NCAADefaultPackerPalette , core::pack::palette::NoDesignPackerPalette , core::pack::palette::PackerPalette , core::pack::rotamer_set::AddResiduesRotamerSetOperation , core::pack::rotamer_set::DeleteAllRotamerSetOperation , core::pack::rotamer_set::RotamerSetOperation , core::pack::rotamer_set::RotamerSetsOperation , core::pack::rotamer_set::UnboundRotamersOperation , core::pack::rotamer_set::WaterPackingInfo , core::pack::task::ALLAA , core::pack::task::ALLAAwc , core::pack::task::ALLAAxc , core::pack::task::APOLA , core::pack::task::APOLAR , core::pack::task::AROMATIC , core::pack::task::AUTO , core::pack::task::CHARGED , core::pack::task::EX , core::pack::task::EX_CUTOFF , core::pack::task::FIX_HIS_TAUTOMER , core::pack::task::NATAA , core::pack::task::NATRO , core::pack::task::NO_ADDUCTS , core::pack::task::NOTAA , core::pack::task::operation::AddBehaviorRLT , core::pack::task::operation::AllResFilter , core::pack::task::operation::AnyResFilter , core::pack::task::operation::AppendResidueRotamerSet , core::pack::task::operation::AppendRotamer , core::pack::task::operation::AppendRotamerSet , core::pack::task::operation::ChainIs , core::pack::task::operation::ChainIsnt , 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::IncludeCurrent , core::pack::task::operation::IncludeCurrentRLT , core::pack::task::operation::InitializeExtraRotsFromCommandline , core::pack::task::operation::InitializeFromCommandline , core::pack::task::operation::InitializeFromOptionCollection , core::pack::task::operation::KeepSequenceSymmetry , core::pack::task::operation::NoRepackDisulfides , core::pack::task::operation::NoResFilter , core::pack::task::operation::OperateOnCertainResidues , core::pack::task::operation::OperateOnResidueSubset , core::pack::task::operation::OptCysHG , core::pack::task::operation::OptH , core::pack::task::operation::PreserveCBeta , core::pack::task::operation::PreserveCBetaRLT , core::pack::task::operation::PreventRepacking , core::pack::task::operation::PreventRepackingRLT , core::pack::task::operation::ProhibitResidueProperties , core::pack::task::operation::ProhibitSpecifiedBaseResidueTypes , core::pack::task::operation::ReadResfile , core::pack::task::operation::ReadResfileAndObeyLengthEvents , core::pack::task::operation::ReplicateTask , core::pack::task::operation::ResFilter , core::pack::task::operation::ResidueHasProperty , core::pack::task::operation::ResidueIndexIs , core::pack::task::operation::ResidueIndexIsnt , core::pack::task::operation::ResidueLacksProperty , core::pack::task::operation::ResidueName3Is , core::pack::task::operation::ResidueName3Isnt , core::pack::task::operation::ResiduePDBIndexIs , core::pack::task::operation::ResiduePDBIndexIsnt , core::pack::task::operation::ResiduePDBInfoHasLabel , core::pack::task::operation::ResiduePDBInfoLacksLabel , 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::RestrictToRepackingRLT , core::pack::task::operation::RestrictToResidueProperties , core::pack::task::operation::RestrictToSpecifiedBaseResidueTypes , core::pack::task::operation::RestrictYSDesign , core::pack::task::operation::RotamerExplosion , core::pack::task::operation::SetRotamerCouplings , core::pack::task::operation::SetRotamerLinks , core::pack::task::operation::TaskOperation , core::pack::task::operation::UseMultiCoolAnnealer , core::pack::task::PackerTask , core::pack::task::PackerTask_ , core::pack::task::PIKAA , core::pack::task::PIKNA , core::pack::task::POLAR , core::pack::task::PROPERTY , core::pack::task::ResfileCommand , core::pack::task::residue_selector::ClashBasedShellSelector , core::pack::task::SCAN , core::pack::task::TARGET , core::pack::task::TaskFactory , core::pack::task::USE_INPUT_SC , core::pose::datacache::CacheableObserver , core::pose::datacache::CacheablePoseRawPtr , core::pose::datacache::LengthEventCollector , core::pose::datacache::PositionConservedResiduesStore , core::pose::datacache::SpecialSegmentsObserver , core::pose::full_model_info::FullModelInfo , core::pose::full_model_info::FullModelParameters , core::pose::full_model_info::SubMotifInfo , core::pose::metrics::PoseMetricCalculator , 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::Pose , core::pose::reference_pose::ReferencePose , core::pose::reference_pose::ReferencePoseSet , core::pose::rna::RNA_DataInfo , core::pose::rna::RNA_FilteredBaseBaseInfo , core::pose::rna::RNA_RawBaseBaseInfo , core::pose::rna::secstruct_legacy::RNA_SecStructLegacyInfo , core::pose::toolbox::AtomID_Mapper , core::pose::toolbox::AtomLevelDomainMap , core::scoring::aa_composition_energy::AACompositionConstraint , core::scoring::aa_composition_energy::AACompositionEnergy , core::scoring::aa_composition_energy::AACompositionEnergySetup , core::scoring::aa_composition_energy::AACompositionPropertiesSet , core::scoring::aa_repeat_energy::AARepeatEnergy , core::scoring::bin_transitions::BinTransitionCalculator , core::scoring::bin_transitions::BinTransitionData , core::scoring::carbon_hbonds::CarbonHBondEnergy , core::scoring::CenListInfo , core::scoring::ChemicalShiftAnisotropy , core::scoring::constraints::AmbiguousConstraint , core::scoring::constraints::AmbiguousNMRConstraint , core::scoring::constraints::AmbiguousNMRDistanceConstraint , core::scoring::constraints::AngleConstraint , core::scoring::constraints::AtomPairConstraint , core::scoring::constraints::BackboneStubConstraint , core::scoring::constraints::BackboneStubLinearConstraint , core::scoring::constraints::BasePairConstraint , core::scoring::constraints::BigBinConstraint , core::scoring::constraints::BoundFunc , core::scoring::constraints::ConstantConstraint , core::scoring::constraints::Constraint , core::scoring::constraints::Constraints , core::scoring::constraints::ConstraintsEnergy , core::scoring::constraints::ConstraintSet , core::scoring::constraints::CoordinateConstraint , core::scoring::constraints::CstEnergyContainer , core::scoring::constraints::CstMinimizationData , core::scoring::constraints::DihedralConstraint , core::scoring::constraints::DihedralPairConstraint , core::scoring::constraints::DistancePairConstraint , core::scoring::constraints::FabConstraint , core::scoring::constraints::KofNConstraint , core::scoring::constraints::LocalCoordinateConstraint , core::scoring::constraints::MembraneSpanConstraint , core::scoring::constraints::MembraneSpanTermZConstraint , core::scoring::constraints::MultiConstraint , core::scoring::constraints::NamedAngleConstraint , core::scoring::constraints::NamedAtomPairConstraint , core::scoring::constraints::NamedDihedralConstraint , core::scoring::constraints::NonResidueTypeConstraint , core::scoring::constraints::OffsetPeriodicBoundFunc , core::scoring::constraints::PeriodicBoundFunc , core::scoring::constraints::ResidueCouplingConstraint , core::scoring::constraints::ResidueTypeConstraint , core::scoring::constraints::ResidueTypeLinkingConstraint , core::scoring::constraints::RTConstraint , core::scoring::constraints::SequenceProfileConstraint , core::scoring::constraints::SiteConstraint , core::scoring::constraints::SiteConstraintResidues , core::scoring::ContextGraph , core::scoring::cryst::XtalMLEnergy , core::scoring::custom_pair_distance::DistanceFunc , core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy , core::scoring::custom_pair_distance::RespairInteractions , core::scoring::DenseEnergyContainer , core::scoring::DipolarCoupling , core::scoring::disulfides::CaCbCb_Angle_Func , core::scoring::disulfides::CaCbCbCa_Dihedral_Func , core::scoring::disulfides::CB_Angle_Func , core::scoring::disulfides::Cb_Distance_Func , core::scoring::disulfides::CBSG_Dihedral_Func , core::scoring::disulfides::Cen_Distance_Func , core::scoring::disulfides::CentroidDisulfideEnergy , core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergy , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::DisulfMinData , core::scoring::disulfides::FullatomDisulfideEnergy , core::scoring::disulfides::FullatomDisulfideEnergyContainer , core::scoring::disulfides::NCaCaC_Dihedral_Func , core::scoring::disulfides::SG_Dist_Func , core::scoring::disulfides::SGSG_Dihedral_Func , core::scoring::dna::BasePartner , core::scoring::dna::DNAChiEnergy , core::scoring::dna::DNATorsionEnergy , core::scoring::DockingScoreFunction , core::scoring::elec::FA_ElecEnergy , core::scoring::elec::FA_ElecEnergyAroAll , core::scoring::elec::FA_ElecEnergyAroAro , core::scoring::elec::FA_GrpElecEnergy , core::scoring::elec::FAElecContextData , core::scoring::elec::RNA_FA_ElecEnergy , core::scoring::electron_density::ElecDensAllAtomCenEnergy , core::scoring::electron_density::ElecDensCenEnergy , core::scoring::electron_density::ElecDensEnergy , core::scoring::electron_density::FastDensEnergy , core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy , core::scoring::electron_density_atomwise::PoseSequence , core::scoring::Energies , core::scoring::epr_deer::DEERDataCache , core::scoring::etable::AnalyticEtableEnergy , core::scoring::etable::coulomb::Coulomb , core::scoring::etable::TableLookupEtableEnergy , core::scoring::FACTSPoseInfo , core::scoring::FACTSResidueInfo , core::scoring::FACTSRotamerSetInfo , core::scoring::fiber_diffraction::CentroidScatter , core::scoring::fiber_diffraction::FAScatter , core::scoring::fiber_diffraction::FiberDiffractionEnergy , core::scoring::fiber_diffraction::FiberDiffractionEnergyDens , core::scoring::func::AmberPeriodicFunc , core::scoring::func::CharmmPeriodicFunc , core::scoring::func::CircularGeneral1D_Func , core::scoring::func::CircularHarmonicFunc , core::scoring::func::CircularPowerFunc , core::scoring::func::CircularSigmoidalFunc , core::scoring::func::CircularSplineFunc , core::scoring::func::ConstantFunc , core::scoring::func::CountViolFunc , core::scoring::func::EtableFunc , core::scoring::func::FadeFunc , core::scoring::func::FlatHarmonicFunc , core::scoring::func::Func , core::scoring::func::GaussianChainDoubleFunc , core::scoring::func::GaussianChainFunc , core::scoring::func::GaussianChainGeneralFunc , core::scoring::func::GaussianChainQuadrupleFunc , core::scoring::func::GaussianChainSingleFunc , core::scoring::func::GaussianChainTripleFunc , core::scoring::func::GaussianFunc , core::scoring::func::HarmonicFunc , core::scoring::func::IdentityFunc , core::scoring::func::KarplusFunc , core::scoring::func::LinearPenaltyFunction , core::scoring::func::MinMultiHarmonicFunc , core::scoring::func::MixtureFunc , core::scoring::func::PeriodicFunc , core::scoring::func::ScalarWeightedFunc , core::scoring::func::SigmoidFunc , core::scoring::func::SkipViolFunc , core::scoring::func::SmoothStepFunc , core::scoring::func::SoedingFunc , core::scoring::func::SOGFunc , core::scoring::func::SplineFunc , core::scoring::func::SquareWell2Func , core::scoring::func::SquareWellFunc , core::scoring::func::SumFunc , core::scoring::func::TopOutFunc , core::scoring::func::USOGFunc , core::scoring::GenBondedExclInfo , core::scoring::GenBornPoseInfo , core::scoring::GenBornResidueInfo , core::scoring::GenBornRotamerSetInfo , core::scoring::geometric_solvation::ContextDependentGeometricSolEnergy , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody , core::scoring::hackaro::HackAroEnergy , core::scoring::hbonds::HBondEnergy , core::scoring::hbonds::HBondResidueMinData , core::scoring::hbonds::HBondResPairMinData , core::scoring::hbonds::HBondSet , core::scoring::hbonds::hbtrie::HBondsTrieVsTrieCachedDataContainer , core::scoring::hbonds::NPDHBondEnergy , core::scoring::hbonds::NPDHBondSet , core::scoring::interface_::DDPscore , core::scoring::lkball::LK_BallEnergy , core::scoring::lkball::LKB_ResidueInfo , core::scoring::lkball::LKB_ResiduesInfo , core::scoring::lkball::LKB_ResPairMinData , core::scoring::loop_graph::LoopCloseEnergy , core::scoring::LREnergyContainer , core::scoring::magnesium::MgEnergy , core::scoring::magnesium::RNA_MgPointEnergy , core::scoring::membrane::FaMPEnvEnergy , core::scoring::membrane::FaMPEnvSmoothEnergy , core::scoring::membrane::FaMPSolvEnergy , core::scoring::membrane::MPCbetaEnergy , core::scoring::membrane::MPEnvEnergy , core::scoring::membrane::MPHelicalityEnergy , core::scoring::membrane::MPNonHelixPenalty , core::scoring::membrane::MPPairEnergy , core::scoring::membrane::MPResidueLipophilicityEnergy , core::scoring::membrane::MPSpanAngleEnergy , core::scoring::membrane::MPSpanInsertionEnergy , core::scoring::membrane::MPTerminiPenalty , core::scoring::membrane::MPTMProjPenalty , core::scoring::Membrane_FAEmbed , core::scoring::MembraneEmbed , core::scoring::MembraneTopology , core::scoring::methods::Abego , core::scoring::methods::ArgCationPiEnergy , core::scoring::methods::AromaticBackboneRestraintEnergy , core::scoring::methods::AspartimidePenaltyEnergy , core::scoring::methods::BranchEnergy , core::scoring::methods::Burial_v2Energy , core::scoring::methods::BurialEnergy , core::scoring::methods::carbohydrates::SugarBackboneEnergy , core::scoring::methods::CartesianBondedEnergy , core::scoring::methods::CenHBEnergy , core::scoring::methods::CenPairEnergy , core::scoring::methods::CenPairMotifDegreeEnergy , core::scoring::methods::CenPairMotifEnergy , core::scoring::methods::CenRotEnvEnergy , core::scoring::methods::CenRotPairEnergy , core::scoring::methods::ChainbreakEnergy , core::scoring::methods::ChemicalShiftAnisotropyEnergy , core::scoring::methods::ContactOrderEnergy , core::scoring::methods::CovalentLabelingEnergy , core::scoring::methods::CovalentLabelingFAEnergy , core::scoring::methods::CustomAtomPairEnergy , core::scoring::methods::D2H_SA_Energy , core::scoring::methods::dfire::DFIRE_Energy , core::scoring::methods::DipolarCouplingEnergy , core::scoring::methods::DirectReadoutEnergy , core::scoring::methods::DistanceChainbreakEnergy , core::scoring::methods::DNA_BaseEnergy , core::scoring::methods::DNA_DihedralEnergy , core::scoring::methods::DNA_EnvPairEnergy , core::scoring::methods::DNA_ReferenceEnergy , core::scoring::methods::EnergyMethod , core::scoring::methods::EnergyMethodOptions , core::scoring::methods::EnvEnergy , core::scoring::methods::EnvSmoothEnergy , core::scoring::methods::Fa_MbenvEnergy , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::methods::FACTSEnergy , core::scoring::methods::FreeDOF_Energy , core::scoring::methods::GaussianOverlapEnergy , core::scoring::methods::GenBornEnergy , core::scoring::methods::GenericBondedEnergy , core::scoring::methods::GoapEnergy , core::scoring::methods::HRF_MSLabelingEnergy , core::scoring::methods::HRFDynamicsEnergy , core::scoring::methods::HybridVDW_Energy , core::scoring::methods::HydroxylTorsionEnergy , core::scoring::methods::IntermolEnergy , core::scoring::methods::LinearBranchEnergy , core::scoring::methods::LinearChainbreakEnergy , core::scoring::methods::LK_hack , core::scoring::methods::LK_PolarNonPolarEnergy , core::scoring::methods::LK_SigmoidalFunc , core::scoring::methods::MembraneCbetaEnergy , core::scoring::methods::MembraneCenPairEnergy , core::scoring::methods::MembraneEnvEnergy , core::scoring::methods::MembraneEnvPenalties , core::scoring::methods::MembraneEnvSmoothEnergy , core::scoring::methods::MembraneLipo , core::scoring::methods::MissingEnergy , core::scoring::methods::MMBondAngleEnergy , core::scoring::methods::MMBondLengthEnergy , core::scoring::methods::MMLJEnergyInter , core::scoring::methods::MMLJEnergyIntra , core::scoring::methods::MMTorsionEnergy , core::scoring::methods::MotifDockEnergy , core::scoring::methods::MultipoleElecEnergy , core::scoring::methods::MultipoleElecResPairMinData , core::scoring::methods::NeighborListData , core::scoring::methods::NMerPSSMEnergy , core::scoring::methods::NMerRefEnergy , core::scoring::methods::NMerSVMEnergy , core::scoring::methods::OmegaTetherEnergy , core::scoring::methods::OtherPoseEnergy , core::scoring::methods::P_AA_Energy , core::scoring::methods::P_AA_pp_Energy , core::scoring::methods::P_AA_ss_Energy , core::scoring::methods::PackStatEnergy , core::scoring::methods::PairEnergy , core::scoring::methods::PBLifetimeCache , core::scoring::methods::PeptideBondEnergy , core::scoring::methods::pHEnergy , core::scoring::methods::PointWaterEnergy , core::scoring::methods::PoissonBoltzmannEnergy , core::scoring::methods::ProClosureEnergy , core::scoring::methods::ProQ_Energy , core::scoring::methods::RamachandranEnergy2B , core::scoring::methods::RamachandranEnergy , core::scoring::methods::RamaPreProEnergy , core::scoring::methods::ReferenceEnergy , core::scoring::methods::ReferenceEnergyNoncanonical , core::scoring::methods::ResidualDipolarCouplingEnergy , core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl , core::scoring::methods::RG_Energy_Fast , core::scoring::methods::RG_LocalEnergy , core::scoring::methods::RG_MinData , core::scoring::methods::RingClosureEnergy , core::scoring::methods::RMS_Energy , core::scoring::methods::SA_Energy , core::scoring::methods::SASAEnergy , core::scoring::methods::SecondaryStructureEnergy , core::scoring::methods::SequenceDependentRefEnergy , core::scoring::methods::SmoothCenPairEnergy , core::scoring::methods::SmoothEnvEnergy , core::scoring::methods::SplitUnfoldedTwoBodyEnergy , core::scoring::methods::SSElementMotifContactEnergy , core::scoring::methods::SuckerEnergy , core::scoring::methods::SymmetricLigandEnergy , core::scoring::methods::UnfoldedStateEnergy , core::scoring::methods::VdWTinkerEnergy , core::scoring::methods::VdWTinkerResPairMinData , core::scoring::methods::WaterAdductHBondEnergy , core::scoring::methods::WaterAdductIntraEnergy , core::scoring::methods::WaterSpecificEnergy , core::scoring::methods::YHHPlanarityEnergy , core::scoring::mhc_epitope_energy::MHCEpitopeConstraint , core::scoring::mhc_epitope_energy::MHCEpitopeEnergy , core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup , core::scoring::mhc_epitope_energy::ScoreCache , core::scoring::MinScoreScoreFunction , core::scoring::MultipoleElecPoseInfo , core::scoring::MultipoleElecResidueInfo , core::scoring::MultipoleElecRotamerSetInfo , core::scoring::MultipoleParameter , core::scoring::NeighborList , core::scoring::netcharge_energy::NetChargeConstraint , core::scoring::netcharge_energy::NetChargeEnergy , core::scoring::netcharge_energy::NetChargeEnergySetup , core::scoring::nmr::pcs::PCSData , core::scoring::nmr::pre::PREData , core::scoring::nmr::rdc::RDCData , core::scoring::nv::NVscore , core::scoring::OneToAllEnergyContainer , core::scoring::orbitals::OrbitalsScore , core::scoring::packing::HolesEnergy , core::scoring::packing::HolesEnergyRes , core::scoring::packing::SurfEnergy , core::scoring::packing::SurfVolEnergy , core::scoring::PolymerBondedEnergyContainer , core::scoring::ResidualDipolarCoupling , core::scoring::ResidualDipolarCoupling_Rohl , core::scoring::ResidueNblistData , core::scoring::ResiduePairNeighborList , core::scoring::rna::chemical_shift::RNA_ChemicalShiftEnergy , core::scoring::rna::data::RNA_ChemicalMappingEnergy , core::scoring::rna::data::RNA_DataBackboneEnergy , core::scoring::rna::RG_Energy_RNA , core::scoring::rna::RNA_BulgeEnergy , core::scoring::rna::RNA_CentroidInfo , core::scoring::rna::RNA_FullAtomStackingEnergy , core::scoring::rna::RNA_FullAtomVDW_BasePhosphate , core::scoring::rna::RNA_JR_SuiteEnergy , core::scoring::rna::RNA_LJ_BaseEnergy , core::scoring::rna::RNA_LowResolutionPotential , core::scoring::rna::RNA_PairwiseLowResolutionEnergy , core::scoring::rna::RNA_PartitionEnergy , core::scoring::rna::RNA_ScoringInfo , core::scoring::rna::RNA_StubCoordinateEnergy , core::scoring::rna::RNA_SugarCloseEnergy , core::scoring::rna::RNA_SuiteEnergy , core::scoring::rna::RNA_TorsionEnergy , core::scoring::rna::RNA_VDW_Energy , core::scoring::rna::RNP_LowResEnergy , core::scoring::rna::RNP_LowResPairDistEnergy , core::scoring::rna::RNP_LowResStackEnergy , core::scoring::rna::StackElecEnergy , core::scoring::rna::TNA_SuiteEnergy , core::scoring::saxs::FastSAXSEnergy , core::scoring::saxs::SAXSEnergy , core::scoring::ScoreFunction , core::scoring::SigmoidWeightedCenList< T > , core::scoring::solid_surface::SurfaceEnergies , core::scoring::SS_Info , core::scoring::SS_Killhairpins_Info , core::scoring::sym_e::symEnergy , core::scoring::symmetry::SymmetricEnergies , core::scoring::TenANeighborGraph , core::scoring::trie::TrieCollection , core::scoring::trie::TrieVsTrieCachedDataContainerBase , core::scoring::TwelveANeighborGraph , core::scoring::util_methods::DumpTrajectoryEnergy , core::scoring::vdwaals::VDW_Energy , core::scoring::VdWTinkerPoseInfo , core::scoring::VdWTinkerResidueInfo , core::scoring::VdWTinkerRotamerSetInfo , 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::CachedResidueSubset , 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::select::util::SelectResiduesByLayer , core::sequence::ChemicalShiftScoringScheme , core::sequence::ChemicalShiftSequence , core::sequence::CompassScoringScheme , core::sequence::CompositeScoringScheme , core::sequence::CompositeSequence , core::sequence::DPScoringScheme , core::sequence::L1ScoringScheme , core::sequence::MatrixScoringScheme , core::sequence::PairScoringScheme , core::sequence::ProfSimScoringScheme , core::sequence::ScoringScheme , core::sequence::Sequence , core::sequence::SequenceAlignment , core::sequence::SequenceProfile , core::sequence::SimpleScoringScheme , 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::SimpleMetricData , 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::FragmentJumpCM , protocols::abinitio::abscript::JumpSampleData , protocols::abinitio::abscript::RigidChunkCM , protocols::abinitio::abscript::StructPerturberCM , protocols::abinitio::ClassicAbinitio , protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::DomainAssembly , protocols::abinitio::FoldConstraints , protocols::abinitio::FragmentSampler , protocols::abinitio::JumpingFoldConstraintsWrapper , protocols::abinitio::KinematicAbinitio , protocols::abinitio::MembraneAbinitio , 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::anchored_design::AnchoredDesignMover , protocols::anchored_design::AnchorMoversData , protocols::antibody::AntibodyCDRGrafter , protocols::antibody::AntibodyDatabaseManager , protocols::antibody::AntibodyInfo , protocols::antibody::AntibodyModelerProtocol , protocols::antibody::AntibodyNumberingConverterMover , protocols::antibody::CDRSetOptions , protocols::antibody::CDRSetOptionsParser , protocols::antibody::clusters::BasicCDRClusterSet , protocols::antibody::clusters::CDRCluster , protocols::antibody::constraints::CDRDihedralConstraintMover , protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover , protocols::antibody::constraints::ParatopeSiteConstraintMover , protocols::antibody::design::AntibodyDesignMover , protocols::antibody::design::AntibodySeqDesignTFCreator , protocols::antibody::design::CDRGraftDesignOptions , protocols::antibody::design::CDRGraftDesignOptionsParser , protocols::antibody::design::CDRSeqDesignOptions , protocols::antibody::design::CDRSeqDesignOptionsParser , protocols::antibody::design::GeneralAntibodyModeler , protocols::antibody::design::NativeAntibodySeq , protocols::antibody::design::ResnumFromStringsWithRangesSelector , protocols::antibody::GraftCDRLoopsProtocol , protocols::antibody::H3PerturbCCD , protocols::antibody::H3RefineCCD , protocols::antibody::LHRepulsiveRamp , protocols::antibody::LHRepulsiveRampLegacy , protocols::antibody::LHSnugFitLegacy , protocols::antibody::residue_selector::AntibodyRegionSelector , protocols::antibody::residue_selector::CDRResidueSelector , protocols::antibody::snugdock::SnugDock , protocols::antibody::snugdock::SnugDockProtocol , 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::antibody_legacy::AntibodyModeler , protocols::backbone_moves::local_backbone_mover::FreePeptide , protocols::backbone_moves::local_backbone_mover::GapCloser , 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::ForceDisulfidesMover , protocols::canonical_sampling::BiasedMonteCarlo , protocols::canonical_sampling::DbTrajectoryRecorder , protocols::canonical_sampling::FixedTemperatureController , protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::MetropolisHastingsMover , protocols::canonical_sampling::ParallelTempering , protocols::canonical_sampling::PDBTrajectoryRecorder , protocols::canonical_sampling::ProgressBarObserver , protocols::canonical_sampling::SidechainMetropolisHastingsMover , protocols::canonical_sampling::SilentTrajectoryRecorder , protocols::canonical_sampling::SimulatedTempering , 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::cluster::AssignToClustersMover , protocols::cluster::ClusterPhilStyle , protocols::cluster::ClusterPhilStyle_Loop , protocols::cluster::ClusterPhilStyle_PoseReporter , protocols::cluster::EnsembleConstraints_Simple , protocols::comparative_modeling::features::ResidueFeature , protocols::comparative_modeling::features::SSFeature , protocols::comparative_modeling::features::TorsionFeature , protocols::comparative_modeling::IgnoreSubsetConstraintSet , protocols::comparative_modeling::LoopRelaxMover , protocols::comparative_modeling::ThreadingMover , protocols::constraint_filters::ConstraintScoreCutoffFilter , protocols::constraint_filters::ConstraintScoreFilter , protocols::constraint_filters::SavePoseConstraintToFileFilter , protocols::constraint_filters::ShowConstraintsFilter , protocols::constraint_generator::AddConstraints , protocols::constraint_generator::AtomPairConstraintGenerator , protocols::constraint_generator::ConstraintGenerator , protocols::constraint_generator::ConstraintsMap , 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::RemoveConstraints , protocols::constraint_generator::ResidueTypeConstraintGenerator , protocols::constraint_generator::TerminiConstraintGenerator , protocols::constraint_movers::AddConstraintsToCurrentConformationMover , protocols::constraint_movers::ClearConstraintsMover , protocols::constraint_movers::ConstraintSetMover , protocols::constraint_movers::CstInfoMover , protocols::constraint_movers::ResidueTypeConstraintMover , protocols::constraints_additional::AmbiguousMultiConstraint , protocols::constraints_additional::BindingSiteConstraint , protocols::constraints_additional::COMCoordinateConstraint , protocols::constraints_additional::MaxSeqSepConstraintSet , protocols::constraints_additional::SequenceCoupling1BDConstraint , protocols::constraints_additional::SequenceCouplingConstraint , 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::cyclic_peptide_predict::HierarchicalHybridJD_JobResultsSummary , protocols::cyclic_peptide_predict::HierarchicalHybridJD_PNearToArbitraryStateSummary , protocols::cyclic_peptide_predict::HierarchicalHybridJD_ResultsSummaryBase , protocols::cyclic_peptide_predict::HierarchicalHybridJD_RMSDToBestSummary , protocols::cyclic_peptide_predict::HierarchicalHybridJD_SASASummary , protocols::cyclic_peptide_predict::PNearCalculator , 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::calculators::CavityCalculator , protocols::denovo_design::components::CompoundPerturber , protocols::denovo_design::components::ConnectionPerturber , protocols::denovo_design::components::DivideAndConqueror , protocols::denovo_design::components::HelixPairing , protocols::denovo_design::components::HelixPerturber , protocols::denovo_design::components::HelixSheetPairing , protocols::denovo_design::components::IdealAbegoGenerator , protocols::denovo_design::components::NullPerturber , 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::components::StructureDataObserver , protocols::denovo_design::components::StructureDataPerturber , protocols::denovo_design::connection::ConnectionArchitect , protocols::denovo_design::constraints::FileConstraintGenerator , 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::SetPoseSecstructFromStructureDataMover , protocols::denovo_design::movers::SetResidueAliasMover , protocols::denovo_design::residue_selectors::NamedSegmentSelector , protocols::denovo_design::residue_selectors::PairedSheetResidueSelector , protocols::denovo_design::task_operations::ConsensusLoopDesignOperation , protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::dna::DesignProteinBackboneAroundDNA , protocols::dna::DnaChains , protocols::dna::DnaInterfaceFinder , protocols::dna::DnaInterfaceMinMover , protocols::dna::DnaInterfaceMultiStateDesign , protocols::dna::DnaInterfacePacker , protocols::dna::RestrictDesignToProteinDNAInterface , protocols::dna::SeparateDnaFromNonDna , protocols::dna::WatsonCrickRotamerCouplings , protocols::dna_dock::DNAClashCheckFilter , protocols::dna_dock::PropagateClashCheckFilter , protocols::docking::DockingHighResFilter , protocols::docking::DockingHighResLegacy , protocols::docking::DockingInitialPerturbation , protocols::docking::DockingLowRes , protocols::docking::DockingLowResEnsemble , protocols::docking::DockingLowResFilter , protocols::docking::DockingProtocol , protocols::docking::DockingSlideIntoContact , protocols::docking::DockMCMCycle , protocols::docking::DockMCMProtocol , protocols::docking::DockSetupMover , protocols::docking::EllipsoidalRandomizationMover , 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::energy_based_clustering::EnergyBasedClusteringOptions , protocols::energy_based_clustering::EnergyBasedClusteringProtocol , protocols::environment::AutoCutData , protocols::environment::claims::CutBiasClaim , protocols::environment::claims::EnvClaim , protocols::environment::claims::EnvLabelSelector , protocols::environment::claims::JumpClaim , protocols::environment::claims::TorsionClaim , protocols::environment::claims::VirtResClaim , protocols::environment::claims::XYZClaim , protocols::environment::CoMTrackerCM , protocols::environment::EnvMover , protocols::environment::ProtectedConformation , protocols::environment::ScriptCM , protocols::enzdes::AddLigandMotifRotamers , protocols::enzdes::AddOrRemoveMatchCsts , protocols::enzdes::AddRigidBodyLigandConfs , protocols::enzdes::BackboneSampler , protocols::enzdes::DetectProteinLigandInterface , 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::ProteinLigandInterfaceUpweighter , protocols::enzdes::RemoveLigandFilter , protocols::enzdes::RepackWithoutLigandFilter , protocols::enzdes::ResidueConformerFilter , protocols::enzdes::SetCatalyticResPackBehavior , protocols::enzdes::UpdateEnzdesHeaderMover , protocols::enzymatic_movers::DNAMethyltransferaseMover , protocols::enzymatic_movers::EnzymaticMover , protocols::enzymatic_movers::GlycosyltransferaseMover , protocols::enzymatic_movers::KinaseMover , protocols::enzymatic_movers::NTerminalAcetyltransferaseMover , protocols::evolution::AASynthesisFitnessCost , protocols::evolution::AlignmentAAFinder , protocols::evolution::AlignmentGapInserter , protocols::evolution::EvolutionaryDynamicsMover , protocols::evolution::NucleotideMutation , protocols::farnesyl::InstallFarnesylMover , protocols::farnesyl::SampleFarnesylMover , protocols::features::InterfaceDdGMover , protocols::features::ReportToDB , protocols::features::TrajectoryReportToDB , 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::MatchResiduesMover , protocols::fldsgn::NcontactsCalculator , protocols::fldsgn::potentials::AACompositionEnergy , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy , protocols::fldsgn::SheetConstraintGenerator , protocols::fldsgn::SheetRemodelConstraintGenerator , protocols::fldsgn::topology::HelixPairing , protocols::fldsgn::topology::HelixPairingSet , protocols::fldsgn::topology::Sheet , protocols::fldsgn::topology::SS_Info2 , protocols::fldsgn::topology::StrandPairing , protocols::fldsgn::topology::StrandPairingSet , protocols::flexpep_docking::FlexPepDockingFlags , protocols::flexpep_docking::FlexPepDockingProtocol , protocols::flxbb::CombinedTaskOperation , protocols::flxbb::FilterStructs , protocols::flxbb::FilterStructs_Packstat , protocols::flxbb::FilterStructs_TotalCharge , protocols::flxbb::FlxbbDesign , protocols::flxbb::InterlockAroma , protocols::flxbb::LayerDesignOperation , protocols::fold_from_loops::constraint_generator::AutomaticSheetConstraintGenerator , protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator , 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::build::Bridge , protocols::forge::build::BuildInstruction , protocols::forge::build::BuildManager , protocols::forge::build::ConnectRight , protocols::forge::build::CountFromLeft , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::forge::build::RelativeConnectRight , protocols::forge::build::RelativeSequencePosition , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap , protocols::forge::components::BDR , protocols::forge::components::VarLengthBuild , protocols::forge::constraints::InverseRotamersRCG , protocols::forge::constraints::InvrotTreeRCG , protocols::forge::constraints::NtoCConstraintGenerator , protocols::forge::constraints::RemoveRemodelCsts , protocols::forge::remodel::GenericRemodelConstraintGenerator , protocols::forge::remodel::RemodelAccumulator , protocols::forge::remodel::RemodelDesignMover , protocols::forge::remodel::RemodelGlobalFrame , protocols::forge::remodel::RemodelLigandHandler , protocols::forge::remodel::RemodelLoopMover , protocols::forge::remodel::RemodelMover , protocols::forge::remodel::RemodelRotamerLinks , protocols::forge::remodel::ResidueVicinityRCG , protocols::frag_picker::FragmentScoreFilter , protocols::frag_picker::nonlocal::NonlocalFrags , protocols::frag_picker::scores::FragmentScoreMap , protocols::frags::TorsionFragment , protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter , protocols::generalized_kinematic_closure::GeneralizedKIC , protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber , protocols::generalized_kinematic_closure::selector::GeneralizedKICselector , protocols::genetic_algorithm::Entity , protocols::genetic_algorithm::EntityElement , 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::hbnet::ConstrainHBondNetwork , protocols::hbnet::HBNet , protocols::hbnet::HBNetScore , protocols::hbnet::HBNetStapleInterface , protocols::hbnet::UnsatSelector , protocols::helical_bundle::BackboneGridSampler , protocols::helical_bundle::BackboneGridSamplerHelper , protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::BundleGridSamplerHelper , protocols::helical_bundle::BundleParametrizationCalculator , protocols::helical_bundle::BundleReporterFilter , protocols::helical_bundle::FitSimpleHelix , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters , protocols::helical_bundle::parameters::BundleParametersSet , protocols::helical_bundle::parameters::OmegaBundleParameter , protocols::helical_bundle::PerturbBundle , protocols::helical_bundle::PerturbBundleHelix , protocols::helical_bundle_predict::HBP_FinalFullatomRefinementMoveGenerator , protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator , protocols::helical_bundle_predict::HBP_MoveGenerator , protocols::helical_bundle_predict::HBP_SigmoidalTemperatureScheduleGenerator , protocols::helical_bundle_predict::HBP_TemperatureScheduleGenerator , protocols::helical_bundle_predict::HBPHelix , protocols::helical_bundle_predict::HBPHelixAssignments , protocols::helical_bundle_predict::HBPHelixParameters , protocols::helical_bundle_predict::HelicalBundlePredictApplication , protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions , protocols::hotspot_hashing::AddSearchPatternRotSetOp , protocols::hotspot_hashing::movers::PlaceSurfaceProbe , protocols::hotspot_hashing::SearchPatternRotSetOp , protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionSampler , protocols::hybridization::CartesianHybridize , protocols::hybridization::CartesianSampler , protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol , protocols::hybridization::MRMover , protocols::hybridization::TemplateHistory , protocols::hydrate::Hydrate , protocols::idealize::IdealizeMover , protocols::indexed_structure_store::filters::FragmentLookupFilter , protocols::indexed_structure_store::movers::DirectSegmentLookupMover , protocols::indexed_structure_store::movers::SegmentSequenceProfileMover , protocols::jd2::InnerJob , protocols::jd2::Job , protocols::jd3::JobTracker , protocols::jumping::ChainbreakDistFunc , protocols::legacy_sewing::Assembly , protocols::legacy_sewing::ContinuousAssembly , protocols::legacy_sewing::DisembodiedAssembly , protocols::legacy_sewing::LegacyAddStartnodeFragments , protocols::legacy_sewing::LegacyAppendAssemblyMover , protocols::legacy_sewing::LegacyAssemblyConstraintsMover , protocols::legacy_sewing::LegacyEnumerateAssemblyMover , protocols::legacy_sewing::LegacyGivenPathAssemblyMover , protocols::legacy_sewing::LegacyGreedyAssemblyMover , protocols::legacy_sewing::LegacyMonteCarloAssemblyMover , protocols::legacy_sewing::LegacyReadNativeRotamersFile , protocols::legacy_sewing::LegacyReadRepeatNativeRotamersFile , protocols::legacy_sewing::LegacyRepeatAssemblyMover , 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::InterfaceScoreCalculator , protocols::ligand_docking::LigandDesign , protocols::ligand_docking::MinimizeBackbone , protocols::ligand_docking::MolarMassFilter , protocols::ligand_docking::MolecularMassFilter , protocols::ligand_docking::ProtLigEnsemble , protocols::ligand_docking::RandomConformers , 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_build::LoopMover_SlidingWindow , protocols::loop_grower::FragmentExtension , protocols::loop_grower::LoopGrower , protocols::loop_modeler::LoopModeler , protocols::loophash::FastGapMover , protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashLibrary , protocols::loophash::LoopHashMoverWrapper , protocols::loophash::LoopHashRelaxProtocol , protocols::loophash::Mover_LoopHashRefine , protocols::loophash::WorkUnit_LoopHash , protocols::LoopRebuild , protocols::loops::filters::LoopAnalyzerFilter , protocols::loops::FoldTreeFromLoops , protocols::loops::loop_closure::ccd::CCDLoopClosureMover , protocols::loops::loop_closure::ccd::RamaCheck1B , protocols::loops::loop_closure::ccd::RamaCheck2B , protocols::loops::loop_closure::ccd::RamaCheckBase , protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover , protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD , protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC , protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD , protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves , protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub , protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::loops::loop_mover::refine::LoopMover_Refine_KIC , protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer , protocols::loops::loop_mover::refine::RepackTrial , protocols::loops::loop_mover::refine::ShearMinCCDTrial , protocols::loops::loop_mover::refine::SmallMinCCDTrial , protocols::loops::Loops , 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::mainchain_potential::GenerateMainchainPotential , protocols::mainchain_potential::GenerateMainchainPotentialOptions , protocols::match::downstream::ClassicMatchAlgorithm , protocols::match::downstream::DownstreamAlgorithm , protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder , protocols::match::downstream::SecondaryMatcherToDownstreamResidue , protocols::match::downstream::SecondaryMatcherToUpstreamResidue , protocols::match::MatcherMover , protocols::match::output::WriteUpstreamCoordinateKinemage , protocols::match::upstream::ProteinUpstreamBuilder , protocols::match::upstream::UpstreamBuilder , protocols::matdes::BuildingBlockInterfaceOperation , protocols::matdes::ClashCheckFilter , protocols::matdes::ExtractSubposeMover , protocols::matdes::GetRBDOFValues , protocols::matdes::InterfacePackingFilter , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator , protocols::matdes::MotifHitsRotamersOperation , protocols::matdes::OligomericAverageDegreeFilter , protocols::matdes::SchemePlaceMotifsMover , protocols::matdes::SymDofMover , protocols::matdes::SymUnsatHbondFilter , protocols::md::CartesianMD , protocols::mean_field::EnergiesByTaskCalculator , protocols::mean_field::GenMeanFieldMover , protocols::medal::MedalExchangeMover , protocols::medal::MedalMover , 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::scoring::FaWaterToBilayerEnergy , protocols::membrane::scoring::MEnvAtomParams , 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::VisualizeEmbeddingMover , protocols::membrane::visualize::VisualizeMembraneMover , protocols::membrane_benchmark::MembraneEnergyLandscapeSampler , protocols::membrane_benchmark::PeptideOrientationMover , protocols::minimization_packing::BoltzmannRotamerMover , protocols::minimization_packing::ChainGroupDiscriminator , protocols::minimization_packing::DisulfideOptimizationMover , protocols::minimization_packing::GroupDiscriminator , protocols::minimization_packing::MinMover , protocols::minimization_packing::MinPackMover , protocols::minimization_packing::PackRotamersMover , protocols::minimization_packing::PertMinMover , protocols::minimization_packing::RepackSidechainsMover , protocols::minimization_packing::RotamerTrialsMinMover , protocols::minimization_packing::RotamerTrialsMover , protocols::minimization_packing::SaneMinMover , protocols::minimization_packing::symmetry::SymMinMover , protocols::minimization_packing::symmetry::SymPackRotamersMover , protocols::minimization_packing::symmetry::TaskAwareSymMinMover , protocols::minimization_packing::TaskAwareMinMover , protocols::minimization_packing::UserDefinedGroupDiscriminator , protocols::monte_carlo::GenericMonteCarloMover , protocols::monte_carlo::GenericSimulatedAnnealer , protocols::monte_carlo::MonteCarloInterface , protocols::monte_carlo::MonteCarloRecover , protocols::monte_carlo::MonteCarloReset , protocols::monte_carlo::MonteCarloTest , protocols::monte_carlo::ResetBaselineMover , protocols::motif_grafting::movers::MotifGraftMover , protocols::motifs::BuildPosition , protocols::motifs::Motif , protocols::motifs::MotifDnaPacker , protocols::motifs::MotifHit , protocols::moves::CycleMover , protocols::moves::CyclicMover , protocols::moves::DsspMover , protocols::moves::FilterReportAsPoseExtraScoresMover , protocols::moves::FilterReporterMover , protocols::moves::IfMover , protocols::moves::IteratedConvergenceMover , protocols::moves::MonteCarlo , protocols::moves::MonteCarloUtil , protocols::moves::Mover , protocols::moves::NullMover , protocols::moves::PyMOLMover , protocols::moves::PyMOLObserver , protocols::moves::RampingMover , protocols::moves::RandomMover , protocols::moves::RepeatMover , protocols::moves::SequenceMover , protocols::moves::StructureRestrictor , protocols::moves::SwitchMover , protocols::moves::TrialMover , protocols::mpi_refinement::WorkUnit_bbGauss , protocols::mpi_refinement::WorkUnit_CombinePose , protocols::mpi_refinement::WorkUnit_FragInsert , protocols::mpi_refinement::WorkUnit_KicCloser , protocols::mpi_refinement::WorkUnit_LoopHash , protocols::mpi_refinement::WorkUnit_MD , protocols::mpi_refinement::WorkUnit_NormalMode , protocols::mpi_refinement::WorkUnit_PartialAbinitio , protocols::mpi_refinement::WorkUnit_RamaPerturber , protocols::mpi_refinement::WorkUnit_Relax , protocols::multistate_design::MultiStateEntity , protocols::multistate_design::PosType , protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopCreatorMover , protocols::ncbb::oop::OopDockDesignProtocol , protocols::ncbb::ResidueReplacementRebuildMover , protocols::ncbb::SecStructFinder , protocols::ncbb::SecStructMinimizeMover , protocols::network::UIObserver , protocols::nmr::ParaNMRScoreMover , protocols::nmr::pcs::PCSEnergy , protocols::nmr::pcs::PCSLigandTransformMover , protocols::nmr::pre::PREEnergy , protocols::nmr::pre::PREMover , protocols::nmr::rdc::RDCEnergy , protocols::noesy_assign::FloatingResonance , protocols::noesy_assign::LabelResonance , protocols::noesy_assign::ProtonResonance , protocols::noesy_assign::Resonance , protocols::nonlocal::HelixRotate , protocols::nonlocal::SheetTranslate , protocols::nonlocal::SingleFragmentMover , protocols::normalmode::NormalModeMinimizer , protocols::normalmode::NormalModeRelaxMover , protocols::optimize_weights::ScaleAnnealerTemperatureOperation , protocols::pack_interface::ProteinProteinInterfaceUpweighter , protocols::pb_potential::SetupPoissonBoltzmannPotential , protocols::pdbinfo_manipulations::AlignPDBInfoToSequences , protocols::peptide_deriver::PeptideDeriverBasicStreamOutputter , protocols::peptide_deriver::PeptideDeriverFilter , protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter , protocols::peptide_deriver::PeptideDeriverOutputterContainer , protocols::peptide_deriver::PeptideDeriverPoseOutputter , protocols::pockets::PocketConstraint , 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::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::ResidueDecompositionByChainCalculator , 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::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::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::GridSet , 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::FragInsertAndAlignMover , protocols::rbsegment_relax::GaussianRBSegmentMover , protocols::rbsegment_relax::HelicalGaussianMover , protocols::rbsegment_relax::IdealizeHelicesMover , protocols::rbsegment_relax::MakeStarTopologyMover , protocols::rbsegment_relax::OptimizeThreadingMover , protocols::rbsegment_relax::SequenceShiftMover , protocols::rbsegment_relax::StrandTwistingMover , 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::CentroidRelax , protocols::relax::ClassicRelax , protocols::relax::FastRelax , protocols::relax::LocalRelax , protocols::relax::membrane::MPFastRelaxMover , protocols::relax::membrane::MPRangeRelaxMover , protocols::relax::MiniRelax , protocols::relax::RelaxScriptFileContents , protocols::relax::RepeatProteinRelax , protocols::relax::WorkUnit_BatchRelax , protocols::relax::WorkUnit_BatchRelax_and_PostRescore , 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::AlignmentEnergy , protocols::rna::denovo::coarse::CoarseRNA_LoopCloser , protocols::rna::denovo::coarse::MultipleDomainMover , protocols::rna::denovo::movers::RNA_DeNovoProtocolMover , protocols::rna::denovo::movers::RNA_FragmentMover , protocols::rna::denovo::movers::RNA_Minimizer , protocols::rna::denovo::RNA_DeNovoProtocol , protocols::rna::movers::ERRASER2Protocol , protocols::rna::movers::RNA_LoopCloser , 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::SavePoseMover , protocols::rotamer_recovery::RotamerRecoveryMover , protocols::score_filters::GeometryFilter , protocols::score_filters::ScoreCutoffFilter , protocols::score_filters::ScoreTypeFilter , protocols::scoring::InterfaceInfo , protocols::scoring::methods::EnsembleEnergy , protocols::scoring::methods::InterchainEnvEnergy , protocols::scoring::methods::InterchainPairEnergy , protocols::scoring::methods::pcs2::PcsDataCenterManager , protocols::scoring::methods::pcs2::PcsEnergy , protocols::scoring::methods::pcs::PCS_data , protocols::scoring::methods::pcs::PCS_Energy , protocols::scoring::methods::pcsTs1::PCS_data_Ts1 , protocols::scoring::methods::pcsTs1::PCS_Energy_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_Ts2 , protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_Ts3 , protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_Ts4 , protocols::scoring::methods::pcsTs4::PCS_Energy_Ts4 , protocols::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments , protocols::scoring::methods::saxs::PDDFEnergy , protocols::scoring::methods::SpecialRotamerEnergy , protocols::scoring::methods::TargetClashEnergy , protocols::scoring::ResidualDipolarCouplingRigidSegments , protocols::scoring::VDW_CachedRepScreenInfo , protocols::scoring::VDW_GridEnergy , 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::data_storage::Basis , protocols::sewing::data_storage::HashedSmartAssembly , protocols::sewing::data_storage::LigandResidue , protocols::sewing::data_storage::LigandSegment , protocols::sewing::data_storage::SmartAssembly , protocols::sewing::data_storage::SmartSegment , protocols::sewing::data_storage::SmartSewingResidue , protocols::sewing::hashing::AlignmentFileGeneratorMover , protocols::sewing::hashing::AlignmentGenerator , protocols::sewing::hashing::BasisMapGenerator , protocols::sewing::hashing::EdgeMapGenerator , protocols::sewing::hashing::Hasher , protocols::sewing::hashing::ModelFileReader , protocols::sewing::movers::AppendAssemblyMover , protocols::sewing::movers::AssemblyMover , protocols::sewing::movers::LigandBindingAssemblyMover , protocols::sewing::requirements::ClashRequirement , protocols::sewing::requirements::DsspSpecificLengthRequirement , protocols::sewing::requirements::KeepLigandContactsRequirement , protocols::sewing::requirements::LengthInResiduesRequirement , protocols::sewing::requirements::LigandClashRequirement , protocols::sewing::requirements::NonTerminalStartingSegmentRequirement , protocols::sewing::requirements::SizeInSegmentsRequirement , 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::AbinitioBaseFilter , 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::COFilter , 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::LongestContinuousApolarSegmentFilter , 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::PackerNeighborGraphFilter , protocols::simple_filters::PackStatFilter , protocols::simple_filters::PDDFScoreFilter , 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::RGFilter , protocols::simple_filters::SaveResfileToDiskFilter , protocols::simple_filters::SAXSScoreFilter , protocols::simple_filters::SecretionPredictionFilter , protocols::simple_filters::SequenceDistance , protocols::simple_filters::ShapeComplementarityFilter , protocols::simple_filters::SheetFilter , 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::bb_sampler::BBDihedralSampler2D , protocols::simple_moves::bb_sampler::BBDihedralSampler3D , protocols::simple_moves::bb_sampler::BBDihedralSampler , protocols::simple_moves::bb_sampler::BBDihedralSamplerBase , protocols::simple_moves::bb_sampler::BBDihedralSamplerND , protocols::simple_moves::bb_sampler::SmallBBSampler , protocols::simple_moves::bb_sampler::SugarBBSampler , protocols::simple_moves::BBDihedralSamplerMover , protocols::simple_moves::BBG8T3AMover , protocols::simple_moves::BBGaussianMover , protocols::simple_moves::bin_transitions::InitializeByBins , protocols::simple_moves::bin_transitions::PerturbByBins , protocols::simple_moves::ChainSplitMover , protocols::simple_moves::ChangeAndResetFoldTreeMover , protocols::simple_moves::ClassicFragmentMover , protocols::simple_moves::ConcatenatePosesMover , protocols::simple_moves::ConstrainToIdealMover , protocols::simple_moves::ContingentAcceptMover , protocols::simple_moves::ConvertRealToVirtualMover , protocols::simple_moves::ConvertVirtualToRealMover , protocols::simple_moves::CopyRotamerMover , protocols::simple_moves::CoupledMover , 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::MissingDensityToJumpMover , protocols::simple_moves::ModifyVariantTypeMover , protocols::simple_moves::MutateResidue , protocols::simple_moves::PDBReloadMover , protocols::simple_moves::PeptideStapleMover , 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::ReturnSidechainMover , 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::ShearMover , 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::SimpleThreadingMover , protocols::simple_moves::SmallMover , protocols::simple_moves::StorePoseSnapshot , protocols::simple_moves::StructProfileMover , protocols::simple_moves::SuperimposeMover , protocols::simple_moves::SwitchChainOrderMover , protocols::simple_moves::SwitchResidueTypeSetMover , protocols::simple_moves::TorsionSetMover , protocols::simple_moves::Tumble , protocols::simple_moves::VirtualRootMover , protocols::simple_moves::WriteFiltersToPose , protocols::simple_moves::WriteSSEMover , protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator , protocols::simple_pose_metric_calculators::NumberHBondsCalculator , protocols::simple_task_operations::DockingNoRepack1 , protocols::simple_task_operations::DockingNoRepack2 , protocols::simple_task_operations::RestrictToInterface , protocols::simple_task_operations::RestrictToLoops , protocols::simple_task_operations::RestrictToLoopsAndNeighbors , protocols::splice::AlignEndsMover , protocols::splice::DesignInterfacesOperation , protocols::splice::FindEndpointsOperation , protocols::splice::RBInMover , protocols::splice::RBOutMover , protocols::splice::RotLibOut , protocols::splice::SampleRotamersFromPDB , protocols::splice::SampleRotamersFromPDB_RotamerSetOperation , protocols::splice::Splice , protocols::splice::SpliceIn , protocols::splice::SpliceInAntibody , protocols::splice::SpliceInTail , protocols::splice::SpliceOut , protocols::splice::SpliceOutAntibody , protocols::splice::SpliceOutTail , protocols::star::StarAbinitio , protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser , protocols::stepwise::modeler::options::StepWiseBasicModelerOptions , protocols::stepwise::modeler::options::StepWiseModelerOptions , protocols::stepwise::modeler::options::StepWiseProteinModelerOptions , protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler , 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::mover::StepWiseMasterMover , protocols::stepwise::monte_carlo::mover::StepWiseMove , protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions , protocols::stepwise::options::StepWiseBasicOptions , protocols::struct_fragment::StructFragmentMover , protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::FullatomRelaxMover , protocols::surface_docking::SurfaceDockingProtocol , protocols::surface_docking::SurfaceParameters , protocols::switches::GraftSwitchMover , protocols::symmetric_docking::membrane::MPSymDockMover , protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockingLowRes , protocols::symmetric_docking::SymDockProtocol , protocols::symmetric_docking::SymRestrictTaskForDocking , protocols::symmetry::DetectSymmetry , protocols::symmetry::ExtractAsymmetricPoseMover , protocols::symmetry::ExtractAsymmetricUnitMover , protocols::symmetry::NCSResMapping , protocols::symmetry::SetupForSequenceSymmetryMover , protocols::symmetry::SetupForSymmetryMover , protocols::symmetry::SetupNCSMover , 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::LimitAromaChi2_RotamerSetOperation , protocols::task_operations::LimitAromaChi2Operation , protocols::task_operations::LinkResidues , protocols::task_operations::ModifyAnnealer , protocols::task_operations::MutationSetDesignOperation , protocols::task_operations::pHVariantTaskOperation , protocols::task_operations::PreventChainFromRepackingOperation , protocols::task_operations::PreventResiduesFromRepackingOperation , protocols::task_operations::ProteinCore , protocols::task_operations::ProteinInterfaceDesignOperation , protocols::task_operations::PruneBuriedUnsats_RotamerSetsOperation , protocols::task_operations::PruneBuriedUnsatsOperation , protocols::task_operations::ReadResfileFromDB , protocols::task_operations::ResfileCommandOperation , protocols::task_operations::ResidueProbDesignOperation , protocols::task_operations::RestrictByCalculatorsOperation , protocols::task_operations::RestrictChainToRepackingOperation , protocols::task_operations::RestrictConservedLowDdgOperation , protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation , protocols::task_operations::RestrictIdentitiesOperation , protocols::task_operations::RestrictInterGroupVectorOperation , protocols::task_operations::RestrictNativeResiduesOperation , protocols::task_operations::RestrictNonSurfaceToRepackingOperation , protocols::task_operations::RestrictOperationsBase , protocols::task_operations::RestrictResiduesToRepackingOperation , protocols::task_operations::RestrictToAlignedSegmentsOperation , protocols::task_operations::RestrictToCDRH3Loop , protocols::task_operations::RestrictToInterfaceOperation , protocols::task_operations::RestrictToInterfaceVectorOperation , protocols::task_operations::RestrictToMoveMapChiOperation , protocols::task_operations::RestrictToNeighborhoodOperation , 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::STMStoredTask , protocols::task_operations::StoreCombinedStoredTasksMover , protocols::task_operations::StoreCompoundTaskMover , protocols::task_operations::StoreTaskMover , protocols::task_operations::ThreadSequenceOperation , protocols::tcr::TCRmodel , protocols::testing::BenchmarkBuildRotamersMover , protocols::toolbox::DummyClass , protocols::toolbox::EnergyLandscapeEvaluator , protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver , protocols::toolbox::match_enzdes_util::InvrotCollector , protocols::toolbox::MulliganPNearEvaluator , protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers , protocols::toolbox::rotamer_set_operations::RigidBodyMoveRSO , protocols::toolbox::rotamer_set_operations::SpecialRotamerRSO , protocols::toolbox::RotamerBoltzmannWeightEvaluator , protocols::toolbox::SF_Replica , protocols::topology_broker::AsymFoldandDockClaimer , protocols::topology_broker::BasicJumpClaimer , protocols::topology_broker::claims::BBClaim , protocols::topology_broker::claims::CutClaim , protocols::topology_broker::claims::DofClaim , protocols::topology_broker::claims::JumpClaim , protocols::topology_broker::claims::LegacyRootClaim , protocols::topology_broker::claims::SequenceClaim , protocols::topology_broker::claims::SymmetryClaim , protocols::topology_broker::ConstraintClaimer , protocols::topology_broker::CoordConstraintClaimer , protocols::topology_broker::CutBiasClaimer , protocols::topology_broker::DensityScoringClaimer , protocols::topology_broker::DisulfJumpClaimer , protocols::topology_broker::FibrilModelingClaimer , protocols::topology_broker::FoldandDockClaimer , protocols::topology_broker::FragmentClaimer , protocols::topology_broker::FragmentJumpClaimer , protocols::topology_broker::MembraneTopologyClaimer , protocols::topology_broker::MetalloClaimer , protocols::topology_broker::PcsEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4 , protocols::topology_broker::RigidChunkClaimer , protocols::topology_broker::SequenceClaimer , protocols::topology_broker::StartStructClaimer , protocols::topology_broker::SymmetryClaimer , protocols::topology_broker::TemplateFragmentClaimer , protocols::topology_broker::TemplateJumpClaimer , protocols::topology_broker::TMHTopologySamplerClaimer , protocols::topology_broker::TopologyClaimer , protocols::ub_e2c::ubi_e2c_modeler , protocols::vardist_solaccess::LoadVarSolDistSasaCalculatorMover , protocols::vardist_solaccess::VarSolDistSasaCalculator , protocols::wum::DatabaseEntryWorkUnit , protocols::wum::WorkUnit_MoverWrapper , protocols::wum::WorkUnit_SilentStructStore , protocols::wum::WorkUnit_Wait , protocols::wum::WorkUnitBase
• clone_as_base_class() : core::scoring::ScoreFunction
• clone_atom_types_from_commandline() : core::chemical::AtomTypeSet
• clone_cache_data() : core::fragment::Frame
• clone_calculators() : core::pose::metrics::PoseMetricContainer
• clone_flipping_chirality() : core::conformation::Residue
• clone_info() : core::pose::full_model_info::FullModelInfo
• clone_modeler() : protocols::stepwise::modeler::StepWiseModeler
• clone_sampler() : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• clone_scorefxn() : protocols::rna::denovo::movers::RNA_Minimizer
• clone_shifted() : core::fragment::FragSet
• clone_with_frags() : core::fragment::Frame
• clone_with_new_sequence_numbering() : core::conformation::PseudoBondCollection
• clone_with_template() : core::fragment::Frame
• cloned_member_constraints() : core::scoring::constraints::MultiConstraint
• Clones : core::conformation::symmetry::SymmetryInfo
• closable() : protocols::stepwise::sampler::rna::RNA_KIC_Sampler
• close() : protocols::dna::DnaNeighbor , protocols::jd2::SingleFileBuffer
• close_ : protocols::dna::DnaNeighbor
• close_all_loops() : protocols::rna::denovo::coarse::MultipleDomainMover
• close_at_all_cutpoints() : protocols::rna::denovo::coarse::CoarseRNA_LoopCloser
• close_at_cutpoint() : protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser
• close_bond() : protocols::generalized_kinematic_closure::GeneralizedKIC
• close_chain_ : protocols::stepwise::screener::PartitionContactScreener
• close_chainbreaks() : protocols::stepwise::modeler::StepWiseMinimizer
• close_channel() : protocols::jd2::MpiFileBuffer
• close_chbrk_ : protocols::abinitio::ClassicAbinitio
• close_contact_threshold_ : core::select::residue_selector::CloseContactResidueSelector
• close_file() : protocols::jd2::MpiFileBuffer
• close_gaps() : protocols::loophash::LoopHashSampler
• close_loop() : protocols::pose_length_moves::NearNativeLoopCloser
• close_loop_in_single_direction() : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• close_loops() : core::import_pose::options::RNA_FragmentMonteCarloOptions , protocols::abinitio::AbrelaxApplication , protocols::rna::denovo::movers::RNA_DeNovoMasterMover
• close_loops_ : core::import_pose::options::RNA_FragmentMonteCarloOptions , protocols::rna::denovo::movers::RNA_DeNovoMasterMover , protocols::rna::denovo::movers::RNA_Minimizer
• close_loops_after_each_move() : core::import_pose::options::RNA_FragmentMonteCarloOptions
• close_loops_after_each_move_ : core::import_pose::options::RNA_FragmentMonteCarloOptions
• close_one_loop_stem() : protocols::antibody_legacy::CloseOneMover
• close_one_loop_stem_helper() : protocols::antibody_legacy::CloseOneMover
• close_the_loop() : protocols::rna::denovo::coarse::CoarseRNA_LoopCloser
• close_threshold_ : protocols::dna::DnaInterfaceFinder , protocols::dna::RestrictDesignToProteinDNAInterface
• close_with_idealization() : protocols::abinitio::AbrelaxMover
• CloseContactResidueSelector() : core::select::residue_selector::CloseContactResidueSelector
• closed_loop() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer
• closed_loop_ : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer
• CloseFold() : protocols::seeded_abinitio::CloseFold
• CloseOneCDRLoop() : protocols::antibody::CloseOneCDRLoop
• CloseOneMover() : protocols::antibody_legacy::CloseOneMover
• closer_ft : protocols::environment::EnvClaimBroker::BrokerResult
• CloserToAtom() : core::scoring::sc::CloserToAtom
• closest_binder() : protocols::fold_from_loops::utils::Nub
• closest_by_dist4() : core::pose::rna::RNA_SuiteName
• closest_interface_residue() : protocols::scoring::Interface , protocols::scoring::InterfaceInfo
• closest_non_overlap_residue() : protocols::pose_creation::MergePDBatOverlapMover , protocols::pose_creation::MergePDBMover
• closest_orient_atoms_msd() : protocols::enzdes::ModifyStoredRBConfs
• closest_rsd_ : protocols::membrane::AddMPLigandMover
• closest_state_on_alt_bb() : protocols::flexpack::interaction_graph::FlexbbNode
• closest_state_on_alt_bb_ : protocols::flexpack::interaction_graph::FlexbbNode
• closest_suite() : core::pose::rna::RNA_SuiteName
• closure() : protocols::simple_moves::BBConRotMover
• closure_cycles_ : protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover
• closure_fragments() : protocols::loops::loop_closure::ccd::LoopClosure , protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• closure_fragments_ : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• closure_frame_ : protocols::loops::loop_closure::ccd::LoopClosure
• closure_protocol() : protocols::abinitio::AbrelaxMover , protocols::abinitio::KinematicAbinitio
• closure_protocol_ : protocols::abinitio::KinematicAbinitio
• closure_success_ : protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover
• closure_type_ : protocols::pose_length_moves::NearNativeLoopCloser
• ClosureProblem() : protocols::kinematic_closure::ClosureProblem , protocols::kinematic_closure::ClosureSolution
• ClosureSolution : protocols::kinematic_closure::ClosureProblem , protocols::kinematic_closure::ClosureSolution
• CloudPDBWriter() : protocols::match::output::CloudPDBWriter
• CLU_RADIUS : protocols::cluster::calibur::Clustering
• clust_cutoff_ : protocols::simple_moves::ExplicitWaterMover
• clust_radius_ : protocols::simple_moves::ExplicitWaterMover
• cluster() : protocols::abinitio::IterativeBase , protocols::antibody::CDRDBPose , protocols::antibody::CDRDBSequence , protocols::antibody::clusters::CDRCluster , protocols::antibody::clusters::ClusterData , protocols::cluster::APCluster , protocols::cluster::calibur::Clustering
• Cluster() : protocols::cluster::Cluster
• cluster() : protocols::comparative_modeling::AlignmentClustering , protocols::hotspot_hashing::HotspotStubSet , protocols::multistage_rosetta_scripts::MRSJobQueen , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::modeler::align::StepWiseClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased , protocols::toolbox::ClusterBase
• Cluster : protocols::toolbox::ClusterBase
• cluster() : protocols::toolbox::KCluster
• cluster_ : core::scoring::packstat::CavityBall , protocols::antibody::clusters::CDRCluster , protocols::forge::remodel::RemodelAccumulator
• cluster_base_ : protocols::cluster::AssignToClustersMover
• cluster_based_CDRDBPose_indexes_ : protocols::antibody::design::AntibodyDesignMover
• cluster_by_ : protocols::energy_based_clustering::EnergyBasedClusteringOptions
• cluster_by_all_atom_ : protocols::cluster::GatherPosesMover
• cluster_by_all_atom_rmsd() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• cluster_by_all_atom_rmsd_ : protocols::stepwise::legacy::screener::SimpleRMSD_Screener , protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased , protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• cluster_by_protein_backbone_ : protocols::cluster::GatherPosesMover
• cluster_center_ : protocols::cluster::Cluster
• cluster_centers_neighbor_list_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• cluster_check() : protocols::loop_grower::LoopPartialSolutionStore
• cluster_conformers_and_set_weights_and_coordinates() : core::scoring::nmr::NMRSpinlabel
• cluster_cyclic_permutations_ : protocols::energy_based_clustering::EnergyBasedClusteringOptions
• cluster_data_ : protocols::antibody::clusters::CDRClusterMatcher
• cluster_data_cutoff_ : protocols::antibody::constraints::CDRDihedralConstraintMover
• cluster_data_for_results_of_stage_ : protocols::multistage_rosetta_scripts::MRSJobQueen
• cluster_fragments() : protocols::loop_grower::FragmentExtension
• cluster_KeyFeatures() : protocols::pockets::GenPharmacophore
• cluster_loop() : protocols::forge::remodel::RemodelAccumulator
• cluster_manager_ : protocols::antibody::CDRSetOptionsParser
• cluster_matcher_ : protocols::antibody::clusters::CDRClusterSet
• Cluster_Member() : protocols::stepwise::legacy::modeler::rna::Cluster_Member
• cluster_metric() : protocols::multistage_rosetta_scripts::MRSJobSummary
• cluster_metric_ : protocols::multistage_rosetta_scripts::MRSJobSummary
• cluster_metric_tag_for_stage_ : protocols::multistage_rosetta_scripts::MRSJobQueen
• cluster_metric_xml_schema_group_name() : protocols::multistage_rosetta_scripts::cluster::ClusterMetricFactory
• cluster_mg() : protocols::magnesium::MgScanner
• cluster_min_volume : core::scoring::packstat::SasaOptions
• cluster_num_ : protocols::make_rot_lib::RotData
• cluster_oversample_ : protocols::electron_density::DockIntoDensityMover
• cluster_pose() : protocols::forge::remodel::RemodelAccumulator
• cluster_pose_list() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection
• cluster_radius : protocols::toolbox::ClusterOptions
• cluster_radius_ : protocols::cluster::ClusterBase , protocols::electron_density::DockIntoDensityMover , protocols::energy_based_clustering::EnergyBasedClusteringOptions , protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased , protocols::toolbox::ClusterPhilStyle
• cluster_rmsd() : protocols::stepwise::modeler::align::StepWiseClusterer , protocols::stepwise::options::StepWiseBasicOptions
• cluster_rmsd_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection , protocols::stepwise::modeler::align::StepWiseClusterer , protocols::stepwise::options::StepWiseBasicOptions
• cluster_rmsds_to_try_with_auto_tune_ : protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• cluster_rotset() : protocols::simple_moves::ExplicitWaterMover
• cluster_sampling_cutoff() : protocols::antibody::CDRSetOptions
• cluster_size_ : protocols::stepwise::modeler::align::StepWiseClusterer
• cluster_switch() : protocols::forge::remodel::RemodelAccumulator
• cluster_switch_ : protocols::forge::remodel::RemodelAccumulator
• cluster_with_auto_tune() : protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• ClusterBase() : protocols::cluster::ClusterBase , protocols::toolbox::ClusterBase
• clustercheck_ : protocols::loop_grower::FragmentExtension , protocols::loop_grower::LoopGrower , protocols::loop_grower::LoopPartialSolutionStore
• clusterCPockets() : protocols::pockets::PocketGrid
• ClusterDisList : protocols::toolbox::KClusterElement
• clustered_best_poses() : protocols::forge::remodel::RemodelAccumulator
• clustered_pose_list() : protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• clustered_top_poses() : protocols::forge::remodel::RemodelAccumulator
• Clusterer() : protocols::mpi_refinement::Clusterer
• clusterer_ : protocols::stepwise::modeler::StepWiseConnectionSampler
• Clustering() : protocols::cluster::calibur::Clustering
• ClusterIterator : protocols::toolbox::ClusterBase
• clusterlist : protocols::cluster::ClusterBase
• ClusterList : protocols::toolbox::ClusterBase
• clusterlist() : protocols::toolbox::ClusterBase
• clusterlist_ : protocols::toolbox::ClusterBase
• ClusterMetric() : protocols::multistage_rosetta_scripts::cluster::ClusterMetric
• ClusterMetricCreator() : protocols::multistage_rosetta_scripts::cluster::ClusterMetricCreator
• ClusterMetricFactory() : protocols::multistage_rosetta_scripts::cluster::ClusterMetricFactory
• ClusterMetricRegistrator() : protocols::multistage_rosetta_scripts::cluster::ClusterMetricRegistrator< T >
• ClusterNdxList : protocols::toolbox::KClusterElement
• ClusterOptions() : protocols::toolbox::ClusterOptions
• ClusterPhilStyle() : protocols::cluster::ClusterPhilStyle , protocols::toolbox::ClusterPhilStyle
• ClusterPhilStyle_Loop() : protocols::cluster::ClusterPhilStyle_Loop
• ClusterPhilStyle_PoseReporter() : protocols::cluster::ClusterPhilStyle_PoseReporter
• ClusterPhilStyleOP : protocols::forge::remodel::RemodelAccumulator
• clusterPockets() : protocols::pockets::PocketGrid
• ClusterPoseSelector() : protocols::pose_selectors::ClusterPoseSelector
• clusters_ : protocols::antibody::clusters::BasicCDRClusterSet , protocols::antibody::clusters::CDRClusterSet , protocols::denovo_design::calculators::CavityCalculator , protocols::pockets::CClusterSet , protocols::pockets::PClusterSet , protocols::pockets::PocketGrid
• ClusterTypList : protocols::toolbox::KClusterElement
• CM_SuggestFixResidue() : protocols::topology_broker::RigidChunkClaimer::CM_SuggestFixResidue
• cmd() : protocols::simple_moves::WriteSSEMover
• cmd_ : core::io::external::PsiPredInterface , protocols::denovo_design::filters::SSPredictionFilter , protocols::simple_filters::HolesFilter , protocols::simple_moves::WriteSSEMover
• cmd_accept_to_best() : protocols::relax::FastRelax
• cmd_line_csts() : protocols::comparative_modeling::LoopRelaxMover
• cmd_line_csts_ : protocols::comparative_modeling::LoopRelaxMover
• cmd_line_operation_ : protocols::antibody::design::GeneralAntibodyModeler , protocols::calc_taskop_movers::CreateSequenceMotifMover
• cmdline_options_activated() : protocols::noesy_assign::NoesyModule
• CmdLineData() : protocols::topology_broker::CmdLineData
• cmp() : core::scoring::packstat::Event
• co_substrates_ : protocols::enzymatic_movers::EnzymaticMover
• coarse_angle_sampling_ : protocols::hotspot_hashing::movers::PlaceSurfaceProbe
• coarse_centering_mode : core::scoring::APBSConfig::I_PARAM
• coarse_rna_ : core::import_pose::libraries::RNA_ChunkLibrary
• coarse_rna_name_to_num_ : protocols::rna::denovo::coarse::CoarseRNA_Fragments
• coarse_sampling_ : protocols::hotspot_hashing::movers::PlaceSurfaceProbe
• CoarseRNA_Fragments() : protocols::rna::denovo::coarse::CoarseRNA_Fragments
• CoarseRNA_LoopCloser() : protocols::rna::denovo::coarse::CoarseRNA_LoopCloser
• code_to_root_map() : core::chemical::carbohydrates::CarbohydrateInfoManager
• code_to_root_map_ : core::chemical::carbohydrates::CarbohydrateInfoManager
• codes_to_root_map_file() : core::chemical::carbohydrates::CarbohydrateInfoManager
• coef1_ : protocols::branch_angle::BranchAngleOptimizer
• coef2_ : protocols::branch_angle::BranchAngleOptimizer
• COEF_DELTA : core::pack::dunbrack::SingleResidueDunbrackLibrary
• coef_map1_ : protocols::branch_angle::BranchAngleOptimizer
• coef_map2_ : protocols::branch_angle::BranchAngleOptimizer
• coeff_grad_x : core::scoring::electron_density::ElectronDensity
• coeff_grad_y : core::scoring::electron_density::ElectronDensity
• coeff_grad_z : core::scoring::electron_density::ElectronDensity
• coeffs_ : protocols::sasa_scores::Poly
• coeffs_density_ : core::scoring::electron_density::ElectronDensity
• coeffs_faatr_ : protocols::ligand_docking::ga_ligand_dock::GridScorer
• coeffs_faelec_ : protocols::ligand_docking::ga_ligand_dock::GridScorer
• coeffs_farep_ : protocols::ligand_docking::ga_ligand_dock::GridScorer
• coeffs_fasol_ : protocols::ligand_docking::ga_ligand_dock::GridScorer
• coeffs_lkball_ : protocols::ligand_docking::ga_ligand_dock::GridScorer
• coeffs_lkbridge_ : protocols::ligand_docking::ga_ligand_dock::GridScorer
• COFilter() : protocols::simple_filters::COFilter
• col2islabel_ : protocols::noesy_assign::PeakFileFormat
• col2proton_ : protocols::noesy_assign::PeakFileFormat
• col_name_ : protocols::simple_filters::JScoreEvaluator
• coldspot_label() : protocols::fold_from_loops::utils::Nub
• coldspots : protocols::fold_from_loops::utils::NubSegment
• coll_radii_ : protocols::vardist_solaccess::VarSolDistSasaCalculator , protocols::vardist_solaccess::VarSolDRotamerDots
• collect() : protocols::abinitio::HedgeArchive
• collect_all_inverse_rotamers() : protocols::toolbox::match_enzdes_util::InvrotTarget , protocols::toolbox::match_enzdes_util::InvrotTree , protocols::toolbox::match_enzdes_util::InvrotTreeNode , protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase
• collect_alternative_decoys() : protocols::abinitio::IterativeBase , protocols::abinitio::IterativeCentroid
• collect_claims() : protocols::environment::EnvClaimBroker
• collect_ddG_of_binding_data() : protocols::optimize_weights::IterativeOptEDriver
• collect_ddG_of_mutation_data() : protocols::optimize_weights::IterativeOptEDriver
• collect_decoy_discrimination_data() : protocols::optimize_weights::IterativeOptEDriver
• collect_dG_of_binding_data() : protocols::optimize_weights::IterativeOptEDriver
• collect_elements() : protocols::environment::EnvClaimBroker
• collect_hedge_structures() : protocols::abinitio::IterativeBase
• collect_hedgeing_decoys_from_batches() : protocols::abinitio::IterativeBase
• collect_HN_S2_and_EF() : protocols::sparta::PDB
• collect_jumps() : core::environment::FoldTreeSketch::Node
• collect_ligand_discrimination_data() : protocols::optimize_weights::IterativeOptEDriver
• collect_rotamer_energies() : protocols::optimize_weights::IterativeOptEDriver
• collect_rotamer_energies_from_slave_cpu() : protocols::optimize_weights::IterativeOptEDriver
• collect_rotamer_energies_from_slave_cpus() : protocols::optimize_weights::IterativeOptEDriver
• collect_rotamer_recovery_data_from_slave_cpu() : protocols::optimize_weights::IterativeOptEDriver
• collect_rotamer_recovery_data_from_slave_cpus() : protocols::optimize_weights::IterativeOptEDriver
• collect_sequence_recovery_data_from_slave_cpu() : protocols::optimize_weights::IterativeOptEDriver
• collect_sequence_recovery_data_from_slave_cpus() : protocols::optimize_weights::IterativeOptEDriver
• collect_target_statistics() : protocols::noesy_assign::PeakCalibrator
• collect_upperbound_statistics() : protocols::noesy_assign::PeakCalibrator , protocols::noesy_assign::StructureDependentPeakCalibrator , protocols::noesy_assign::StructureIndependentPeakCalibrator
• collectInsertionPose() : protocols::forge::remodel::RemodelData
• collector_ : protocols::frag_picker::quota::QuotaSelector
• collector_to_picker() : protocols::struct_fragment::StructFragmentMover
• collision_check_id_2_restype_id() : protocols::toolbox::match_enzdes_util::LigandConformer
• collision_check_id_2_restype_id_ : protocols::toolbox::match_enzdes_util::LigandConformer
• colonyE() : protocols::hotspot_hashing::HotspotStubSet
• colonyE_ : protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover , protocols::protein_interface_design::movers::SetupHotspotConstraintsMover
• color_ : protocols::qsar::RenderGridsToKinemage
• color_data_ : protocols::qsar::RenderGridsToKinemage
• Color_mode : protocols::viewer::GraphicsState
• color_mode_ : protocols::qsar::RenderGridsToKinemage
• color_name : protocols::qsar::ColorGradient
• color_value : protocols::qsar::ColorGradient
• ColorGradient() : protocols::qsar::ColorGradient
• coloumb_ : protocols::ligand_docking::rdf::RDFElecFunction
• cols() : core::sequence::DP_Matrix
• column_labels_ : protocols::noesy_assign::PeakFileFormat
• column_names_ : protocols::contact_map::ContactMap , protocols::frag_picker::CSTalosIO , protocols::frag_picker::PhiPsiTalosIO
• column_width_ : protocols::rotamer_recovery::RRReporterHuman
• com : core::scoring::methods::RG_MinData , protocols::features::helixAssembly::HelicalFragment , protocols::ligand_docking::ga_ligand_dock::Pharmacophore
• CoM() : protocols::pockets::FingerprintBase
• COM : protocols::toolbox::DecoySetEvaluation
• com_ : protocols::features::helixAssembly::HelicalFragment , protocols::ligand_docking::ga_ligand_dock::Pharmacophore
• CoM_ : protocols::pockets::FingerprintBase
• com_jump_name_ : protocols::environment::CoMTrackerCM
• com_name_ : protocols::environment::CoMTrackerCM
• COM_target_ : protocols::constraints_additional::COMCoordinateConstraint
• com_vector_criterion_ : protocols::match::NumNeighborsMPM
• comatms : core::scoring::elec::ElecGroup
• CombinationMode : protocols::denovo_design::components::CompoundPerturber
• combine() : protocols::noesy_assign::Resonance
• combine_chains() : protocols::pose_length_moves::NearNativeLoopCloser
• combine_exclude_file() : protocols::abinitio::abscript::ConstraintPreparer
• combine_exclude_res() : protocols::abinitio::abscript::ConstraintPreparer
• combine_exclude_res_ : protocols::abinitio::abscript::ConstraintPreparer , protocols::topology_broker::ConstraintClaimer
• combine_helical_silent_file_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• combine_history_ : protocols::simple_moves::CombinePoseMover
• combine_long_loop_mode() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• combine_long_loop_mode_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• combine_permutations() : protocols::denovo_design::architects::BetaSheetArchitect
• combine_permutations_rec() : protocols::denovo_design::architects::BetaSheetArchitect
• combine_ratio() : protocols::abinitio::abscript::ConstraintPreparer , protocols::topology_broker::ConstraintClaimer
• combine_ratio_ : protocols::abinitio::abscript::ConstraintPreparer , protocols::topology_broker::ConstraintClaimer
• combine_residue_selections() : core::select::residue_selector::SSElementSelector
• combine_resis_ : protocols::enzdes::PoseFoundResiduesCombination
• combine_rot_dbs() : protocols::splice::SampleRotamersFromPDB
• combine_score : protocols::stepwise::modeler::rna::Combine_Tags_Info
• combine_segment_names() : protocols::denovo_design::connection::ConnectionArchitect
• Combine_Tags_Info() : protocols::stepwise::modeler::rna::Combine_Tags_Info
• combine_xyz_lists() : protocols::pockets::NonPlaidFingerprint
• CombineChainsMover() : protocols::domain_assembly::CombineChainsMover
• combined_filters_ : protocols::matdes::MatDesGreedyOptMutationMover
• CombinedConstraintEvaluator() : protocols::constraints_additional::CombinedConstraintEvaluator
• CombinedConstraintEvaluatorCreator() : protocols::constraints_additional::CombinedConstraintEvaluatorCreator
• CombinedFilter() : protocols::filters::CombinedFilter
• CombinedTaskOperation() : protocols::flxbb::CombinedTaskOperation
• CombinePoseMover() : protocols::simple_moves::CombinePoseMover
• combos_ : protocols::hbnet::HBNetStapleInterface
• COMCoordinateConstraint() : protocols::constraints_additional::COMCoordinateConstraint
• COMM_ : core::scoring::rna::chemical_shift::RNA_CS_parameters
• comm_size_ : protocols::canonical_sampling::AsyncMPITemperingBase
• command : protocols::denovo_design::movers::RelaxScriptCommand , protocols::relax::RelaxScriptCommand
• command_ : protocols::rpc::JSON_RPC , protocols::simple_filters::ExternalEvaluator , protocols::task_operations::ResfileCommandOperation
• command_map_ : protocols::task_operations::ResfileCommandOperation
• command_string() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• commands_ : core::pack::task::ResfileContents , protocols::task_operations::ResfileCommandOperation , protocols::task_operations::SequenceMotifTaskOperation
• commands_for_residue() : core::pack::task::ResfileContents
• comment : core::io::HELIXInformation , core::io::ModifiedResidueInformation , core::sequence::SequenceAlignment
• comment_exists() : protocols::simple_filters::PoseComment
• comment_exists_ : protocols::simple_filters::PoseComment
• comment_from_line() : core::io::silent::SilentStruct
• comment_line() : core::io::silent::SilentFileData
• comment_lines() : core::io::silent::SilentFileData
• comment_lines_ : core::io::silent::SilentFileData
• comment_name() : protocols::simple_filters::PoseComment
• comment_name_ : protocols::simple_filters::PoseComment
• comment_value() : protocols::simple_filters::PoseComment
• comment_value_ : protocols::simple_filters::PoseComment
• comments() : core::io::rna::RDAT , core::sequence::SequenceAlignment
• comments_ : core::io::rna::RDAT , core::sequence::SequenceAlignment
• commit_alt_bb_substitution() : protocols::flexpack::interaction_graph::MinimalistFlexbbNode
• commit_change() : core::pack::interaction_graph::NPDHBSimpleInteractionGraph , core::pack::interaction_graph::SimpleEdge , core::pack::interaction_graph::SimpleInteractionGraph , core::pack::interaction_graph::SimpleNode
• commit_change_no_res_pointer_update() : core::pack::interaction_graph::NPDHBSimpleNode , core::pack::interaction_graph::SimpleNode
• commit_change_npd() : core::pack::interaction_graph::NPDHBSimpleNode
• commit_considered_backbone_move() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph , protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph
• commit_considered_substitution() : core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty , core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy , core::pack::interaction_graph::AnnealableGraphBase , core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::FASTERNode , 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::LazyInteractionGraph , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::MultiplexedAnnealableGraph , core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > , core::pack::interaction_graph::NPDHBondNode< V, E, G > , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::ResidueArrayAnnealingEvaluator , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistInteractionGraph , core::pack::interaction_graph::SymmMinimalistNode , core::scoring::annealing::ResidueArrayAnnealableEnergy , core::scoring::mhc_epitope_energy::MHCEpitopeEnergy , protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph , protocols::flexpack::interaction_graph::MinimalistFlexbbNode
• commit_considered_substitution_surface() : core::pack::interaction_graph::SurfaceNode< V, E, G >
• COMMIT_LIMIT_BETWEEN_UPDATES : core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistInteractionGraph , protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• commit_relaxation() : core::pack::interaction_graph::FASTERInteractionGraph
• common_block_precedes_job_blocks_ : protocols::jd3::standard::StandardJobQueen
• common_block_tags() : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::standard::StandardJobQueen
• common_block_tags_ : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::standard::StandardJobQueen
• common_delta_omega1_ : protocols::helical_bundle_predict::HBPHelixAssignments
• COMMON_DENOMINATOR : core::scoring::ResidualDipolarCoupling
• common_omega0_ : protocols::helical_bundle_predict::HBPHelixAssignments
• common_r0_ : protocols::helical_bundle_predict::HBPHelixAssignments
• communicator_handle_ : protocols::jd2::MPIMultiCommJobDistributor
• comp : protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering >
• comp_constraint_aas_ : protocols::fldsgn::potentials::AACompositionEnergy , protocols::fldsgn::potentials::SetAACompositionPotential
• comp_file_contents_D_alpha_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• comp_file_contents_D_beta_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• comp_file_contents_L_alpha_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• comp_file_contents_L_beta_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• comp_id() : protocols::indexed_structure_store::ResidueEntry , protocols::indexed_structure_store::StructureEntry
• compact_bbindex() : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• compact_residue_schema_ : protocols::features::ProteinResidueConformationFeatures , protocols::features::ResidueConformationFeatures
• Comparator() : protocols::environment::Comparator
• comparator_ : protocols::frag_picker::BestTotalScoreSelector , protocols::frag_picker::CustomScoreSelector
• compare() : protocols::hbnet::NetworkStateScoreComparator , protocols::loophash::BackboneSegment
• compare_all_to_ground_state_ : protocols::multistate_design::PartitionAggregateFunction
• compare_by_superposition() : protocols::simple_filters::ResidueDepthFilter
• compare_composites() : protocols::simple_filters::SimpleMetricFilter
• compare_energy_to_ground_state_ : protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• compare_input_pose_geometry_to_reference() : protocols::minimization_packing::GreenPacker
• compare_metric() : protocols::simple_filters::SimpleMetricFilter
• compare_SizeRealPairs() : protocols::enzdes::EnzdesFlexibleRegion
• compare_to_native() : protocols::enzdes::DesignVsNativeComparison
• compare_to_ref() : protocols::matdes::SymUnsatHbondFilter
• compare_to_ref_ : protocols::matdes::SymUnsatHbondFilter
• compare_topo_strings() : protocols::simple_filters::SpanTopologyMatchPoseFilter
• CompareByScoreCombination() : protocols::frag_picker::CompareByScoreCombination
• compareCoverage() : protocols::pockets::ComparisonGrid
• CompareMode : protocols::enzdes::ValueEvaluator
• comparer_ : protocols::features::RotamerRecoveryFeatures , protocols::rotamer_recovery::RotamerRecovery
• comparer_name_ : protocols::rotamer_recovery::RRReporterHuman , protocols::rotamer_recovery::RRReporterSQLite
• comparer_params_ : protocols::rotamer_recovery::RRReporterHuman , protocols::rotamer_recovery::RRReporterSQLite
• comparer_types_ : protocols::rotamer_recovery::RotamerRecoveryFactory
• CompareScoreComponent() : protocols::frag_picker::CompareScoreComponent
• CompareTags() : protocols::jd2::CompareTags
• CompareTotalScore() : protocols::frag_picker::CompareTotalScore
• ComparisonGrid : protocols::pockets::CCluster , protocols::pockets::CClusterSet , protocols::pockets::ComparisonGrid , protocols::pockets::PCluster , protocols::pockets::PClusterSet , protocols::pockets::PocketGrid
• CompassScoringScheme() : core::sequence::CompassScoringScheme
• compatibility_check() : protocols::forge::build::BuildManager
• compatible() : protocols::abinitio::AlternativePairings , protocols::abinitio::PairingStatEntry , protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder , protocols::match::upstream::OriginalBackboneBuildPoint , protocols::match::upstream::ProteinUpstreamBuilder , protocols::match::upstream::ScaffoldBuildPoint , protocols::match::upstream::UpstreamBuilder
• compatible_restype() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• compatible_with() : protocols::forge::build::BuildInstruction
• compatible_with_current_format() : protocols::noesy_assign::PeakFileFormat , protocols::noesy_assign::PeakFileFormat_Base
• complete() : protocols::genetic_algorithm::GeneticAlgorithmBase , protocols::jd3::job_distributors::JobExtractor
• complete_ : protocols::jd3::job_distributors::JobExtractor
• complete_deltaE_prediction_for_bbmove() : protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph
• complete_larval_job_maturation() : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::standard::StandardJobQueen , protocols::multistage_rosetta_scripts::MRSJobQueen , protocols::rosetta_scripts::RosettaScriptsJobQueen
• complete_moving_atom_id_map_ : protocols::stepwise::modeler::align::StepWisePoseAligner
• complete_partial_state_assignment() : core::pack::interaction_graph::FASTERNode , protocols::flexpack::interaction_graph::MinimalistFlexbbNode
• complete_state_assignment() : core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode
• CompleteConnectionsFilter() : protocols::ligand_docking::CompleteConnectionsFilter
• completed() : protocols::jd2::Job , protocols::jd3::LarvalJob
• completed_ : protocols::jd2::Job , protocols::jd3::LarvalJob
• completed_first_round1_hit_building_ : protocols::match::downstream::ClassicMatchAlgorithm
• completed_job_summary() : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::JobQueen , protocols::jd3::standard::StandardJobQueen , protocols::multistage_rosetta_scripts::MRSJobQueen
• completed_jobs() : protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::JobTracker
• completed_jobs_ : protocols::jd3::JobTracker
• completed_jobs_by_dag_node_ : protocols::jd3::JobTracker
• completed_jobs_for_node() : protocols::jd3::JobTracker
• completed_quenches_ : protocols::carbohydrates::GlycanTreeModeler
• CompletedJobOutput() : protocols::jd3::CompletedJobOutput
• CompletionMessage : protocols::jd2::archive::ArchiveManager , protocols::jd2::archive::MPIArchiveJobDistributor::CompletionMessage
• CompletionMessages : protocols::jd2::archive::ArchiveManager
• complex_object_name() : protocols::fold_from_loops::utils::Nub
• complex_total_energy : protocols::analysis::InterfaceData
• complex_type_gen() : protocols::rigid::UniformRigidBodyMover
• complex_type_generator_for_anchored_graft_mover() : protocols::grafting::AnchoredGraftMover
• complex_type_generator_for_backbone_mover() : protocols::simple_moves::BackboneMover
• complex_type_generator_for_fast_relax() : protocols::relax::FastRelax
• complex_type_generator_for_logical_selector() : protocols::pose_selectors::LogicalSelector
• complex_type_generator_for_loop_protocol() : protocols::loop_modeling::LoopProtocol
• complex_type_generator_for_min_mover() : protocols::minimization_packing::MinMover
• complex_type_generator_for_pack_rotamers_mover() : protocols::minimization_packing::PackRotamersMover
• complex_type_generator_for_rotamer_trials_mover() : protocols::minimization_packing::RotamerTrialsMover
• complex_type_generator_for_simple_metric() : core::simple_metrics::SimpleMetric
• complex_type_name_for_architect() : protocols::denovo_design::architects::DeNovoArchitectFactory
• complex_type_name_for_chunk_library_inputter() : protocols::jd3::chunk_library_inputters::ChunkLibraryInputterFactory
• complex_type_name_for_constraint_generator() : protocols::constraint_generator::ConstraintGeneratorFactory
• complex_type_name_for_full_model_inputter() : protocols::jd3::full_model_inputters::FullModelInputterFactory
• complex_type_name_for_pairing() : protocols::denovo_design::components::SegmentPairing
• complex_type_name_for_pose_inputter() : protocols::jd3::pose_inputters::PoseInputterFactory
• complex_type_name_for_pose_outputter() : protocols::jd3::pose_outputters::PoseOutputterFactory
• complex_type_name_for_pose_reporter() : protocols::rosetta_scripts::PosePropertyReporterFactory
• complex_type_name_for_pose_selector() : protocols::rosetta_scripts::PoseSelectorFactory
• complex_type_name_for_secondary_pose_outputter() : protocols::jd3::pose_outputters::PoseOutputterFactory
• complexed_energy : protocols::analysis::PerResidueInterfaceData
• complexed_interface_score : protocols::analysis::InterfaceData
• complexed_SASA : protocols::analysis::InterfaceData
• complexed_sasa : protocols::analysis::PerResidueInterfaceData
• component() : protocols::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• component_bounds_ : core::conformation::symmetry::SymmetryInfo
• component_file_ : protocols::simple_moves::ConcatenatePosesMover
• component_id_ : protocols::frag_picker::CompareScoreComponent
• component_membership_ : core::pack::interaction_graph::InteractionGraphBase
• component_weights_ : protocols::optimize_weights::IterativeOptEDriver , protocols::optimize_weights::OptEMultifunc
• components_ : core::conformation::symmetry::SymmData , core::conformation::symmetry::SymmetryInfo , protocols::frag_picker::CompareByScoreCombination , protocols::frag_picker::quota::ABEGO_SS_Pool , protocols::frag_picker::quota::SecondaryStructurePool
• components_moved_by_jump() : core::conformation::symmetry::SymmData , core::conformation::symmetry::SymmetryInfo
• compose_atomnames() : core::chemical::sdf::MolWriter
• compose_atoms() : core::chemical::sdf::MolWriter
• compose_bonds() : core::chemical::sdf::MolWriter
• compose_ctab() : core::chemical::sdf::MolWriter
• compose_job_info() : core::chemical::sdf::MolWriter
• compose_metadata() : core::chemical::sdf::MolWriter
• compose_naming() : core::chemical::sdf::MolWriter
• compose_nbr_atom() : core::chemical::sdf::MolWriter
• compose_properties() : core::chemical::sdf::MolWriter
• compose_rosetta_properties() : core::chemical::sdf::MolWriter
• compose_typeinfo() : core::chemical::sdf::MolWriter
• ComposeSearchPatterns() : protocols::hotspot_hashing::ComposeSearchPatterns
• composite_action_ : protocols::simple_filters::SimpleMetricFilter
• composite_real_data_ : core::simple_metrics::SimpleMetricStruct
• composite_string_data_ : core::simple_metrics::SimpleMetricStruct
• CompositeEnergyMetric() : core::simple_metrics::composite_metrics::CompositeEnergyMetric
• CompositeFragmentSelector() : protocols::frag_picker::CompositeFragmentSelector
• CompositeRealMetric() : core::simple_metrics::CompositeRealMetric , core::simple_metrics::MetricKey
• CompositeScoringScheme() : core::sequence::CompositeScoringScheme
• CompositeSegmentMoveSet_ : protocols::rbsegment_relax::RBSegmentRelax
• CompositeSequence() : core::sequence::CompositeSequence
• CompositeSequenceCreator() : core::sequence::CompositeSequenceCreator
• CompositeStringMetric() : core::simple_metrics::CompositeStringMetric , core::simple_metrics::MetricKey
• CompositionMover() : protocols::moves::CompositionMover
• compound_factory_ : protocols::task_operations::StoreCompoundTaskMover
• compound_filters_ : protocols::matdes::MatDesGreedyOptMutationMover
• compound_in_progress() : core::io::HeaderInformation
• compound_in_progress_ : core::io::HeaderInformation
• compound_statement_ : protocols::filters::CompoundFilter
• compound_task_ : protocols::task_operations::StoreCompoundTaskMover
• compound_token_to_string() : core::io::HeaderInformation
• CompoundArchitect() : protocols::denovo_design::architects::CompoundArchitect
• CompoundDesignableTask() : protocols::task_operations::StoreCompoundTaskMover
• CompoundFactory : protocols::task_operations::StoreCompoundTaskMover
• CompoundFilter() : protocols::filters::CompoundFilter
• CompoundPackableTask() : protocols::task_operations::StoreCompoundTaskMover
• CompoundPerturber() : protocols::denovo_design::components::CompoundPerturber
• compounds() : core::io::HeaderInformation
• Compounds : core::io::HeaderInformation
• compounds_ : core::io::HeaderInformation
• CompoundStatement : protocols::filters::CompoundFilter
• CompoundTask : protocols::task_operations::StoreCompoundTaskMover
• CompoundToken : core::io::HeaderInformation
• CompoundToken_max : core::io::HeaderInformation
• CompoundTranslate() : protocols::ligand_docking::CompoundTranslate
• compprob() : core::scoring::packstat::PackingScore
• compprob_ : core::scoring::packstat::PackingScore
• COMPUTATION_TYPE : core::scoring::nmr::pcs::PCSSingleSet , core::scoring::nmr::rdc::RDCMultiSet
• computation_type_ : core::scoring::nmr::pcs::PCSSingleSet , core::scoring::nmr::rdc::RDCMultiSet
• compute() : core::scoring::dna::TorsionFourierComponent , core::scoring::dssp::Dssp , core::scoring::dssp::StrandPairingSet , core::scoring::membrane::MPSpanAngleEnergy , core::scoring::membrane::MPSpanInsertionEnergy , core::scoring::packstat::LeeRichards , core::scoring::packstat::Slice , core::select::util::SelectResiduesByLayer , protocols::abinitio::PairingStatistics , protocols::calc_taskop_filters::MultipleSigmoids , protocols::calc_taskop_filters::Operator , protocols::calc_taskop_filters::RelativePoseFilter , protocols::calc_taskop_filters::RotamerBoltzmannWeight , protocols::calc_taskop_filters::Sigmoid , protocols::constraint_filters::SavePoseConstraintToFileFilter , protocols::constraint_filters::ShowConstraintsFilter , protocols::cryst::ReportGradientsMover , protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter , 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::enzdes::DiffAtomSasaFilter , protocols::enzdes::EnzScoreFilter , protocols::enzdes::LigBurialFilter , protocols::enzdes::LigDSasaFilter , protocols::enzdes::LigInterfaceEnergyFilter , protocols::enzdes::RepackWithoutLigandFilter , protocols::evolution::AASynthesisFitnessCost , protocols::features::InterfaceDdGMover , protocols::filters::CalculatorFilter , protocols::filters::CombinedFilter , protocols::filters::CompoundFilter , protocols::filters::IfThenFilter , protocols::filters::ReplicateFilter , protocols::filters::TimeFilter , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::filters::FragQualFilter , protocols::fldsgn::filters::HelixBendFilter , 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::MatchResidues , protocols::fold_from_loops::filters::ConstraintFulfilmentFilter , protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter , protocols::fold_from_loops::filters::ScorePoseSegmentFromResidueSelectorFilter , protocols::frag_picker::FragmentScoreFilter , protocols::hbnet::UnsatSelector , protocols::helical_bundle::BundleReporterFilter , protocols::indexed_structure_store::filters::FragmentLookupFilter , protocols::jumping::SameStrand , protocols::matdes::ClashCheckFilter , protocols::matdes::GetRBDOFValues , protocols::matdes::InterfacePackingFilter , protocols::matdes::OligomericAverageDegreeFilter , protocols::matdes::SymUnsatHbondFilter , 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::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::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::Torsion , protocols::score_filters::GeometryFilter , protocols::score_filters::ScoreTypeFilter , protocols::simple_ddg::DdgFilter , 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::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::ReadPoseExtraScoreFilter , protocols::simple_filters::ReportFilter , protocols::simple_filters::ResidueBurialFilter , protocols::simple_filters::ResidueChiralityFilter , protocols::simple_filters::ResidueCountFilter , 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::SecretionPredictionFilter , protocols::simple_filters::SequenceDistance , protocols::simple_filters::ShapeComplementarityFilter , protocols::simple_filters::SidechainRmsdFilter , protocols::simple_filters::SimpleHbondsToAtomFilter , protocols::simple_filters::SpanTopologyMatchPoseFilter , protocols::simple_filters::SSElementLengthFilter , protocols::simple_filters::SSElementMotifContactFilter , 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::toolbox::CalcInterNeighborGroup , protocols::toolbox::ClusterPhilStyle , protocols::toolbox::EnergyLandscapeEvaluator , protocols::toolbox::MulliganPNearEvaluator , protocols::toolbox::RotamerBoltzmannWeightEvaluator
• compute_ : protocols::frag_picker::FragmentScoreFilter
• compute_aas_after_disallowing() : protocols::denovo_design::task_operations::ConsensusLoopDesignOperation
• compute_absent_energies() : protocols::minimization_packing::GreenPacker
• compute_absent_lrci_energies_for_residue_pair() : protocols::minimization_packing::GreenPacker
• compute_absent_srci_energies_for_residue_pair() : protocols::minimization_packing::GreenPacker
• compute_acceptor_atom_energy() : core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy
• compute_aggregate_score() : protocols::pack_daemon::MultistateFitnessFunction
• compute_all_units() : protocols::denovo_design::components::DivideAndConqueror
• compute_alt_weights_for_hbonds() : core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G > , core::pack::interaction_graph::NPDHBondNode< V, E, G > , core::pack::interaction_graph::NPDHBSimpleNode
• compute_altbbconf_alternate_state_energy() : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• compute_anchor_transform() : protocols::features::LoopAnchorFeatures
• compute_angle() : protocols::fldsgn::filters::HSSTripletFilter
• compute_average_distances() : protocols::noesy_assign::FragsToAtomDist
• compute_average_structure() : protocols::toolbox::DecoySetEvaluation
• compute_avg_dist() : core::scoring::epr_deer::DEERData
• compute_best_allowed_aas() : protocols::denovo_design::task_operations::ConsensusLoopDesignOperation
• compute_best_solution() : protocols::denovo_design::components::FoldGraph
• compute_beta_topology() : protocols::abinitio::IterativeBase
• compute_bias() : protocols::rigid::RigidBodyMotionMover
• compute_boltz_probability() : protocols::calc_taskop_filters::RotamerBoltzmannWeight
• compute_boltz_sum() : protocols::denovo_design::filters::SSPredictionFilter
• compute_boltz_weight_packrotamers() : protocols::pose_metric_calculators::RotamerBoltzCalculator
• compute_Boltzmann_weight() : protocols::calc_taskop_filters::RotamerBoltzmannWeight
• compute_bounding_box() : core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid
• compute_burial() : core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid
• compute_cb_frame() : protocols::match::upstream::ProteinUpstreamBuilder
• compute_centroid_environment() : core::scoring::CenRotEnvPairPotential , core::scoring::EnvPairPotential , core::scoring::SmoothEnvPairPotential
• compute_chi() : core::scoring::saxs::SAXSEnergy , protocols::scoring::methods::saxs::PDDFEnergy
• compute_chi_with_fit() : core::scoring::saxs::SAXSEnergy
• compute_closure_metrics() : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• compute_comb() : protocols::fldsgn::MatchResidues
• compute_connection_candidates() : protocols::denovo_design::connection::ConnectionArchitect
• compute_cores() : protocols::abinitio::IterativeBase
• compute_csascore() : core::scoring::ChemicalShiftAnisotropy
• compute_d2() : protocols::simple_filters::SymmetricMotifFilter
• compute_dcentroid_environment() : core::scoring::CenRotEnvPairPotential , core::scoring::SmoothEnvPairPotential
• compute_dcscore() : core::scoring::DipolarCoupling
• compute_ddg() : protocols::calc_taskop_filters::RotamerBoltzmannWeight2
• compute_derivatives() : core::scoring::packstat::Slice
• compute_designable_neighbors() : protocols::enzdes::PackRotamersMoverPartGreedy
• compute_dipscore() : core::scoring::ResidualDipolarCoupling
• compute_dipscore_nls() : core::scoring::ResidualDipolarCoupling
• compute_dipscore_nlsDa() : core::scoring::ResidualDipolarCoupling
• compute_dipscore_nlsDaR() : core::scoring::ResidualDipolarCoupling
• compute_dipscore_nlsR() : core::scoring::ResidualDipolarCoupling
• compute_dist() : protocols::fldsgn::filters::HSSTripletFilter
• compute_dist_map() : core::kinematics::ShortestPathInFoldTree
• compute_distance_histogram() : core::scoring::saxs::SAXSEnergy
• compute_distance_matrix() : protocols::toolbox::DecoySetEvaluation
• compute_donor_atom_energy() : core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy
• compute_energies() : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::symmetry::SymmetricRotamerSets , protocols::features::StructureScoresFeatures , protocols::minimization_packing::GreenPacker
• compute_energy() : core::pack::interaction_graph::SimpleEdge
• compute_energy_for_assignment() : protocols::pack_daemon::DaemonSet , protocols::pack_daemon::PackDaemon
• compute_entropy_reduction() : protocols::calc_taskop_filters::RotamerBoltzmannWeight
• compute_entropy_reduction_ : protocols::calc_taskop_filters::RotamerBoltzmannWeight
• compute_events() : core::scoring::packstat::Slice
• compute_fa_deriv() : core::scoring::membrane::FaMPEnvEnergy
• compute_fa_proj() : core::scoring::membrane::FaMPEnvEnergy , core::scoring::membrane::FaMPSolvEnergy
• compute_fa_proj_coord() : core::scoring::membrane::FaMPEnvEnergy
• compute_fa_projection() : core::scoring::Membrane_FAPotential
• compute_folding_energies() : protocols::evolution::NucleotideMutation
• compute_fractions() : core::fragment::SecondaryStructure
• compute_frag_bias() : protocols::hybridization::FragmentBiasAssigner
• compute_fragment_bias() : protocols::hybridization::CartesianSampler
• compute_from_selector() : protocols::denovo_design::filters::SSShapeComplementarityFilter
• compute_from_ss_info() : protocols::denovo_design::filters::SSShapeComplementarityFilter
• compute_fully_buried_ene() : core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy
• compute_func() : core::scoring::func::SoedingFunc
• compute_grid_constant() : core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy
• compute_grid_scores_ : protocols::ligand_docking::InterfaceScoreCalculator
• compute_gunn() : protocols::frag_picker::scores::GunnCost , protocols::simple_moves::GunnCost
• compute_hash() : protocols::qsar::scoring_grid::GridManager
• compute_hbonds() : protocols::simple_filters::InterfaceHbondsFilter
• compute_Hbonds_for_residue() : protocols::simple_pose_metric_calculators::NumberHBondsCalculator
• compute_helix_pairing_set() : protocols::fldsgn::filters::HelixPairingFilter
• compute_input_set() : protocols::residue_selectors::HBondSelector
• compute_insert_pos() : protocols::abinitio::AllResiduesChanged , protocols::hybridization::AllResiduesChanged
• compute_intensities() : core::scoring::saxs::SAXSEnergy
• compute_interface() : protocols::scoring::InterchainPotential
• compute_interface_delta_hbond_unsat() : protocols::analysis::InterfaceAnalyzerMover
• compute_interface_delta_hbond_unsat_ : protocols::analysis::InterfaceAnalyzerMover
• compute_interface_energy() : protocols::analysis::InterfaceAnalyzerMover
• compute_interface_energy_ : protocols::analysis::InterfaceAnalyzerMover
• compute_interface_packstat() : protocols::analysis::InterfaceAnalyzerMover
• compute_interface_sc() : protocols::analysis::InterfaceAnalyzerMover
• compute_interface_sc_ : protocols::analysis::InterfaceAnalyzerMover
• compute_jump() : protocols::simple_filters::SSMotifFinder
• compute_jumpout_diff() : core::scoring::geometric_solvation::DatabaseOccSolEne
• compute_L1() : core::scoring::saxs::SAXSEnergy , protocols::scoring::methods::saxs::PDDFEnergy
• compute_ligand_natoms() : protocols::pockets::PlaidFingerprint
• compute_ligand_natoms_with_hydrogens() : protocols::pockets::PlaidFingerprint
• compute_ligand_nconformers() : protocols::pockets::PlaidFingerprint
• compute_ligand_resnum() : protocols::pockets::PlaidFingerprint
• compute_ligand_score_bonus() : protocols::coupled_moves::CoupledMovesProtocol
• compute_matching_energy() : core::scoring::disulfides::DisulfideMatchingPotential
• compute_max_ : protocols::calc_taskop_filters::RotamerBoltzmannWeight
• compute_max_branch_depth() : core::scoring::trie::RotamerTrie< AT, CPDATA >
• compute_membrane_embedding() : core::scoring::MembranePotential
• compute_metrics() : core::scoring::motif::MotifHits
• compute_metrics_for_residue_subset() : protocols::enzdes::EnzdesScorefileFilter
• compute_mg_sol_for_hydrogens_ : core::scoring::magnesium::MgEnergy
• compute_mismatch_prob() : protocols::denovo_design::filters::SSPredictionFilter
• compute_model_weights() : protocols::abinitio::PairingStatistics
• compute_modified_ddg() : protocols::calc_taskop_filters::RotamerBoltzmannWeight2
• compute_modified_ddG() : protocols::calc_taskop_filters::RotamerBoltzmannWeight
• compute_modified_residue_energy() : protocols::calc_taskop_filters::RotamerBoltzmannWeight2
• compute_mpair_score() : core::scoring::membrane::MPPairEnergy
• compute_mpcbeta_score() : core::scoring::membrane::MPCbetaEnergy
• compute_mpenv_score() : core::scoring::membrane::MPEnvEnergy
• compute_Nk() : protocols::noesy_assign::PeakAssignmentResidueMap
• compute_nonhelix_penalty() : core::scoring::membrane::MPNonHelixPenalty
• compute_normalization() : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• compute_number_cavities() : protocols::vip::VIP_Mover
• compute_one_and_two_body_energies() : core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• compute_one_body_energies() : core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset , core::pack::rotamer_set::symmetry::SymmetricRotamerSet_
• compute_one_body_energies_for_otf_ig() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• compute_one_body_energy_maps() : core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• compute_onebody_interactions_with_background() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• compute_orb_orb_E() : core::scoring::orbitals::OrbitalsScore
• compute_packstat_ : protocols::analysis::InterfaceAnalyzerMover , protocols::features::InterfaceFeatures
• compute_pair_energy_for_alternate_state() : core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode
• compute_pair_energy_for_current_state() : core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode
• compute_paired_residues() : protocols::fldsgn::filters::SheetTopologyFilter
• compute_pairwise_score() : protocols::scoring::ResidualDipolarCouplingRigidSegments
• compute_pcs_values_and_score_from_tensor() : core::scoring::nmr::pcs::PCSSingleSet
• compute_pddf() : protocols::scoring::methods::saxs::PDDFEnergy
• compute_pddf_without_ff() : protocols::scoring::methods::saxs::PDDFEnergy
• compute_penalty() : core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty
• compute_per_residue_probabilities() : protocols::medal::MedalMover
• compute_permutations() : protocols::denovo_design::architects::StrandArchitect
• compute_pnear_and_dgfolding() : protocols::cyclic_peptide_predict::PNearCalculator
• compute_polar_group_sol_energy() : core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy
• compute_pose_hpatch_score() : core::pack::interaction_graph::SurfacePotential
• compute_pose_surface_energy() : core::pack::interaction_graph::SurfacePotential
• compute_pre_score_from_current_data() : core::scoring::nmr::pre::PREMultiSet
• compute_pre_score_from_point_vector() : core::scoring::nmr::pre::PREMultiSet
• compute_pre_score_from_single_point() : core::scoring::nmr::pre::PREMultiSet
• compute_proline_correction_energies_for_otf_graph() : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::symmetry::SymmetricRotamerSets
• compute_proposal_density() : protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover , protocols::simple_moves::sidechain_moves::PerturbChiSidechainMover , protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• compute_proton_chi_samplings() : core::pack::rotamers::SingleResidueRotamerLibrary
• compute_rama_score() : protocols::loops::loop_closure::ccd::RamaCheck1B , protocols::loops::loop_closure::ccd::RamaCheck2B , protocols::loops::loop_closure::ccd::RamaCheckBase
• compute_rdc_values_and_score_from_tensor() : core::scoring::nmr::rdc::RDCMultiSet
• compute_rdf() : protocols::ligand_docking::ComputeLigandRDF
• compute_reference_intragroup_rpes() : protocols::minimization_packing::GreenPacker
• compute_residual() : protocols::simple_filters::DisulfideEntropyFilter
• compute_residue() : protocols::simple_filters::NMerPSSMEnergyFilter
• compute_residue_pairings() : protocols::fldsgn::filters::SheetTopologyFilter
• compute_residue_pairs() : protocols::fldsgn::SheetConstraintGenerator
• compute_residue_selection() : protocols::simple_filters::BuriedSurfaceAreaFilter
• compute_residue_subset() : protocols::denovo_design::residue_selectors::NamedSegmentSelector , protocols::relax::AtomCoordinateCstMover
• compute_residue_subset_for_segment() : protocols::denovo_design::residue_selectors::NamedSegmentSelector
• compute_residue_surface_energy() : core::pack::interaction_graph::SurfacePotential
• compute_resnums() : protocols::simple_filters::ResidueIEFilter
• compute_rmsd() : protocols::comparative_modeling::LoopRelaxMover , protocols::simple_ddg::ddG
• compute_rmsd_ : protocols::comparative_modeling::LoopRelaxMover , protocols::simple_ddg::ddG
• compute_rmsd_with_super() : protocols::simple_ddg::ddG
• compute_rotamer_energies_for_assigned_pdbs() : protocols::optimize_weights::IterativeOptEDriver
• compute_rotamer_pair_energy() : core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::SymmOnTheFlyNode
• compute_rotamers_around_ligands() : protocols::optimize_weights::IterativeOptEDriver
• compute_rotdensities() : protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover , protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover
• compute_salt_bridges() : protocols::simple_filters::InterfaceHbondsFilter
• compute_samebbconf_alternate_state_energy_first_node() : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• compute_samebbconf_alternate_state_energy_second_node() : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• compute_score() : core::scoring::nmr::pcs::PCSMultiSet , protocols::calc_taskop_filters::RotamerBoltzmannWeight2
• compute_score_all_media() : core::scoring::nmr::rdc::RDCData
• compute_score_all_spinlabel() : core::scoring::nmr::pre::PREData
• compute_score_all_tags() : core::scoring::nmr::pcs::PCSData
• compute_scores() : core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric
• compute_selected_residues() : protocols::simple_moves::BackboneMover
• compute_separated_sasa() : protocols::analysis::InterfaceAnalyzerMover
• compute_separated_sasa_ : protocols::analysis::InterfaceAnalyzerMover
• compute_sho_acceptor_atom_energy() : core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy
• compute_sho_donor_atom_energy() : core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy
• compute_simple() : protocols::denovo_design::filters::PreProlineFilter
• compute_size() : protocols::stepwise::modeler::protein::InputStreamWithResidueInfo
• compute_slice_com() : protocols::membrane::MPLipidAccessibility
• compute_smooth_nb() : core::scoring::packing::PoseBalls
• compute_spline() : protocols::denovo_design::filters::PreProlineFilter
• compute_sr_one_body_energies_for_flexsets() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• compute_state_energies() : protocols::pack_daemon::MPIMultistateFitnessFunction , protocols::pack_daemon::MultistateFitnessFunction
• compute_subfilter() : protocols::filters::CompoundFilter
• compute_surface() : core::scoring::packstat::Slice
• compute_surrounding_sasa() : core::scoring::packstat::MultiProbePerSphereAccumulator
• compute_swap_trim_CSPs() : protocols::ub_e2c::ubi_e2c_modeler
• compute_symm_rotations() : core::scoring::electron_density::ElectronDensity
• compute_target_residues() : protocols::denovo_design::movers::AlignResiduesMover
• compute_tempered_rotamer_probabilities() : protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover
• compute_template_residues() : protocols::denovo_design::movers::AlignResiduesMover
• compute_tensor_stats() : core::scoring::ResidualDipolarCoupling
• compute_termini_penalty() : core::scoring::membrane::MPTerminiPenalty
• compute_tmproj_penalty() : core::scoring::membrane::MPTMProjPenalty
• compute_total_score() : protocols::scoring::ResidualDipolarCouplingRigidSegments
• compute_total_volume_of_current_residues() : core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid
• compute_transform_and_write_to_db() : protocols::features::LoopAnchorFeatures
• compute_trim_CSPs() : protocols::ub_e2c::ubi_e2c_modeler
• compute_unsats_all_nodes() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph
• compute_unsats_changed_nodes() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph
• compute_unsats_for_node() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph
• compute_valid_atoms() : protocols::constraint_generator::HydrogenBondConstraintGenerator
• compute_volume_of_this_buried_rotamer() : core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid
• compute_volumes_of_buried_rotamers() : core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid
• compute_zero_intensity() : core::scoring::saxs::SAXSEnergy
• computeAllBoltz() : protocols::pose_metric_calculators::RotamerBoltzCalculator
• computeBoltzSum() : protocols::pose_metric_calculators::RotamerBoltzCalculator
• computeBoltzWeight() : protocols::pose_metric_calculators::RotamerBoltzCalculator
• computeBoltzWeight_lazy() : protocols::pose_metric_calculators::RotamerBoltzCalculator
• computeCrystParams() : core::scoring::electron_density::ElectronDensity , core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• computed_ : core::scoring::DenseEnergyContainer , core::scoring::DenseNeighborConstIterator , core::scoring::DenseNeighborIterator , core::scoring::OneToAllEnergyContainer , core::scoring::OneToAllNeighborConstIterator , core::scoring::OneToAllNeighborIterator , core::scoring::PolymerBondedEnergyContainer
• computeGradient() : protocols::viewer::triangleIterator
• computeGradients() : core::scoring::electron_density::ElectronDensity
• computeGunnTuples() : protocols::frag_picker::scores::GunnCostScore
• ComputeLigandRDF() : protocols::ligand_docking::ComputeLigandRDF
• computeStats() : core::scoring::electron_density::ElectronDensity
• ComputeTotalDistCst() : protocols::abinitio::ComputeTotalDistCst
• CoMTrackerCM() : protocols::environment::CoMTrackerCM
• concatenate_all_options() : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::standard::StandardJobQueen
• concatenate_poses() : protocols::simple_moves::ConcatenatePosesMover
• concatenate_rot_matrix() : protocols::splice::SampleRotamersFromPDB
• concatenate_topology() : core::conformation::membrane::SpanningTopology
• concatenated_input_source_names() : protocols::jd3::InnerLarvalJob
• ConcatenatePosesMover() : protocols::simple_moves::ConcatenatePosesMover
• concave : core::scoring::sc::_RESULTS
• concavity_direction() : protocols::fldsgn::filters::StrandCurvatureByLevels
• concavity_direction_ : protocols::fldsgn::filters::StrandCurvatureByLevels
• concavity_reference_residue() : protocols::fldsgn::filters::StrandCurvatureByLevels
• concavity_reference_residue_ : protocols::fldsgn::filters::StrandCurvatureByLevels
• ConcurrencyTest() : protocols::features::helixAssembly::ConcurrencyTest
• condist_ : protocols::fldsgn::NcontactsCalculator
• condition_ : protocols::protein_interface_design::movers::LoopOver
• conditional_erase() : core::pose::PDBPoseMap
• conditionally_add_edge() : core::scoring::ContextGraph , core::scoring::TenANeighborGraph , core::scoring::TwelveANeighborGraph
• cone_angle_cos_ : protocols::scoring::methods::pcs::GridSearchIterator , protocols::scoring::methods::pcsTs1::GridSearchIterator_Ts1 , protocols::scoring::methods::pcsTs2::GridSearchIterator_Ts2 , protocols::scoring::methods::pcsTs3::GridSearchIterator_Ts3 , protocols::scoring::methods::pcsTs4::GridSearchIterator_Ts4
• cone_distance_cutoff_ : core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyEnergy
• cone_distance_cutoff_sq_ : core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid
• cone_dotproduct_cutoff_ : core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyEnergy , core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid
• conf_ : core::environment::DofPassport , core::pose::PDBInfo , protocols::ligand_docking::ga_ligand_dock::GriddedAtomTreeMultifunc
• conf_event_link_ : protocols::boinc::BoincCurrentPoseObserver
• conf_num_ : protocols::docking::DockingEnsemble
• conf_size() : protocols::docking::DockingEnsemble
• conf_size_ : protocols::docking::DockingEnsemble
• confidence() : core::fragment::SecondaryStructure , protocols::filters::StochasticFilter
• confidence_ : core::fragment::SecondaryStructure , protocols::filters::StochasticFilter
• config : core::scoring::APBSWrapper , protocols::indexed_structure_store::DirectSegmentLookup
• Config : protocols::indexed_structure_store::DirectSegmentLookup
• config : protocols::indexed_structure_store::SegmentSequenceProfile
• Config : protocols::indexed_structure_store::SegmentSequenceProfile
• config_file_ : protocols::topology_broker::TemplateFragmentClaimer
• config_filename_ : core::scoring::PoissonBoltzmannPotential
• configure() : protocols::abinitio::abscript::RigidChunkCM
• configure_from_filter_tag() : protocols::cyclic_peptide::PeptideInternalHbondsMetric
• configure_from_options_system() : core::scoring::methods::DNA_DihedralEnergy
• configure_hbond_options() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph
• configure_master_mover() : protocols::rna::movers::ERRASER2Protocol
• configure_new_scorefunction() : protocols::optimize_weights::IterativeOptEDriver
• configure_rotameric_single_residue_dunbrack_library() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser
• configure_score_fxn() : protocols::coupled_moves::CoupledMovesProtocol
• configure_voxel_grid() : core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyEnergy
• confine_to_user_defined_helices() : protocols::helical_bundle_predict::HBPHelixAssignments
• confine_to_user_defined_helices_ : protocols::helical_bundle_predict::HBPHelixAssignments
• confirm_sequence() : protocols::forge::remodel::RemodelMover
• Conformation : core::chemical::ICoorAtomID , core::conformation::Conformation , core::conformation::signals::ConnectionEvent
• conformation : core::conformation::signals::ConnectionEvent
• Conformation : core::conformation::signals::GeneralEvent
• conformation : core::conformation::signals::GeneralEvent
• Conformation : core::pose::Pose
• conformation() : core::pose::Pose
• Conformation : core::scoring::constraints::Constraints , core::scoring::constraints::SequenceProfileConstraint , core::scoring::func::FourPointsFunc , core::scoring::func::XYZ_Func , protocols::constraints_additional::SequenceCoupling1BDConstraint , protocols::constraints_additional::SequenceCouplingConstraint , protocols::environment::EnvClaimBroker , protocols::environment::Environment
• conformation : protocols::network::UIObserver
• conformation_ : core::pose::Pose , core::scoring::func::ConformationXYZ , protocols::environment::DofUnlock
• conformation_energy() : core::scoring::constraints::Constraints
• conformation_event_link_ : protocols::moves::PyMOLObserver , protocols::network::UIObserver
• conformation_obs_hub_ : core::pose::Pose
• conformation_observer : protocols::moves::PyMOLObserver
• conformation_pt_ : core::scoring::constraints::ConstraintSet
• conformation_ptr() : core::pose::Pose
• conformation_size : core::conformation::signals::LengthEvent
• ConformationAP : protocols::environment::Environment
• ConformationCOP : core::pose::Pose , protocols::environment::EnvClaimBroker , protocols::environment::Environment
• ConformationEvent : core::pose::Pose , core::pose::signals::ConformationEvent , protocols::boinc::BoincCurrentPoseObserver
• conformationEvent() : protocols::moves::PyMOLObserver , protocols::network::UIObserver
• ConformationKinWriter() : core::conformation::ConformationKinWriter
• ConformationOP : core::pose::Pose , protocols::environment::EnvClaimBroker , protocols::environment::Environment
• conformations_for_flexible_segments_ : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• ConformationXYZ() : core::scoring::func::ConformationXYZ
• conformer() : core::scoring::nmr::NMRDummySpinlabelAtom
• conformer_ : core::scoring::nmr::NMRDummySpinlabelAtom
• conformer_bins : core::chemical::carbohydrates::LinkageConformerData
• CONFORMER_FILTER : core::scoring::nmr::NMRSpinlabel
• conformer_found() : protocols::carbohydrates::LinkageConformerMover
• conformer_found_ : protocols::carbohydrates::LinkageConformerMover
• conformer_group_for_conformer_ : protocols::match::downstream::LigandConformerBuilder
• conformer_group_indices_ : protocols::match::downstream::LigandConformerBuilder
• conformer_switch_probability_ : protocols::sewing::movers::AssemblyMover
• conformer_table_ : core::scoring::nmr::NMRDummySpinlabelEnsemble
• Conformers : protocols::sparta::PDB
• conformers_ : core::chemical::rings::RingConformerManager
• conformers_for_ring_size_and_type() : core::chemical::rings::RingConformerManager
• ConformerSwitchMover() : protocols::docking::ConformerSwitchMover
• conjug_ : core::chemical::Bond
• conjugability() : core::chemical::Bond
• conjugated_ : core::chemical::gasteiger::GasteigerAtomTypeData
• conn_dat() : core::scoring::etable::etrie::CountPairDataGeneric
• conn_dist() : 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
• conn_id_ : core::chemical::ResConnID
• connect() : core::scoring::mhc_epitope_energy::MHCEpitopePredictorExternal , protocols::denovo_design::connection::ConnectionArchitect , protocols::pockets::SmallMol
• connect_atom() : core::conformation::Residue
• connect_atom_ : core::chemical::AddConnect
• connect_atoms() : core::chemical::ResidueTypeFinder
• connect_atoms_ : core::chemical::ResidueTypeFinder
• connect_from_ : protocols::protein_interface_design::movers::SetAtomTree
• connect_info_cutoff() : core::io::StructFileRepOptions
• connect_info_cutoff_ : core::io::StructFileRepOptions
• connect_map() : core::conformation::Residue
• connect_map_ : core::conformation::Residue
• connect_map_size() : core::conformation::Residue
• connect_segments() : protocols::denovo_design::components::StructureData
• connect_to_ : protocols::protein_interface_design::movers::SetAtomTree
• ConnectChainsMover() : protocols::pose_length_moves::ConnectChainsMover
• connected() : core::kinematics::FoldTree , protocols::pockets::SmallMol
• connected_by_twobonds() : core::scoring::methods::GoapRsdType
• connected_by_twobonds_ : core::scoring::methods::GoapRsdType
• connected_components() : protocols::match::HitNeighborFinder
• connected_indices : core::io::AtomInformation
• connected_movable_groups() : protocols::denovo_design::connection::AreConnectablePredicate
• connected_orders : core::io::AtomInformation
• connected_residue_at_lower() : core::conformation::Residue
• connected_residue_at_resconn() : core::conformation::Residue
• connected_residue_at_upper() : core::conformation::Residue
• connected_resonance_ids() : protocols::noesy_assign::Resonance
• connected_resonance_ids_ : protocols::noesy_assign::Resonance
• connected_resonance_ptrs_ : protocols::noesy_assign::Resonance
• connected_resonances() : protocols::noesy_assign::Resonance
• connected_segments() : protocols::denovo_design::components::StructureData
• connection : core::conformation::carbohydrates::GlycanNode
• connection_atom_sets_ : core::scoring::mm::MMBondAngleResidueTypeParam
• connection_distance() : core::conformation::Residue
• connection_distance_ : core::scoring::etable::etrie::CountPairData_1_1
• connection_distances_ : core::scoring::etable::etrie::CountPairData_1_2 , core::scoring::etable::etrie::CountPairData_1_3
• connection_exists_to_residue() : core::scoring::trie::RotamerTrieBase
• connection_gaps_ : core::scoring::etable::etrie::TrieCountPairGeneric
• connection_id_ : protocols::ligand_docking::AddHydrogen
• connection_id_for_residue() : core::scoring::trie::RotamerTrieBase
• connection_incomplete() : core::conformation::Residue
• connection_index() : core::scoring::mm::MMBondAngleResidueTypeParam
• connection_index_ : core::scoring::mm::MMBondAngleResidueTypeParam
• connection_obs_hub_ : core::conformation::Conformation
• connection_pair() : core::scoring::mm::MMBondAngleResidueTypeParam
• connection_theta0() : core::scoring::mm::MMBondAngleResidueTypeParam
• connection_theta0_ : core::scoring::mm::MMBondAngleResidueTypeParam
• connection_use_theta0() : core::scoring::mm::MMBondAngleResidueTypeParam
• connection_use_theta0_ : core::scoring::mm::MMBondAngleResidueTypeParam
• ConnectionArchitect() : protocols::denovo_design::connection::ConnectionArchitect
• ConnectionArchitectCOPs : protocols::denovo_design::movers::BuildDeNovoBackboneMover
• ConnectionEvent : core::conformation::Conformation , core::conformation::signals::ConnectionEvent
• ConnectionPerturber() : protocols::denovo_design::components::ConnectionPerturber
• connections() : core::import_pose::RNA_BasePairHandler
• connections_ : protocols::denovo_design::architects::CompoundArchitect
• connections_ct_naming_func() : protocols::denovo_design::movers::BuildDeNovoBackboneMover
• connections_match() : core::conformation::Residue
• connections_to_residue() : core::conformation::Residue
• connections_to_residues_ : core::conformation::Residue
• connectivity_index() : protocols::toolbox::ResidueNetwork
• ConnectRight() : protocols::forge::build::ConnectRight
• ConnectSulfurAndMakeVirtualProton() : core::chemical::ConnectSulfurAndMakeVirtualProton
• connid() : core::chemical::ResConnID
• connid_for_entry_connpoint() : core::scoring::trie::CPDataCorrespondence
• cons_design_data_source_ : protocols::antibody::task_operations::AddCDRProfilesOperation
• cons_task_ : protocols::antibody::task_operations::AddCDRProfilesOperation
• consensus_residues : core::enzymes::EnzymeData
• consensus_sequence : core::enzymes::EnzymeData
• ConsensusDesignMover() : protocols::calc_taskop_movers::ConsensusDesignMover
• ConsensusLoopDatabase() : protocols::denovo_design::task_operations::ConsensusLoopDatabase
• ConsensusLoopDesignOperation() : protocols::denovo_design::task_operations::ConsensusLoopDesignOperation
• conservation_ : core::pose::datacache::PositionConservedResiduesStore
• conservation_cutoff_ : protocols::task_operations::RestrictConservedLowDdgOperation
• conservation_cutoff_aligned_segments() : protocols::task_operations::SeqprofConsensusOperation
• conservation_cutoff_aligned_segments_ : protocols::task_operations::SeqprofConsensusOperation
• conservation_cutoff_protein_interface_design() : protocols::task_operations::SeqprofConsensusOperation
• conservation_cutoff_protein_interface_design_ : protocols::task_operations::SeqprofConsensusOperation
• ConservationMap : core::pose::datacache::PositionConservedResiduesStore
• ConservativeDesignOperation() : protocols::task_operations::ConservativeDesignOperation
• ConservativeDesignOperationCreator() : protocols::task_operations::ConservativeDesignOperationCreator
• conserve_foldtree_ : protocols::protein_interface_design::movers::DockAndRetrieveSidechains
• conserved_mutations_ : protocols::task_operations::ConservativeDesignOperation
• conserved_pos_taskop_ : protocols::calc_taskop_filters::ConservedPosMutationFilter
• ConservedPosMutationFilter() : protocols::calc_taskop_filters::ConservedPosMutationFilter
• consider_already_bonded() : protocols::cyclic_peptide::TryDisulfPermutations
• consider_already_bonded_ : protocols::cyclic_peptide::TryDisulfPermutations
• consider_alternate_state() : core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::NPDHBondNode< V, E, G >
• consider_alternate_state_step1() : core::pack::interaction_graph::NPDHBondBackgroundEdge< V, E, G > , core::pack::interaction_graph::NPDHBondEdge< V, E, G >
• consider_alternate_state_step2() : core::pack::interaction_graph::NPDHBondBackgroundEdge< V, E, G > , core::pack::interaction_graph::NPDHBondEdge< V, E, G >
• consider_backbone_move() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph , protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph
• consider_bbmove_w_state_substitution() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph , protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph
• consider_mainchain_only() : protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter , protocols::hbnet::UnsatSelector
• consider_mainchain_only_ : protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter , protocols::hbnet::UnsatSelector
• consider_substitution() : core::pack::interaction_graph::AnnealableGraphBase , core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::MultiplexedAnnealableGraph , core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > , core::pack::interaction_graph::NPDHBSimpleInteractionGraph , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::ResidueArrayAnnealingEvaluator , core::pack::interaction_graph::SimpleInteractionGraph , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistInteractionGraph , protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph
• consider_topN_frags_ : protocols::simple_moves::StructProfileMover
• considered_energy_ : core::pack::interaction_graph::ResidueArrayAnnealingEvaluator
• considered_node_ : core::pack::interaction_graph::ResidueArrayAnnealingEvaluator
• considered_scores_ : core::scoring::mhc_epitope_energy::ScoreCache
• considered_start_ : core::scoring::mhc_epitope_energy::ScoreCache
• considered_state_ : core::pack::interaction_graph::ResidueArrayAnnealingEvaluator
• considered_stop_ : core::scoring::mhc_epitope_energy::ScoreCache
• considered_total_ : core::scoring::mhc_epitope_energy::MHCEpitopeEnergy
• considering_alternate_state() : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode
• consolidate_matches() : protocols::match::MatcherTask
• consolidate_matches_ : protocols::match::MatcherTask
• const_data_cache() : core::pose::Pose
• const_data_cache_ : protocols::jd3::InnerLarvalJob
• const_data_map() : protocols::jd3::InnerLarvalJob
• const_decoy_iterator : protocols::jd2::archive::ArchiveBase
• const_factory_iterator : protocols::task_operations::StoreCompoundTaskMover
• const_full_to_sub() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• const_iterator : core::conformation::Conformation , core::environment::DofPassport , core::io::raw_data::RawFileData::const_iterator , core::io::raw_data::RawFileData::iterator , core::io::silent::SilentFileData::const_iterator , core::io::silent::SilentFileData::iterator , core::kinematics::FoldTree , core::optimization::MinimizerMap , core::optimization::symmetry::SymMinimizerMap , core::pack::interaction_graph::MultiplexedAnnealableGraph , core::pack::task::TaskFactory , core::pose::Pose , core::scoring::constraints::Constraints , core::scoring::constraints::ResidueConstraints , core::scoring::dssp::StrandPairingSet , core::scoring::EMapVector , protocols::abinitio::abscript::ResidueChunkSelection , protocols::abinitio::PairingStatistics , protocols::abinitio::Templates , protocols::constraint_generator::ConstraintsMap , protocols::filters::CompoundFilter , protocols::hotspot_hashing::HotspotStubSet , protocols::jumping::JumpSelector , protocols::jumping::JumpSetup , protocols::jumping::ResiduePairJumpSetup , protocols::legacy_sewing::coord_equal_to , protocols::loops::Loops , protocols::mean_field::jagged_array< T, A > , protocols::noesy_assign::CrossPeak , protocols::noesy_assign::CrossPeakList , protocols::noesy_assign::MethylNames , protocols::noesy_assign::ResonanceList , protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::rosetta_scripts::ParsedProtocol , protocols::sewing::hashing::coord_equal_to , protocols::splice::ResidueBBDofs , protocols::topology_broker::TopologyBroker , protocols::wum::SilentStructStore , protocols::wum::WorkUnitManager , protocols::wum::WorkUnitQueue
• const_ligands_ : protocols::sewing::data_storage::SmartAssembly
• const_my_group() : core::scoring::MultipoleElecResidueInfo
• const_neighbor_iterator_begin() : core::scoring::constraints::CstEnergyContainer , core::scoring::DenseEnergyContainer , core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer , core::scoring::LREnergyContainer , core::scoring::OneToAllEnergyContainer , core::scoring::PolymerBondedEnergyContainer
• const_neighbor_iterator_end() : core::scoring::constraints::CstEnergyContainer , core::scoring::DenseEnergyContainer , core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer , core::scoring::LREnergyContainer , core::scoring::OneToAllEnergyContainer , core::scoring::PolymerBondedEnergyContainer
• const_out_of_bounds_func() : core::scoring::aa_composition_energy::AACompositionEnergySetup , core::scoring::netcharge_energy::NetChargeEnergySetup
• const_pdb_segments() : protocols::sewing::data_storage::SmartAssembly , protocols::sewing::hashing::AlignmentGenerator , protocols::sewing::hashing::BasisMapGenerator , protocols::sewing::hashing::EdgeMapGenerator , protocols::sewing::hashing::Hasher
• const_pointer : protocols::mean_field::jagged_array< T, A >
• const_pose_apply() : protocols::features::InterfaceDdGMover
• const_reference : core::id::AtomID_Map< T > , core::id::DOF_ID_Map< T > , core::id::NamedAtomID_Map< T > , protocols::mean_field::jagged_array< T, A >
• const_reference_segment_ : protocols::sewing::data_storage::SmartSegment
• const_residue_() : core::conformation::Conformation
• const_residues() : core::conformation::Conformation
• const_reverse_iterator : protocols::mean_field::jagged_array< T, A >
• CONST_SCORE : protocols::frag_picker::scores::ConstScore
• const_states() : protocols::multistate_design::MultiStateFitnessFunction
• const_sub_to_full() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• const_task_iterator : protocols::task_operations::StoreCompoundTaskMover
• const_upper_neighbor_iterator_begin() : core::scoring::constraints::CstEnergyContainer , core::scoring::DenseEnergyContainer , core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer , core::scoring::LREnergyContainer , core::scoring::OneToAllEnergyContainer , core::scoring::PolymerBondedEnergyContainer
• const_upper_neighbor_iterator_end() : core::scoring::constraints::CstEnergyContainer , core::scoring::DenseEnergyContainer , core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer , core::scoring::LREnergyContainer , core::scoring::OneToAllEnergyContainer , core::scoring::PolymerBondedEnergyContainer
• ConstAbinitioMoverWeight() : protocols::topology_broker::weights::ConstAbinitioMoverWeight
• constant_cache_ : core::pose::Pose
• ConstantConstraint() : core::scoring::constraints::ConstantConstraint
• ConstantFunc() : core::scoring::func::ConstantFunc
• ConstantLengthFragSet() : core::fragment::ConstantLengthFragSet , core::fragment::ConstantLengthFragSetIterator_
• ConstantLengthFragSetIterator_() : core::fragment::ConstantLengthFragSetIterator_
• ConstantLengthFragSetOP : protocols::forge::components::VarLengthBuild
• ConstantScoreBase() : protocols::qsar::scoring_grid::ConstantScoreBase
• ConstDaemonList : protocols::pack_daemon::DaemonSet
• ConstDaemonListIter : protocols::pack_daemon::DaemonSet
• ConstDataMap : core::pose::Pose
• ConstDataMapOP : core::pose::Pose
• ConstFrameIterator() : core::fragment::ConstFrameIterator , core::fragment::FrameIteratorWorker_
• ConstIterator : protocols::mean_field::jagged_array< T, A >
• ConstPattern() : protocols::hotspot_hashing::ConstPattern
• ConstPointer : protocols::mean_field::jagged_array< T, A >
• constrain_ : protocols::ncbb::SecStructFinder , protocols::ncbb::SecStructMinimizeMover
• constrain_bb_angle_ : protocols::fldsgn::SheetConstraintGenerator
• constrain_bb_cacb_dihedral_ : protocols::fldsgn::SheetConstraintGenerator
• constrain_bb_dihedral_ : protocols::fldsgn::SheetConstraintGenerator
• constrain_ca_ca_dist_ : protocols::fldsgn::SheetConstraintGenerator
• constrain_coords() : protocols::relax::RelaxProtocolBase
• constrain_coords_ : protocols::relax::RelaxProtocolBase
• constrain_linker() : protocols::cyclic_peptide::CrosslinkerMover
• constrain_linker_ : protocols::cyclic_peptide::CrosslinkerMover
• constrain_phosphate() : protocols::rna::movers::ErraserMinimizerMover
• constrain_phosphate_ : protocols::rna::movers::ErraserMinimizerMover
• constrain_relax_segments() : protocols::relax::RelaxProtocolBase
• constrain_relax_segments_ : protocols::relax::RelaxProtocolBase
• constrain_relax_to_native_coords() : protocols::relax::RelaxProtocolBase
• constrain_relax_to_native_coords_ : protocols::relax::RelaxProtocolBase
• constrain_relax_to_start_coords() : protocols::relax::RelaxProtocolBase
• constrain_relax_to_start_coords_ : protocols::relax::RelaxProtocolBase
• constrain_to_antigen_chains() : protocols::antibody::constraints::ParatopeSiteConstraintMover
• constrain_to_closest_ : protocols::constraint_generator::MetalContactsConstraintGenerator
• constrain_to_epitope_residues() : protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover
• constrain_to_ideal() : protocols::rna::movers::RNAIdealizeMover
• constrain_to_paratope_cdrs() : protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover , protocols::antibody::constraints::ParatopeSiteConstraintMover
• constrain_to_paratope_residues() : protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover , protocols::antibody::constraints::ParatopeSiteConstraintMover
• constrain_to_reference() : protocols::relax::RangeRelaxMover
• constrain_vlvh_qq() : protocols::antibody::snugdock::SnugDockProtocol
• constrain_vlvh_qq_ : protocols::antibody::AntibodyModelerProtocol , protocols::antibody::snugdock::SnugDockProtocol
• constrainable_atoms_ : protocols::frag_picker::scores::AtomBasedConstraintsScore
• constrained_lig_atoms() : protocols::enzdes::EnzdesConstraintReporter
• constrained_lig_atoms_ : protocols::enzdes::EnzdesConstraintReporter
• constrained_nonligand_atoms() : protocols::enzdes::EnzdesConstraintReporter
• constrained_nonligand_atoms_ : protocols::enzdes::EnzdesConstraintReporter
• ConstrainHBondNetwork() : protocols::hbnet::ConstrainHBondNetwork
• Constraint() : core::scoring::constraints::Constraint
• constraint() : protocols::aa_composition::AddCompositionConstraintMover , protocols::aa_composition::AddMHCEpitopeConstraintMover , protocols::aa_composition::AddNetChargeConstraintMover
• constraint_ : protocols::aa_composition::AddCompositionConstraintMover , protocols::aa_composition::AddMHCEpitopeConstraintMover , protocols::aa_composition::AddNetChargeConstraintMover
• constraint_definition : protocols::forge::remodel::LineObject
• constraint_energy() : protocols::enzdes::LigInterfaceEnergyFilter
• constraint_file() : protocols::constraint_movers::ConstraintSetMover
• constraint_file_ : core::import_pose::FullModelPoseBuilder , protocols::fldsgn::BluePrintBDR
• constraint_func_ : protocols::forge::constraints::InverseRotamersRCG
• CONSTRAINT_GENERATOR : core::pose::datacache::CacheableDataType
• constraint_generator_name() : protocols::denovo_design::constraints::FileConstraintGeneratorCreator , protocols::fldsgn::SheetConstraintGeneratorCreator
• constraint_generator_xml_schema_group_name() : protocols::constraint_generator::ConstraintGeneratorFactory
• constraint_ref_pose_ : protocols::topology_broker::ConstraintClaimer
• constraint_reporter_ : protocols::enzdes::PredesignPerturbMover
• constraint_set() : core::pose::Pose , protocols::constraint_movers::ConstraintSetMover
• constraint_set_ : core::pose::Pose , core::scoring::constraints::CstEnergyContainer , protocols::rna::denovo::RNA_FragmentMonteCarlo
• constraint_set_high_res_ : protocols::constraint_movers::ConstraintSetMover
• constraint_set_low_res_ : protocols::constraint_movers::ConstraintSetMover
• constraint_setup() : protocols::rna::denovo::movers::RNA_DeNovoProtocolMover
• constraint_threshold_ : protocols::abinitio::FoldConstraints
• constraint_weight_ : protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints , protocols::simple_moves::DisulfideInsertionMover
• constraint_weights_ : protocols::enzdes::EnzdesBaseProtocol
• ConstraintClaimer() : protocols::topology_broker::ConstraintClaimer
• ConstraintCOPs : protocols::constraint_generator::ConstraintsManager , protocols::constraint_generator::ConstraintsMap
• ConstraintCreator() : core::scoring::constraints::ConstraintCreator
• ConstraintCreatorMap : core::scoring::constraints::ConstraintFactory
• ConstraintEdge() : core::scoring::constraints::ConstraintEdge
• ConstraintedOptimizationWeightFunc() : protocols::optimize_weights::ConstraintedOptimizationWeightFunc
• ConstraintEvaluator() : protocols::constraints_additional::ConstraintEvaluator
• ConstraintEvaluatorCreator() : protocols::constraints_additional::ConstraintEvaluatorCreator
• ConstraintEvaluatorWrapper() : protocols::topology_broker::ConstraintEvaluatorWrapper
• ConstraintEvaluatorWrapperCreator() : protocols::topology_broker::ConstraintEvaluatorWrapperCreator
• ConstraintFactory() : core::scoring::constraints::ConstraintFactory
• ConstraintFragmentSampler() : protocols::abinitio::ConstraintFragmentSampler
• ConstraintFulfilmentFilter() : protocols::fold_from_loops::filters::ConstraintFulfilmentFilter
• ConstraintGenerator() : protocols::constraint_generator::ConstraintGenerator
• ConstraintGeneratorCOP : protocols::denovo_design::movers::BuildDeNovoBackboneMover
• ConstraintGeneratorCOPs : protocols::constraint_filters::ConstraintScoreFilter , protocols::denovo_design::movers::BuildDeNovoBackboneMover
• ConstraintGeneratorFactory() : protocols::constraint_generator::ConstraintGeneratorFactory
• ConstraintGeneratorLoader() : protocols::parser::ConstraintGeneratorLoader
• ConstraintGeneratorOP : protocols::denovo_design::movers::BuildDeNovoBackboneMover
• ConstraintGeneratorRegistrator() : protocols::constraint_generator::ConstraintGeneratorRegistrator< T >
• ConstraintGraph() : core::scoring::constraints::ConstraintGraph
• ConstraintInfo() : protocols::ligand_docking::ga_ligand_dock::ConstraintInfo
• ConstraintIO() : core::scoring::constraints::ConstraintIO
• ConstraintNode() : core::scoring::constraints::ConstraintNode
• ConstrainToIdealMover() : protocols::simple_moves::ConstrainToIdealMover
• ConstraintOP : core::scoring::constraints::SequenceProfileConstraint , protocols::constraints_additional::SequenceCoupling1BDConstraint , protocols::constraints_additional::SequenceCouplingConstraint
• ConstraintPreparer() : protocols::abinitio::abscript::ConstraintPreparer
• ConstraintRegistrator() : core::scoring::constraints::ConstraintRegistrator< T >
• ConstraintResidueSelector() : protocols::fold_from_loops::selectors::ConstraintResidueSelector
• constraints() : core::scoring::constraints::BasePairConstraint , core::scoring::constraints::Constraints
• Constraints() : core::scoring::constraints::Constraints
• constraints() : core::scoring::constraints::CstMinimizationData , protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints , protocols::abinitio::Template , protocols::forge::remodel::RemodelConstraintGenerator , protocols::hotspot_hashing::HotspotStubSet , protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• constraints_ : core::scoring::constraints::BasePairConstraint , core::scoring::constraints::Constraints , core::scoring::constraints::CstMinimizationData , protocols::abinitio::abscript::AbscriptStageMover , protocols::abinitio::abscript::ConstraintPreparer , protocols::abinitio::ComputeTotalDistCst , protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints , protocols::abinitio::ShowViolation , protocols::constraint_filters::ConstraintScoreCutoffFilter , protocols::constraints_additional::ConstraintEvaluator , protocols::hotspot_hashing::HotspotStubSet , protocols::ligand_docking::LigandDockMain , protocols::ligand_docking::MinimizeBackbone , protocols::noesy_assign::DistanceScoreMover , protocols::noesy_assign::StructureDependentPeakCalibrator , protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo , protocols::topology_broker::ConstraintClaimer , protocols::topology_broker::CoordConstraintClaimer
• constraints_combine_ratio_ : protocols::constraints_additional::ConstraintEvaluator
• constraints_energy_filter_multiplier() : protocols::cyclic_peptide::CrosslinkerMover
• constraints_energy_filter_multiplier_ : protocols::cyclic_peptide::CrosslinkerMover
• constraints_file_contents_ : protocols::energy_based_clustering::EnergyBasedClusteringProtocol
• constraints_from_link_records() : core::io::StructFileRepOptions
• constraints_from_link_records_ : core::io::StructFileRepOptions
• constraints_NtoC_ : protocols::fldsgn::BluePrintBDR , protocols::flxbb::FlxbbDesign
• constraints_only() : protocols::idealize::IdealizeMover
• constraints_only_ : protocols::idealize::IdealizeMover , protocols::simple_moves::SetupMetalsMover
• constraints_ready_ : core::scoring::dna::DNATorsionEnergy
• constraints_sheet_ : protocols::fldsgn::BluePrintBDR , protocols::flxbb::FlxbbDesign
• ConstraintScoreCutoffFilter() : protocols::constraint_filters::ConstraintScoreCutoffFilter
• ConstraintScoreFilter() : protocols::constraint_filters::ConstraintScoreFilter
• ConstraintsEnergy() : core::scoring::constraints::ConstraintsEnergy
• ConstraintSet() : core::scoring::constraints::ConstraintSet , protocols::aa_composition::AddCompositionConstraintMover , protocols::aa_composition::AddMHCEpitopeConstraintMover , protocols::aa_composition::AddNetChargeConstraintMover , protocols::aa_composition::ClearCompositionConstraintsMover , protocols::comparative_modeling::IgnoreSubsetConstraintSet , protocols::constraint_movers::ConstraintSetMover , protocols::forge::remodel::RemodelGlobalFrame , protocols::forge::remodel::RemodelLigandHandler
• ConstraintSetCOP : core::pose::Pose , protocols::aa_composition::AddCompositionConstraintMover , protocols::aa_composition::AddMHCEpitopeConstraintMover , protocols::aa_composition::AddNetChargeConstraintMover , protocols::aa_composition::ClearCompositionConstraintsMover , protocols::constraint_movers::ConstraintSetMover
• ConstraintSetMover() : protocols::constraint_movers::ConstraintSetMover
• ConstraintSetOP : core::pose::Pose , protocols::aa_composition::AddCompositionConstraintMover , protocols::aa_composition::AddMHCEpitopeConstraintMover , protocols::aa_composition::AddNetChargeConstraintMover , protocols::aa_composition::ClearCompositionConstraintsMover , protocols::comparative_modeling::IgnoreSubsetConstraintSet , protocols::constraint_movers::ConstraintSetMover , protocols::constraints_additional::MaxSeqSepConstraintSet , protocols::forge::remodel::RemodelGlobalFrame , protocols::forge::remodel::RemodelLigandHandler
• ConstraintSetScore() : protocols::sic_dock::ConstraintSetScore
• ConstraintsManager() : protocols::constraint_generator::ConstraintsManager
• ConstraintsMap() : protocols::constraint_generator::ConstraintsMap
• ConstReference : core::id::AtomID_Map< T > , core::id::DOF_ID_Map< T > , core::id::NamedAtomID_Map< T > , protocols::mean_field::jagged_array< T, A >
• ConstReverseIterator : protocols::mean_field::jagged_array< T, A >
• construct_and_dump_outpose() : protocols::enzdes::PoseFoundResiduesCombination
• construct_aqueous_pore() : protocols::membrane::AqueousPoreFinder
• construct_from_pose() : core::scoring::power_diagram::PowerDiagram
• construct_job_result_input_list() : protocols::jd3::job_distributors::VanillaJobDistributor
• construct_one_body_energy_work_vector() : core::pack::rotamer_set::RotamerSets
• construct_rotamer_trie() : core::scoring::trie::RotamerTrie< AT, CPDATA >
• construction_time_ : core::simple_metrics::metrics::TimingProfileMetric
• ConstScore() : protocols::frag_picker::scores::ConstScore
• Contact() : protocols::contact_map::Contact
• contact() : protocols::dna::DnaNeighbor
• Contact() : protocols::frag_picker::Contact
• contact_ : protocols::dna::DnaNeighbor
• contact_atom_name : protocols::sewing::data_storage::ContactDescription
• contact_atom_num : protocols::sewing::data_storage::ContactDescription
• contact_buried_problematic_res() : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• contact_buried_problematic_res_ : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• contact_dis : protocols::sic_dock::CBScoreVisitor
• contact_dis_ : protocols::sic_dock::CBScore
• contact_dist() : protocols::cryst::MakeLatticeMover , protocols::cryst::MakeLayerMover , protocols::matdes::InterfacePackingFilter
• contact_dist2_ : protocols::fldsgn::filters::InterlockingAromaFilter
• contact_dist_ : protocols::cryst::DockLatticeMover , protocols::cryst::MakeLatticeMover , protocols::cryst::MakeLayerMover , protocols::matdes::BuildingBlockInterfaceOperation , protocols::matdes::ExtractSubposeMover , protocols::matdes::InterfacePackingFilter
• contact_dist_cutoff_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• contact_distance() : protocols::fldsgn::filters::InterlockingAromaFilter , protocols::fldsgn::NcontactsCalculator
• contact_distance_cutoff_ : protocols::sewing::requirements::KeepLigandContactsRequirement
• contact_label() : protocols::fold_from_loops::utils::Nub
• contact_list() : protocols::scoring::Interface
• contact_list_ : protocols::scoring::Interface
• contact_order() : core::scoring::dssp::StrandPairing , protocols::abinitio::PairingStatEntry
• contact_order_score() : protocols::sewing::scoring::SegmentContactOrderScorer
• contact_resnum : protocols::sewing::data_storage::ContactDescription
• contact_resnum_string : protocols::sewing::data_storage::ContactDescription
• contact_resnum_string_ : protocols::constraint_generator::MetalContactsConstraintGenerator
• contact_resnums_string_ : protocols::simple_moves::SetupMetalsMover
• contact_selector_ : protocols::constraint_generator::MetalContactsConstraintGenerator , protocols::simple_moves::SetupMetalsMover
• contact_threshold_ : protocols::dna::DnaInterfaceFinder , protocols::dna::RestrictDesignToProteinDNAInterface
• contact_types_ : protocols::frag_picker::FragmentPicker
• ContactCounts() : protocols::frag_picker::ContactCounts
• ContactDescription() : protocols::sewing::data_storage::ContactDescription
• ContactMap() : protocols::contact_map::ContactMap
• ContactMapEvaluator() : protocols::simple_filters::ContactMapEvaluator
• ContactMapEvaluatorCreator() : protocols::simple_filters::ContactMapEvaluatorCreator
• ContactMolecularSurfaceCalculator() : core::scoring::sc::ContactMolecularSurfaceCalculator , protocols::simple_filters::ContactMolecularSurfaceFilter
• ContactMolecularSurfaceFilter() : protocols::simple_filters::ContactMolecularSurfaceFilter
• ContactOrderEnergy() : core::scoring::methods::ContactOrderEnergy
• ContactPartner() : protocols::contact_map::ContactPartner
• contacts : protocols::sic_dock::CorrectionVisitor , protocols::sic_dock::Rose
• contacts_ : protocols::contact_map::ContactMap , protocols::frag_picker::nonlocal::NonlocalPair
• contacts_between_ssElement_threshold_ : protocols::simple_filters::SSElementMotifContactFilter
• contacts_dist_cutoff_squared_ : protocols::frag_picker::FragmentPicker
• contacts_dist_cutoffs_squared_ : protocols::frag_picker::FragmentPicker
• contacts_min_seq_sep_ : protocols::frag_picker::FragmentPicker
• contacts_naive() : protocols::sic_dock::Rose
• contacts_remaining() : protocols::sewing::hashing::LigandBindingResPlacer
• contacts_to_make_ : protocols::sewing::hashing::LigandBindingResPlacer
• containing_cones_cutoff_ : core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyEnergy , core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid
• contains() : core::scoring::dssp::StrandPairing , core::scoring::hbonds::graph::AtomInfoSet , core::scoring::packstat::Circle , core::scoring::packstat::Octree2D , protocols::denovo_design::components::Segment , protocols::dna::DnaChains , protocols::forge::build::Interval
• contains_atom_type() : core::chemical::gasteiger::GasteigerAtomTypeSet , core::chemical::MMAtomTypeSet
• contains_bond_length() : core::chemical::IdealBondLengthSet
• contains_carbohydrate_residues() : core::conformation::Conformation
• contains_carbohydrate_residues_ : core::conformation::Conformation
• contains_catalytic_res() : protocols::enzdes::EnzdesFlexibleRegion
• contains_element_type() : core::chemical::ElementSet
• contains_position() : protocols::toolbox::match_enzdes_util::EnzConstraintIO , protocols::toolbox::match_enzdes_util::EnzCstTemplateResCache , protocols::toolbox::match_enzdes_util::EnzdesCstCache , protocols::toolbox::match_enzdes_util::EnzdesCstParamCache
• contains_seqpos() : core::fragment::Frame
• contents_ : protocols::checkpoint::FileBuffer
• contents_in_pose_store() : protocols::forge::remodel::RemodelAccumulator
• context_chain_selector() : protocols::fold_from_loops::NubInitioMover
• context_clash_hash_ : protocols::scoring::methods::TargetClashEnergy
• context_dependent_ : core::scoring::elec::FA_GrpElecEnergy
• context_derivative_empty() : core::scoring::FACTSPoseInfo
• context_derivative_empty_ : core::scoring::FACTSPoseInfo
• context_graph() : core::scoring::Energies
• context_graphs() : core::scoring::Energies
• context_graphs_ : core::scoring::Energies
• context_graphs_required_ : core::scoring::ScoreFunctionInfo
• context_label() : protocols::fold_from_loops::utils::Nub
• context_minstrength_ : core::scoring::elec::FA_GrpElecEnergy
• context_pdbname_ : protocols::protein_interface_design::filters::ClashWithTargetFilter
• context_pose_ : protocols::flexpack::OtherContextScoreFunction
• context_poses_ : protocols::optimize_weights::IterativeOptEDriver
• context_update_step() : protocols::md::MDBase
• context_update_step_ : protocols::md::MDBase
• ContextDependentGeometricSolEnergy() : core::scoring::geometric_solvation::ContextDependentGeometricSolEnergy
• ContextDependentLRTwoBodyEnergy() : core::scoring::methods::ContextDependentLRTwoBodyEnergy
• ContextDependentOneBodyEnergy() : core::scoring::methods::ContextDependentOneBodyEnergy
• ContextDependentTwoBodyEnergy() : core::scoring::methods::ContextDependentTwoBodyEnergy
• ContextGraph() : core::scoring::ContextGraph
• ContextIndependentGeometricSolEnergy() : core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy
• ContextIndependentLRTwoBodyEnergy() : core::scoring::methods::ContextIndependentLRTwoBodyEnergy
• ContextIndependentOneBodyEnergy() : core::scoring::methods::ContextIndependentOneBodyEnergy
• ContextIndependentTwoBodyEnergy() : core::scoring::methods::ContextIndependentTwoBodyEnergy
• contiguous_monomers() : core::conformation::symmetry::SymmetryInfo
• contiguous_monomers_ : core::conformation::symmetry::SymmetryInfo
• ContingentAcceptMover() : protocols::simple_moves::ContingentAcceptMover
• ContingentFilter() : protocols::filters::ContingentFilter
• continue_if_silent() : protocols::evolution::NucleotideMutation
• continue_if_silent_ : protocols::evolution::NucleotideMutation
• continue_slide() : protocols::symmetry::SymmetrySlider
• continue_until_none_missing() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• continue_until_none_missing_ : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• continuous() : core::scoring::methods::GoapEnergy
• continuous_ : core::scoring::methods::GoapEnergy
• continuous_sheets_ : protocols::loop_grower::FragmentExtension , protocols::loop_grower::LoopGrower
• continuous_weight_ : protocols::loop_grower::FragmentExtension , protocols::loop_grower::LoopGrower
• ContinuousAssembly() : protocols::legacy_sewing::ContinuousAssembly
• ContinuousRotamerSet() : core::pack::rotamer_set::ContinuousRotamerSet
• ContinuousRotamerSets() : core::pack::rotamer_set::ContinuousRotamerSets
• control_grid_param() : protocols::scoring::methods::pcs2::PcsGridSearchParameter , protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• controlling_chi_for_atom() : protocols::match::upstream::UpstreamResTypeGeometry
• controlling_chi_for_atom_ : protocols::match::upstream::UpstreamResTypeGeometry
• convention_ : core::scoring::nmr::NMRTensor
• conventional_chains() : core::pose::full_model_info::FullModelInfo , core::pose::full_model_info::FullModelParameters
• conventional_chains_ : core::pose::full_model_info::FullModelParameters
• conventional_numbering() : core::pose::full_model_info::FullModelInfo , core::pose::full_model_info::FullModelParameters
• conventional_numbering_ : core::pose::full_model_info::FullModelParameters
• conventional_segids() : core::pose::full_model_info::FullModelInfo , core::pose::full_model_info::FullModelParameters
• conventional_segids_ : core::pose::full_model_info::FullModelParameters
• conventional_to_full() : core::pose::full_model_info::FullModelParameters
• converge() : protocols::mean_field::MeanField
• converged() : protocols::optimize_weights::IterativeOptEDriver
• convergence_checks_ : protocols::moves::MonteCarlo
• convert_aa_to_index() : core::scoring::rna::RNP_LowResPairDistPotential
• convert_angle() : core::conformation::parametric::RealValuedParameter
• convert_cart_to_spherical_and_round() : protocols::pockets::NonPlaidFingerprint
• convert_charged_res_to_ala_ : protocols::simple_ddg::SSElementBisectddGFilter
• convert_energies_to_alt_rm() : protocols::mean_field::MeanField
• convert_FArray2D_to_vector0() : core::scoring::TMscore
• convert_GeomSampleInfo_to_FuncOP() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• convert_matrix_to_xyz() : protocols::hybridization::TMalign
• convert_nucleic_acid_residue_info_to_standard() : core::io::pose_from_sfr::PoseFromSFRBuilder
• convert_profile_to_probs() : core::sequence::SequenceProfile
• convert_protein_centroid() : core::import_pose::options::RNA_FragmentMonteCarloOptions
• convert_protein_centroid_ : core::import_pose::options::RNA_FragmentMonteCarloOptions
• convert_scores_to_probabilities() : protocols::task_operations::SeqprofConsensusOperation
• convert_scores_to_probabilities_ : protocols::task_operations::SeqprofConsensusOperation
• convert_silent_file_to_pose_data_list() : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• convert_spherical_list_to_cartesian_list() : protocols::pockets::NonPlaidFingerprint
• convert_string_to_computation_type() : core::scoring::nmr::pcs::PCSSingleSet , core::scoring::nmr::rdc::RDCMultiSet
• convert_string_to_conformer_filter_type() : core::scoring::nmr::NMRSpinlabel
• convert_string_to_residues() : core::select::residue_selector::SSElementSelector
• convert_to_centroid() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• convert_to_degrees_ : core::scoring::func::CircularSplineFunc
• convert_to_fasta() : core::io::external::PsiPredInterface
• convert_to_full_pose() : protocols::ligand_docking::Transform , protocols::ligand_docking::TransformEnsemble
• convert_to_parameter_values_at_res() : core::pose::full_model_info::FullModelParameters
• convert_to_res_lists_by_value() : core::pose::full_model_info::FullModelParameters
• convert_to_ResidueType() : core::chemical::sdf::MolFileIOMolecule
• convert_to_rotation_matrix() : protocols::stepwise::sampler::rigid_body::EulerAngles
• convert_to_torsion_crd() : protocols::normalmode::NormalMode
• convert_vector_to_xyz() : protocols::hybridization::TMalign
• convert_xyz_to_matrix() : protocols::hybridization::TMalign
• convert_xyz_to_vector() : protocols::hybridization::TMalign
• convert_xyz_v_to_vectors() : protocols::hybridization::TMalign
• convertPSERtoASP() : protocols::flexpep_docking::FlexPepDockingAbInitio
• convertPSERtoGLU() : protocols::flexpep_docking::FlexPepDockingAbInitio
• ConvertRealToVirtualMover() : protocols::simple_moves::ConvertRealToVirtualMover
• ConvertVirtualToRealMover() : protocols::simple_moves::ConvertVirtualToRealMover
• convex : core::scoring::sc::_RESULTS
• convolute_single_residue_ : protocols::electron_density::DockIntoDensityMover
• cool() : core::pack::annealer::MultiCoolAnnealer
• coor : core::scoring::sc::_DOT
• coor_const() : protocols::splice::Splice
• coor_const_ : protocols::splice::Splice
• coor_constraint_stack_ : protocols::protein_interface_design::movers::PlaceStubMover
• coor_cst_cutoff_ : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• coord() : core::pack::scmin::ResidueAtomTreeCollectionMomento , protocols::ligand_docking::ga_ligand_dock::ConstraintInfo , protocols::match::downstream::TargetRotamerCoords
• Coord : protocols::sparta::PDB_Entry
• coord1 : protocols::cluster::calibur::Clustering
• coord2 : protocols::cluster::calibur::Clustering
• coord2key() : protocols::canonical_sampling::HamiltonianExchange
• coord_atom_index : protocols::sewing::hashing::LigandCoordInfo
• coord_constrain_sidechains() : protocols::relax::RelaxProtocolBase
• coord_constrain_sidechains_ : protocols::relax::RelaxProtocolBase
• coord_cst_res_ : protocols::hybridization::HybridizeProtocol
• coord_cst_std_ : protocols::protein_interface_design::movers::PlaceStubMover
• coord_cst_weight_ : protocols::rna::denovo::movers::RNA_Minimizer
• coord_csts() : protocols::protein_interface_design::movers::CoordinateConstraintStack
• coord_csts_ : protocols::protein_interface_design::movers::CoordinateConstraintStack
• coord_dev() : protocols::constraint_movers::AddConstraintsToCurrentConformationMover
• coord_dev_ : protocols::constraint_movers::AddConstraintsToCurrentConformationMover
• coord_frame_ref() : core::scoring::MultipoleElecResidueInfo
• coord_frame_ref_ : core::scoring::MultipoleElecResidueInfo
• coord_res_name : protocols::sewing::hashing::LigandCoordInfo
• coord_sdev() : protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots
• coord_sdev_ : protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots , protocols::rna::denovo::movers::RNA_Minimizer
• coord_type() : core::scoring::MultipoleParameter
• coord_type_ : core::scoring::MultipoleParameter
• coordA : protocols::sparta::RingData
• CoordConstraintClaimer() : protocols::topology_broker::CoordConstraintClaimer
• coordfile_ : protocols::loop_grower::FragmentExtension , protocols::loop_grower::LoopGrower
• Coordinate : protocols::indexed_structure_store::search::StructureData , protocols::indexed_structure_store::search::StructurePairQuery , protocols::indexed_structure_store::search::StructureSingleQuery
• coordinate_buffer : protocols::indexed_structure_store::search::StructureData
• coordinate_cacher() : protocols::match::output::PDBWriter
• coordinate_cacher_ : protocols::match::output::PDBWriter , protocols::match::output::WriteKinemageOutputter
• coordinate_constraint_energy() : core::scoring::constraints::ConstraintEdge
• coordinate_constraint_energy_ : core::scoring::constraints::ConstraintEdge
• coordinate_constraint_weight() : protocols::idealize::IdealizeMover
• coordinate_constraint_weight_ : protocols::abinitio::LoopJumpFoldCst , protocols::idealize::IdealizeMover
• coordinate_constraint_weights_ : protocols::abinitio::LoopJumpFoldCst
• coordinate_constraints_during_minimize() : protocols::stepwise::modeler::options::StepWiseBasicModelerOptions
• coordinate_constraints_during_minimize_ : protocols::stepwise::modeler::options::StepWiseBasicModelerOptions
• coordinate_filter() : protocols::loop_grower::LoopGrower
• coordinate_for_nonchi_atom_in_ideal_frame() : protocols::match::upstream::UpstreamResTypeGeometry
• coordinate_in_D3_frame() : protocols::toolbox::match_enzdes_util::LigandConformer
• coordinate_in_global_frame() : protocols::toolbox::match_enzdes_util::LigandConformer
• coordinate_transform_from_target_site() : core::scoring::nmr::NMRDummySpinlabelEnsemble
• coordinate_transform_onto_target_site() : core::scoring::nmr::NMRDummySpinlabelEnsemble
• CoordinateConstraint() : core::scoring::constraints::CoordinateConstraint
• CoordinateConstraintCreator() : core::scoring::constraints::CoordinateConstraintCreator
• CoordinateConstraintGenerator() : protocols::constraint_generator::CoordinateConstraintGenerator
• CoordinateConstraintKC() : protocols::abinitio::CoordinateConstraintKC
• CoordinateConstraintStack() : protocols::protein_interface_design::movers::CoordinateConstraintStack
• CoordinateCst() : protocols::seeded_abinitio::CoordinateCst
• CoordinateMatrix : protocols::indexed_structure_store::search::StructureData , protocols::indexed_structure_store::search::StructurePairQuery , protocols::indexed_structure_store::search::StructureSingleQuery
• coordinates() : core::chemical::rotamers::StoredRotamerLibrarySpecification , protocols::pockets::SmallMol
• coordinates_ : core::chemical::rotamers::StoredRotamerLibrarySpecification
• coordinates_assigned_ : core::io::pose_from_sfr::PoseFromSFRBuilder
• coordinates_from_hit() : protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder
• coordinates_from_orientation() : protocols::toolbox::match_enzdes_util::LigandConformer
• coordinates_per_fragment() : protocols::indexed_structure_store::FragmentSpecification
• Coordinates_Tetrahedral_bondedto3atoms_helper() : core::chemical::orbitals::AssignOrbitals
• Coordinates_TriganolPlanar_bondedto1atom_helper() : core::chemical::orbitals::AssignOrbitals
• coords() : core::grid::CartGrid< T > , core::io::raw_data::DecoyStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RNA_SilentStruct
• Coords : core::io::StructFileRep
• coords() : core::pose::MiniPose , core::pose::UnrecognizedAtomRecord , protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD , protocols::toolbox::DecoySetEvaluation , protocols::toolbox::KClusterData
• coords_ : core::conformation::UltraLightResidue , core::fragment::BBTorsionSRFD , core::io::raw_data::DecoyStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RNA_SilentStruct , core::pack::scmin::ResidueAtomTreeCollectionMomento , core::pose::MiniPose , core::pose::UnrecognizedAtomRecord , core::scoring::nmr::VoxelGridPoint , core::sequence::Cell , protocols::canonical_sampling::mc_convergence_checks::DataBuffer , protocols::legacy_sewing::SewAtom , protocols::ligand_docking::ga_ligand_dock::ConstraintInfo , protocols::match::downstream::TargetRotamerCoords , protocols::match::output::UpstreamDownstreamCollisionFilter , protocols::nmr::pcs::AtomGridPoint , protocols::simple_moves::WaterRot , protocols::toolbox::DecoySetEvaluation
• coords_for_clash_checking_ : protocols::match::downstream::TargetRotamerCoords
• coords_receiving_buffer_ : protocols::canonical_sampling::mc_convergence_checks::DataBuffer
• coords_transfer_buffer_ : protocols::canonical_sampling::mc_convergence_checks::DataBuffer
• coords_vector() : core::conformation::UltraLightResidue
• coordTransformFromThreePoints() : protocols::rbsegment_relax::RBSegmentMover
• CoordVector : core::scoring::nmr::pre::PREMultiSet , protocols::evaluation::PCA
• COP : protocols::canonical_sampling::BiasEnergy::Histogram< T > , protocols::genetic_algorithm::Entity , protocols::genetic_algorithm::EntityRandomizer , protocols::genetic_algorithm::FitnessFunction , protocols::genetic_algorithm::PositionSpecificRandomizer , protocols::multistate_design::MultiStateAggregateFunction , protocols::multistate_design::PartitionAggregateFunction
• copies_pitch() : protocols::helical_bundle::parameters::OmegaBundleParameter
• COPs : protocols::genetic_algorithm::Entity
• copy() : core::fragment::AnnotatedFragData , core::fragment::FragData , core::pack::interaction_graph::RotamerDots , core::pose::PDBInfo , protocols::docking::DockSetupMover , protocols::docking::TemperedDocking , protocols::vardist_solaccess::VarSolDRotamerDots
• copy_all_chi_ : protocols::simple_moves::ReturnSidechainMover
• copy_all_o2prime_torsions() : protocols::stepwise::modeler::rna::o2prime::O2PrimePacker
• copy_alternate_to_current() : protocols::flexpack::interaction_graph::FlexbbEdge , protocols::flexpack::interaction_graph::FlexbbNode
• copy_atom_info() : core::chemical::MutableResidueType , core::chemical::ResidueType
• copy_bb_donor_acceptor_arrays() : core::scoring::hbonds::HBondSet
• copy_begin : protocols::forge::remodel::RemodelWorkingSet
• copy_CCD_torsions() : protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker
• copy_CCD_torsions_general() : protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker
• copy_clone() : core::scoring::electron_density_atomwise::PoseSequence , core::scoring::MultipoleElecResidueInfo , core::scoring::VdWTinkerResidueInfo
• copy_comments() : protocols::calc_taskop_filters::RelativePoseFilter
• copy_comments_ : protocols::calc_taskop_filters::RelativePoseFilter
• copy_context_graphs() : core::scoring::Energies
• copy_coord() : protocols::toolbox::KMedoid
• copy_coordinates() : protocols::frag_picker::DiversifyCrmsdByClustering , protocols::frag_picker::DiversifyCrmsdSelector
• copy_coords() : core::kinematics::AtomTree , core::kinematics::tree::Atom , core::kinematics::tree::BondedAtom , core::kinematics::tree::JumpAtom , core::pack::scmin::ResidueAtomTreeCollectionMomento , protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• copy_data() : core::chemical::AtomProperties , core::chemical::carbohydrates::CarbohydrateInfo , core::chemical::rings::RingConformerSet , protocols::canonical_sampling::BiasEnergy::Histogram< T > , protocols::carbohydrates::RingPlaneFlipMover , protocols::carbohydrates::TautomerizeAnomerMover , protocols::denovo_design::components::StructureData , protocols::hydrate::Hydrate , protocols::loops::loop_closure::ccd::CCDLoopClosureMover , protocols::loops::loop_closure::ccd::RamaCheck1B , protocols::loops::loop_closure::ccd::RamaCheck2B , protocols::loops::loop_closure::ccd::RamaCheckBase , protocols::match::output::MatchScoreWriter , protocols::mean_field::AAMatrix , protocols::mean_field::AAProb , protocols::mean_field::RotMatrix , protocols::mean_field::RotProb , protocols::simple_moves::RingConformationMover , protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::FullatomRelaxMover , protocols::surface_docking::SurfaceDockingProtocol
• copy_dna_chains() : protocols::dna::DnaInterfaceMultiStateDesign , protocols::dna::RestrictDesignToProteinDNAInterface
• copy_DOF_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• copy_dof_movers_ : protocols::stepwise::sampler::copy_dofs::CopyDofStepWiseSampler
• copy_dofs_ : protocols::stepwise::sampler::copy_dofs::ResidueListStepWiseSampler
• copy_dofs_from_pose() : core::optimization::CartesianMinimizerMap , core::optimization::MinimizerMap , core::optimization::symmetry::SymMinimizerMap
• copy_dofs_from_source() : protocols::splice::SpliceOut
• copy_dofs_info() : core::pose::copydofs::CopyDofs , protocols::simple_moves::CopyDofMover
• copy_dofs_info_ : core::pose::copydofs::CopyDofs , protocols::simple_moves::CopyDofMover
• copy_dofs_rotamer() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueList
• copy_dofs_rotamer_ : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueList
• copy_dofs_to_pose() : core::optimization::CartesianMinimizerMap , core::optimization::MinimizerMap , core::optimization::symmetry::SymMinimizerMap
• copy_end : protocols::forge::remodel::RemodelWorkingSet
• copy_fragments() : protocols::frags::FragLib , protocols::frags::SingleResidueTorsionFragmentLibrary , protocols::frags::TorsionFragmentLibrary
• copy_from() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyEdge , core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode , core::pack::interaction_graph::NPDHBSimpleEdge , core::pack::interaction_graph::NPDHBSimpleNode , core::pack::interaction_graph::SimpleEdge , core::pack::interaction_graph::SimpleNode , core::scoring::constraints::ConstraintEdge , core::scoring::constraints::ConstraintNode , core::scoring::constraints::Constraints , core::scoring::EnergyEdge , core::scoring::EnergyNode , core::scoring::MinimizationEdge , core::scoring::MinimizationNode , core::scoring::TenANeighborEdge , core::scoring::TenANeighborNode , core::scoring::TwelveANeighborEdge , core::scoring::TwelveANeighborNode , protocols::jd3::JobDirectedEdge , protocols::jd3::JobDirectedNode , protocols::legacy_sewing::ModelNode
• copy_from_parameters_index() : core::conformation::parametric::Parameter
• copy_from_parameters_index_ : core::conformation::parametric::Parameter
• copy_from_ref() : protocols::scoring::methods::pcs::PCS_tensor , protocols::scoring::methods::pcsTs1::PCS_tensor_Ts1 , protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2 , protocols::scoring::methods::pcsTs3::PCS_tensor_Ts3 , protocols::scoring::methods::pcsTs4::PCS_tensor_Ts4
• copy_hit() : protocols::match::downstream_hit , protocols::match::upstream_hit
• copy_i_bins_to_iplus1() : core::scoring::bin_transitions::BinTransitionData
• copy_identity_ : protocols::simple_moves::CopyRotamerMover
• copy_interface() : protocols::dna::RestrictDesignToProteinDNAInterface
• copy_layer_residues() : protocols::flxbb::LayerDesignOperation
• copy_length_events() : core::pose::datacache::LengthEventCollector
• copy_lr_energy_containers() : core::scoring::Energies
• copy_native_packertask_logic() : protocols::optimize_weights::IterativeOptEDriver
• copy_native_structure() : protocols::abinitio::AbrelaxApplication
• copy_nblists() : core::scoring::Energies
• copy_next_pose_segment() : protocols::stepwise::modeler::protein::InputStreamWithResidueInfo
• copy_node_and_connected_edges() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph
• copy_o2prime_hydrogens_ : protocols::stepwise::modeler::packer::SideChainCopier
• copy_old_data_into_new_table() : core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >
• copy_operations() : core::pack::task::TaskFactory
• copy_opts_swapped() : core::scoring::motif::ResPairMotifQuery
• copy_other_info() : core::chemical::MutableResidueType , core::chemical::ResidueType
• copy_params_from_previous_helices() : protocols::helical_bundle::MakeBundleHelix
• copy_params_from_previous_helices_makebundlehelix_style() : protocols::helical_bundle::BundleParametrizationCalculator
• copy_params_from_previous_helices_perturbbundle_style() : protocols::helical_bundle::BundleParametrizationCalculator
• copy_pdbinfo() : protocols::grafting::GraftMoverBase
• copy_pdbinfo_ : protocols::grafting::GraftMoverBase , protocols::grafting::simple_movers::InsertPoseIntoPoseMover , protocols::grafting::simple_movers::ReplaceRegionMover
• copy_phi_psi_omega() : protocols::simple_moves::RepeatPropagationMover
• copy_phosphates() : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• copy_pitch_from_parameter() : protocols::helical_bundle::parameters::OmegaBundleParameter
• copy_res_ : protocols::stepwise::modeler::packer::SideChainCopier
• copy_residue() : protocols::denovo_design::movers::AlignResiduesMover
• copy_residue_conenctions_and_variants() : core::pack::rotamer_set::RotamerSets
• copy_residue_connections() : core::conformation::Residue
• copy_residue_connections_from() : core::conformation::Residue
• copy_rna_chi() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• copy_rotamer_matrix() : protocols::splice::SampleRotamersFromPDB_RotamerSetOperation
• copy_scores() : core::io::silent::SilentStruct
• copy_segment() : core::conformation::Conformation , core::pose::Pose
• copy_sequence() : protocols::pose_creation::MergePDBMover
• copy_sidechains() : protocols::comparative_modeling::LoopRelaxMover
• copy_sidechains_ : protocols::comparative_modeling::LoopRelaxMover , protocols::seeded_abinitio::SwapSegment
• copy_ss_torsion_only_ : protocols::hybridization::InsertChunkMover
• copy_stored_jacobians_ : protocols::recces::sampler::rna::MC_RNA_KIC_Sampler
• copy_stretch() : protocols::calc_taskop_filters::RelativePoseFilter , protocols::splice::Splice
• copy_stretch_ : protocols::calc_taskop_filters::RelativePoseFilter
• copy_structure() : protocols::abinitio::AbrelaxApplication
• copy_structure_keep_fold_tree() : protocols::rna::denovo::RNA_FragmentMonteCarlo
• copy_suffix() : core::conformation::parametric::Parameter
• copy_suffix_ : core::conformation::parametric::Parameter
• copy_targeted_dna() : protocols::dna::DnaInterfaceMultiStateDesign , protocols::dna::RestrictDesignToProteinDNAInterface
• copy_to_centroid() : protocols::metal_interface::ZincHeterodimerMover
• copy_torsions_ : protocols::simple_moves::CopyRotamerMover
• copy_unset_params_from_globals() : protocols::helical_bundle::BundleParametrizationCalculator , protocols::helical_bundle::MakeBundleHelix
• copy_value_from_parameter() : 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
• copy_values() : core::pose::rna::RNA_RawBaseBaseInfo
• copy_without_output() : protocols::jd2::Job
• CopyDofMover() : protocols::simple_moves::CopyDofMover
• CopyDofs() : core::pose::copydofs::CopyDofs
• CopyDofsInfo() : core::pose::copydofs::CopyDofsInfo
• CopyDofStepWiseSampler() : protocols::stepwise::sampler::copy_dofs::CopyDofStepWiseSampler
• CopyEdge() : core::chemical::CopyEdge< Graph1, Graph2 >
• copying_information_was_set() : core::conformation::parametric::Parameter
• copying_side_chains() : protocols::seeded_abinitio::SwapSegment
• CopyRotamerMover() : protocols::simple_moves::CopyRotamerMover
• CopyVertex() : core::chemical::CopyVertex< Graph1, Graph2 >
• cor_opt_ : core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty
• COradius2() : core::scoring::FACTSRsdTypeInfo
• COradius2_ : core::scoring::FACTSRsdTypeInfo
• core() : protocols::abinitio::IterativeBase
• core15_ : protocols::abinitio::IterativeBase
• core2_ : protocols::abinitio::IterativeBase
• core3_ : protocols::abinitio::IterativeBase
• core4_ : protocols::abinitio::IterativeBase
• core::environment::EnvCore : core::environment::DofPassport
• core_ : protocols::simple_filters::LoopRmsdEvaluator , protocols::task_operations::SelectBySASAOperation
• core_asa_ : protocols::task_operations::SelectBySASAOperation
• core_chunks_ : protocols::hybridization::HybridizeFoldtreeDynamic
• core_cutoff_ : protocols::pose_metric_calculators::SequenceComparison
• core_residues_ : protocols::hbnet::HBNet
• core_selector_ : protocols::hbnet::HBNet
• CoreDunbrackFilter() : protocols::fldsgn::filters::CoreDunbrackFilter
• CornerPoints : protocols::match::Bool3DGrid
• corners() : protocols::match::Bool3DGrid
• correct_arrays_for_symmetry() : core::scoring::ScoreFunction
• correct_bb_O_placements() : protocols::splice::Splice
• correct_finalize_score() : core::scoring::ScoreFunction
• correct_for_duplicated_mainchain_data() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser
• correct_for_incomplete_strand_pairings() : protocols::fldsgn::filters::SecondaryStructureFilter
• correct_jump_atoms_for_fragments() : protocols::jumping::JumpSample
• correct_LJtruncation_ : protocols::simple_moves::PeriodicBoxMover
• correct_polymer_dependent_atoms() : protocols::generalized_kinematic_closure::GeneralizedKIC
• correct_polymer_dependent_atoms_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• correct_range() : core::conformation::parametric::RealValuedParameter , core::conformation::parametric::SizeValuedParameter , core::conformation::parametric::SizeVectorValuedParameter
• correct_rotamer_well_order_on_read_ : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser
• correct_sign() : core::scoring::nmr::rdc::RDCMultiSet
• correct_sign_ : core::scoring::nmr::rdc::RDCMultiSet
• correct_termini_derivatives() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >
• correct_values() : core::conformation::parametric::RealVectorValuedParameter
• correction : protocols::sic_dock::CorrectionVisitor
• correction_weights() : protocols::fold_from_loops::NubInitioMover
• CorrectionVisitor() : protocols::sic_dock::CorrectionVisitor
• correctly_copy_HO2prime_positions() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• correlation_weight_ : protocols::ligand_docking::HighResEnsemble , protocols::ligand_docking::ProtLigEnsemble
• correspondence() : protocols::pack_daemon::PackDaemon
• correspondence_ : protocols::pack_daemon::PackDaemon
• correspondence_file_name_ : protocols::pack_daemon::StructureFileNames
• corresponding_atom_id_map_ : protocols::stepwise::legacy::screener::SimpleRMSD_Screener , protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• corresponding_res_block() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• corresponding_res_block_ : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• corresponding_res_num_in_block_ : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• corresponding_residue_in_current() : core::pose::Pose , core::pose::reference_pose::ReferencePose , core::pose::reference_pose::ReferencePoseSet
• cos_flipped_ANGLE_CUTOFF_HIGH : core::scoring::methods::LK_SigmoidalFunc
• cos_flipped_ANGLE_CUTOFF_LOW : core::scoring::methods::LK_SigmoidalFunc
• cos_r_cell_angles : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• cos_theta() : core::scoring::power_diagram::SAnode , core::scoring::SAnode
• cos_theta_ : core::scoring::power_diagram::SAnode , core::scoring::SAnode
• cosAHD_fade_lookup() : core::scoring::hbonds::HBondDatabase
• cosAHD_fade_lookup_ : core::scoring::hbonds::HBondDatabase
• cosAHD_long_poly_lookup() : core::scoring::hbonds::HBondDatabase
• cosAHD_long_poly_lookup_ : core::scoring::hbonds::HBondDatabase
• cosAHD_short_poly_lookup() : core::scoring::hbonds::HBondDatabase
• cosAHD_short_poly_lookup_ : core::scoring::hbonds::HBondDatabase
• cosBAH2_fade_lookup() : core::scoring::hbonds::HBondDatabase
• cosBAH2_fade_lookup_ : core::scoring::hbonds::HBondDatabase
• cosBAH2_poly_lookup() : core::scoring::hbonds::HBondDatabase
• cosBAH2_poly_lookup_ : core::scoring::hbonds::HBondDatabase
• cosBAH_fade_lookup() : core::scoring::hbonds::HBondDatabase
• cosBAH_fade_lookup_ : core::scoring::hbonds::HBondDatabase
• cosBAH_long_poly_lookup() : core::scoring::hbonds::HBondDatabase
• cosBAH_long_poly_lookup_ : core::scoring::hbonds::HBondDatabase
• cosBAH_short_poly_lookup() : core::scoring::hbonds::HBondDatabase
• cosBAH_short_poly_lookup_ : core::scoring::hbonds::HBondDatabase
• cosine_distance() : protocols::mean_field::AAMatrix
• cosRcellAngles : core::scoring::electron_density::ElectronDensity
• cost_ : protocols::hybridization::WeightedFragmentSmoothTrialMover , protocols::simple_moves::SmoothFragmentMover
• could_be_accepted() : protocols::frag_picker::quota::ABEGO_SS_Pool , protocols::frag_picker::quota::QuotaPool , protocols::frag_picker::quota::SecondaryStructurePool
• CouldHaveHybridization() : core::chemical::gasteiger::PossibleAtomTypesForAtom
• coulomb() : core::scoring::elec::FA_ElecEnergy , core::scoring::elec::FA_GrpElecEnergy , core::scoring::elec::GroupElec
• Coulomb() : core::scoring::etable::coulomb::Coulomb
• coulomb() : core::scoring::rna::StackElecEnergy
• coulomb_ : core::scoring::elec::FA_ElecEnergy , core::scoring::elec::FA_GrpElecEnergy , core::scoring::elec::GroupElec , core::scoring::rna::StackElecEnergy , protocols::ligand_docking::ga_ligand_dock::GridScorer
• count() : core::import_pose::atom_tree_diffs::AtomTreeDiff , core::scoring::elec::CountPairRepresentative , core::scoring::etable::count_pair::CountPair1B< CrossoverBehavior > , core::scoring::etable::count_pair::CountPair2B< CrossoverBehavior > , core::scoring::etable::count_pair::CountPairAll , core::scoring::etable::count_pair::CountPairFunction , core::scoring::etable::count_pair::CountPairGeneric , core::scoring::etable::count_pair::CountPairIntraRes< CrossoverBehavior > , core::scoring::etable::count_pair::CountPairNone , core::scoring::hbonds::graph::AtomInfo , core::scoring::motif::ResPairMotif , core::sequence::CompositeScoringScheme , protocols::make_rot_lib::running_average_pair , protocols::nmr::pre::PREDistanceRecord , protocols::stepwise::screener::StepWiseScreener
• count_ : core::scoring::motif::ResPairMotif , protocols::contact_map::Contact , protocols::denovo_design::components::EnumeratedVectorSelector< T > , protocols::denovo_design::components::RandomVectorSelector< T > , protocols::features::TopCountOfAllInputs , protocols::features::TopCountOfEachInput , protocols::nmr::pre::PREDistanceRecord , protocols::noesy_assign::FragsToAtomDist::DistanceRecord , protocols::pockets::CCluster , protocols::pockets::PCluster , protocols::rna::setup::RNA_MonteCarloJobDistributor , protocols::stepwise::modeler::align::StepWiseClusterer , protocols::stepwise::screener::StepWiseScreener , protocols::task_operations::DatabaseThread
• count_AA_with_direction_ : protocols::features::strand_assembly::SandwichFeatures
• count_accepted() : protocols::canonical_sampling::MultiTemperatureTrialCounter , protocols::moves::TrialCounter
• count_as_percentage_ : protocols::simple_filters::ResidueCountFilter
• count_assignments() : protocols::noesy_assign::CrossPeakList
• count_at_path_distance() : core::scoring::etable::count_pair::CountPairCrossover34 , core::scoring::etable::count_pair::CountPairCrossover3 , core::scoring::etable::count_pair::CountPairCrossover3full , core::scoring::etable::count_pair::CountPairCrossover4
• count_atoms() : core::scoring::APBSWrapper
• count_atoms_in_common() : core::scoring::trie::RotamerDescriptor< AT, CPDAT >
• count_bad_residues_ : protocols::score_filters::GeometryFilter
• count_bb_atoms() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• count_bb_atoms_in_residue() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• count_candidates() : 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::QuotaPool , protocols::frag_picker::quota::SecondaryStructurePool
• count_checkpoint_recoveries_ : protocols::checkpoint::CheckPointer
• count_children() : protocols::loop_modeling::LoopMover
• count_cis_peptide_bonds() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• count_clashes_between_two_poses() : protocols::motif_grafting::movers::MotifGraftMover
• count_components() : protocols::frag_picker::scores::FragmentScoreManager
• count_connected_components_and_initialize_vertex_groups() : core::pack::interaction_graph::InteractionGraphBase
• count_contacts() : protocols::fold_from_loops::NubInitioMover
• count_data() : protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker
• count_data_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection , protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker , protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker , protocols::stepwise::modeler::StepWiseConnectionSampler , protocols::stepwise::screener::BaseCentroidScreener
• count_decoys_ : protocols::noesy_assign::DistanceScoreMover
• count_dynamic_memory() : core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > , 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::DensePDInteractionGraph , core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::EdgeBase , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::FirstClassEdge< V, E, G > , core::pack::interaction_graph::FirstClassNode< V, E, G > , 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::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::LinearMemoryInteractionGraph , 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::NPDHBondInteractionGraph< V, E, G > , core::pack::interaction_graph::NPDHBondNode< V, E, G > , core::pack::interaction_graph::NPDHBSimpleEdge , core::pack::interaction_graph::NPDHBSimpleInteractionGraph , core::pack::interaction_graph::NPDHBSimpleNode , core::pack::interaction_graph::OnTheFlyEdge , core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SimpleEdge , core::pack::interaction_graph::SimpleInteractionGraph , core::pack::interaction_graph::SimpleNode , 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::SurfaceInteractionGraph< 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::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistEdge , core::pack::interaction_graph::SymmMinimalistInteractionGraph , core::pack::interaction_graph::SymmMinimalistNode , core::pack::interaction_graph::SymmOnTheFlyEdge , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyNode , core::scoring::constraints::ConstraintEdge , core::scoring::constraints::ConstraintGraph , core::scoring::constraints::ConstraintNode , core::scoring::ContextGraph , core::scoring::EnergyEdge , core::scoring::EnergyGraph , core::scoring::EnergyNode , core::scoring::hbonds::graph::HBondEdge , core::scoring::hbonds::graph::HBondGraph , core::scoring::hbonds::graph::HBondNode , core::scoring::MinimizationEdge , core::scoring::MinimizationGraph , core::scoring::MinimizationNode , core::scoring::TenANeighborEdge , core::scoring::TenANeighborGraph , core::scoring::TenANeighborNode , core::scoring::TwelveANeighborEdge , core::scoring::TwelveANeighborGraph , core::scoring::TwelveANeighborNode , protocols::flexpack::interaction_graph::FlexbbEdge , protocols::flexpack::interaction_graph::FlexbbInteractionGraph , protocols::flexpack::interaction_graph::FlexbbNode , protocols::flexpack::interaction_graph::MinimalistFlexbbEdge , protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph , protocols::flexpack::interaction_graph::MinimalistFlexbbNode , protocols::flexpack::interaction_graph::OTFFlexbbEdge , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::flexpack::interaction_graph::OTFFlexbbNode , protocols::jd3::JobDigraph , protocols::jd3::JobDirectedEdge , protocols::jd3::JobDirectedNode
• count_energy_drop() : protocols::canonical_sampling::MultiTemperatureTrialCounter , protocols::moves::TrialCounter
• count_energy_to_node_in_my_fragtotalE() : protocols::flexpack::interaction_graph::FlexbbNode
• count_eps_ : protocols::simple_filters::NMerSVMEnergyFilter
• count_ff() : core::scoring::saxs::FormFactorManager
• count_file_reads() : protocols::pack_daemon::DynamicAggregateFunction
• count_fixed_residues() : core::kinematics::FoldTree
• count_gly_as_polar() : protocols::simple_filters::LongestContinuousPolarSegmentFilter
• count_gly_as_polar_ : protocols::simple_filters::LongestContinuousPolarSegmentFilter
• count_good_pairings() : protocols::fldsgn::filters::SheetTopologyFilter
• count_grid_ : protocols::canonical_sampling::BiasEnergy
• count_hbonds() : protocols::cyclic_peptide::PeptideInternalHbondsMetric
• count_inserted() : protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering >
• count_motifs() : core::scoring::motif::MotifHash
• count_moveable_residues() : protocols::forge::remodel::RemodelLoopMover
• count_n_matches() : protocols::match::MatchCounter
• count_ntrial() : protocols::flxbb::FilterStructs
• count_num_covered() : core::pack::interaction_graph::DotSphere
• count_num_npd_properties() : protocols::pack_daemon::DynamicAggregateFunction
• count_pair_bs() : core::scoring::methods::DNA_ReferenceEnergy
• count_pair_full() : core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::methods::EnergyMethodOptions
• count_pair_full_ : core::scoring::elec::FA_ElecEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::methods::EnergyMethodOptions
• count_pair_hybrid() : core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::methods::EnergyMethodOptions
• count_pair_hybrid_ : core::scoring::elec::FA_ElecEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::methods::EnergyMethodOptions
• count_per_rotamer_combo_ : protocols::match::output::LimitHitsPerRotamerFilter
• count_pools() : protocols::frag_picker::quota::QuotaCollector , protocols::frag_picker::quota::QuotaConfig
• count_primary : protocols::electron_density::DensitySymmInfo
• count_protein_residues() : protocols::cyclic_peptide::SymmetricCycpepAlign
• count_query_ss() : protocols::frag_picker::FragmentPicker
• count_recovered_ : protocols::optimize_weights::IterativeOptEDriver
• count_removed_structures() : protocols::jd2::archive::ArchiveBase
• count_residue_pairings() : protocols::fldsgn::filters::SheetTopologyFilter
• count_residues() : protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter
• count_residues_ : protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter
• count_rotamer() : protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• count_rotamer_as_native() : protocols::optimize_weights::PNatRotOptEPositionData
• count_rotamer_for_lastseen_restype_ : protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• count_rotamers_per_target_restype_ : protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• count_rotamers_recovered_ : protocols::optimize_weights::IterativeOptEDriver
• count_sc_hbonds_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• count_scoring_atoms() : core::scoring::saxs::SAXSEnergy
• count_SD_NE1_ : protocols::protein_interface_design::filters::AtomicContactCountFilter
• count_segments() : protocols::fold_from_loops::movers::SplitAndMixPoseMover
• count_static_memory() : 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::DensePDInteractionGraph , core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::EdgeBase , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::FASTERInteractionGraph , 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::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::LinearMemoryInteractionGraph , 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::NPDHBondInteractionGraph< V, E, G > , core::pack::interaction_graph::NPDHBondNode< V, E, G > , core::pack::interaction_graph::NPDHBSimpleEdge , core::pack::interaction_graph::NPDHBSimpleInteractionGraph , core::pack::interaction_graph::NPDHBSimpleNode , core::pack::interaction_graph::OnTheFlyEdge , core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SimpleEdge , core::pack::interaction_graph::SimpleInteractionGraph , core::pack::interaction_graph::SimpleNode , 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::SurfaceInteractionGraph< 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::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistEdge , core::pack::interaction_graph::SymmMinimalistInteractionGraph , core::pack::interaction_graph::SymmMinimalistNode , core::pack::interaction_graph::SymmOnTheFlyEdge , core::pack::interaction_graph::SymmOnTheFlyNode , core::scoring::constraints::ConstraintEdge , core::scoring::constraints::ConstraintGraph , core::scoring::constraints::ConstraintNode , core::scoring::ContextGraph , core::scoring::EnergyEdge , core::scoring::EnergyGraph , core::scoring::EnergyNode , core::scoring::hbonds::graph::HBondEdge , core::scoring::hbonds::graph::HBondGraph , core::scoring::hbonds::graph::HBondNode , core::scoring::MinimizationEdge , core::scoring::MinimizationGraph , core::scoring::MinimizationNode , core::scoring::TenANeighborEdge , core::scoring::TenANeighborGraph , core::scoring::TenANeighborNode , core::scoring::TwelveANeighborEdge , core::scoring::TwelveANeighborGraph , core::scoring::TwelveANeighborNode , protocols::flexpack::interaction_graph::MinimalistFlexbbEdge , protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph , protocols::flexpack::interaction_graph::MinimalistFlexbbNode , protocols::jd3::JobDigraph , protocols::jd3::JobDirectedEdge , protocols::jd3::JobDirectedNode
• count_structure() : protocols::jd2::archive::ArchiveBase
• count_trial() : protocols::canonical_sampling::MultiTemperatureTrialCounter , protocols::moves::TrialCounter
• count_viols_ : core::scoring::func::CountViolFunc , core::scoring::func::SkipViolFunc
• count_visited_pairs_with_segment() : protocols::denovo_design::components::SolutionPredicate
• count_water() : core::select::residue_selector::NumNeighborsSelector
• count_water_ : core::select::residue_selector::NumNeighborsSelector
• countable_nonheavy_unsats_ : protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator
• counted_residue_description() : protocols::simple_filters::LongestContinuousApolarSegmentFilter , protocols::simple_filters::LongestContinuousPolarSegmentFilter
• counter_ : protocols::cyclic_peptide::PeptideCyclizeMover , protocols::kinematic_closure::pivot_pickers::StandardPivots , protocols::moves::MonteCarlo
• counter_segment_ : protocols::sewing::data_storage::SmartAssembly
• counters_ : protocols::canonical_sampling::MultiTemperatureTrialCounter , protocols::canonical_sampling::TrialCounterObserver
• CountPair1B() : core::scoring::etable::count_pair::CountPair1B< CrossoverBehavior >
• CountPair2B() : core::scoring::etable::count_pair::CountPair2B< CrossoverBehavior >
• CountPairAll() : core::scoring::etable::count_pair::CountPairAll
• CountPairData_1_1() : core::scoring::etable::etrie::CountPairData_1_1
• CountPairDataGeneric() : core::scoring::etable::etrie::CountPairDataGeneric
• CountPairFunction() : core::scoring::etable::count_pair::CountPairFunction
• CountPairFunctionCOP : core::scoring::ResidueNblistData
• CountPairGeneric() : core::scoring::etable::count_pair::CountPairGeneric
• CountPairIntraRes() : core::scoring::etable::count_pair::CountPairIntraRes< CrossoverBehavior >
• CountPairNone() : core::scoring::etable::count_pair::CountPairNone
• CountPairRepMap() : core::scoring::elec::CountPairRepMap
• CountPairRepresentative() : core::scoring::elec::CountPairRepresentative
• counts() : protocols::frag_picker::ContactCounts , protocols::indexed_structure_store::SegmentSequenceProfileResult
• counts_ : core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser , protocols::canonical_sampling::SimulatedTempering , protocols::denovo_design::components::SegmentCounts , protocols::frag_picker::ContactCounts
• CountUnsaturatedNeighbors() : core::chemical::gasteiger::PossibleAtomTypesForAtom
• CountViolFunc() : core::scoring::func::CountViolFunc
• CoupledMover() : protocols::simple_moves::CoupledMover
• CoupledMovesProtocol() : protocols::coupled_moves::CoupledMovesProtocol
• couplings_ : core::pack::rotamer_set::RotamerCouplings
• cov_bond_only_flag_ : protocols::ub_e2c::ubi_e2c_modeler
• covalent_bonds_ : protocols::denovo_design::components::StructureData
• covalent_bonds_begin() : protocols::denovo_design::components::StructureData
• covalent_bonds_end() : protocols::denovo_design::components::StructureData
• covalent_compliance_ : protocols::noesy_assign::PeakAssignment
• covalent_compliance_weight_ : protocols::noesy_assign::PeakAssignmentParameters
• covalent_connections() : protocols::toolbox::match_enzdes_util::EnzdesCstParamCache
• covalent_connections_ : protocols::toolbox::match_enzdes_util::EnzdesCstParamCache
• covalent_distances_ : protocols::noesy_assign::CovalentCompliance
• covalent_labeling_fa_input() : core::scoring::methods::EnergyMethodOptions
• covalent_labeling_fa_input_ : core::scoring::methods::EnergyMethodOptions
• covalent_labeling_fa_input_file_ : core::scoring::methods::CovalentLabelingFAEnergy
• covalent_labeling_input() : core::scoring::methods::EnergyMethodOptions
• covalent_labeling_input_ : core::scoring::methods::EnergyMethodOptions
• covalent_labeling_input_file_ : core::scoring::methods::CovalentLabelingEnergy
• CovalentCompliance() : protocols::noesy_assign::CovalentCompliance
• CovalentConnectionReplaceInfo() : protocols::toolbox::match_enzdes_util::CovalentConnectionReplaceInfo
• CovalentLabelingEnergy() : core::scoring::methods::CovalentLabelingEnergy
• CovalentLabelingFAEnergy() : core::scoring::methods::CovalentLabelingFAEnergy
• CovalentRadius : core::chemical::Element
• CovalentRadiusAromaticBond : core::chemical::gasteiger::GasteigerAtomTypeData
• CovalentRadiusDoubleBond : core::chemical::gasteiger::GasteigerAtomTypeData
• CovalentRadiusSingleBond : core::chemical::gasteiger::GasteigerAtomTypeData
• CovalentRadiusTripleBond : core::chemical::gasteiger::GasteigerAtomTypeData
• coverage_ : protocols::pose_metric_calculators::FragQualCalculator
• covered_by_chunk_ : core::import_pose::libraries::RNA_ChunkLibrary
• cp_byname() : core::scoring::elec::CountPairRepMap
• cp_data() : core::scoring::trie::RotamerDescriptorAtom< AT, CPDAT > , core::scoring::trie::TrieNode< AT, CPDATA >
• cp_data_ : core::scoring::trie::RotamerDescriptorAtom< AT, CPDAT > , core::scoring::trie::TrieNode< AT, CPDATA >
• cp_half : core::scoring::etable::count_pair::CountPairFunction
• CP_parameters : core::chemical::rings::RingConformer
• cp_rep_map_ : core::scoring::elec::CountPairRepMap , core::scoring::elec::FA_ElecEnergy
• cp_rep_map_byname_ : core::scoring::elec::CountPairRepMap , core::scoring::ScoringManager
• CPDataCorrespondence() : core::scoring::trie::CPDataCorrespondence
• cpfxn_weight_ : core::scoring::elec::GroupElec
• cprev_n_bond_length_params() : core::scoring::methods::ResidueCartBondedParameters
• cprev_n_bond_length_params_ : core::scoring::methods::ResidueCartBondedParameters
• cpu_time : protocols::boinc::BoincSharedMemory
• cpu_time_ : protocols::boinc::Boinc
• cRad : protocols::pockets::PocketExemplarMultifunc
• crankshaft_alpha_gamma() : protocols::stepwise::monte_carlo::rna::RNA_TorsionMover
• cranny_packer() : protocols::vip::VIP_Mover
• crash_log() : protocols::jd2::JD2Failure
• crd() : core::scoring::methods::ProQ_Energy
• create() : core::chemical::rotamers::BasicRotamerLibrarySpecificationCreator , core::chemical::rotamers::CenrotRotamerLibrarySpecificationCreator , core::chemical::rotamers::DunbrackRotamerLibrarySpecificationCreator , core::chemical::rotamers::NCAARotamerLibrarySpecificationCreator , core::chemical::rotamers::PDBRotamerLibrarySpecificationCreator , core::chemical::rotamers::RotamerLibrarySpecificationCreator , core::chemical::rotamers::StoredRotamerLibrarySpecificationCreator , core::fragment::BBTorsionAndAnglesSRFD , core::fragment::BBTorsionSRFD , core::fragment::DownJumpSRFD , core::fragment::IndependentBBTorsionSRFD , core::fragment::SecstructSRFD , core::fragment::SingleResidueFragData , core::fragment::UpJumpSRFD , core::pack::dunbrack::cenrot::SingleResidueCenrotLibraryCreator , core::pack::dunbrack::SingleResidueDunbrackLibraryCreator , core::pack::rotamers::SingleBasicRotamerLibraryCreator , core::pack::rotamers::SingleLigandRotamerLibraryCreator , core::pack::rotamers::SingleNCAARotamerLibraryCreator , core::pack::rotamers::SingleResidueRotamerLibraryCreator , core::pack::rotamers::StoredRotamerLibraryCreator , core::pose::datacache::CacheableObserver , core::pose::datacache::LengthEventCollector , core::pose::datacache::SpecialSegmentsObserver , protocols::denovo_design::components::SegmentPairing , protocols::denovo_design::components::StructureDataObserver , protocols::denovo_design::components::StructureDataPerturber , protocols::forge::build::BuildManager , protocols::moves::Mover , protocols::moves::PyMOLObserver , protocols::network::UIObserver , protocols::toolbox::DummyClass , protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver
• create_aa_composition_energy_setup_instance() : core::scoring::ScoringManager
• create_ambiguous_constraint() : protocols::constraint_generator::CoordinateConstraintGenerator
• create_and_attach_task_factory() : protocols::docking::DockTaskFactory
• create_and_init_inner_larval_job_from_preliminary() : protocols::jd3::standard::StandardJobQueen
• create_and_initialize_annealing_graph() : core::pack::interaction_graph::InteractionGraphFactory
• create_and_initialize_two_body_interaction_graph() : core::pack::interaction_graph::InteractionGraphFactory
• create_and_set_initial_job_dag() : protocols::jd3::JobQueen
• create_and_store_output_specification_for_job_result() : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::standard::StandardJobQueen
• create_annealer() : core::pack::annealer::AnnealerFactory
• create_architect() : protocols::denovo_design::architects::BetaSheetArchitectCreator , protocols::denovo_design::architects::BlueprintArchitectCreator , protocols::denovo_design::architects::CompoundArchitectCreator , protocols::denovo_design::architects::DeNovoArchitectCreator , protocols::denovo_design::architects::HelixArchitectCreator , protocols::denovo_design::architects::PoseArchitectCreator , protocols::denovo_design::architects::StrandArchitectCreator
• create_assembly() : protocols::legacy_sewing::AssemblyFactory
• create_assembly_scorer() : protocols::sewing::scoring::AssemblyScorerCreator , protocols::sewing::scoring::InterModelMotifScorerCreator , protocols::sewing::scoring::IntraDesignTerminusMotifScorerCreator , protocols::sewing::scoring::LigandScorerCreator , protocols::sewing::scoring::MotifScorerCreator , protocols::sewing::scoring::PartnerMotifScorerCreator , protocols::sewing::scoring::SegmentContactOrderScorerCreator , protocols::sewing::scoring::StartingNodeMotifScorerCreator , protocols::sewing::scoring::SubsetPartnerMotifScorerCreator , protocols::sewing::scoring::TerminusMotifScorerCreator , protocols::sewing::scoring::TopNMotifScorerCreator
• create_atom_id_map() : core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric
• create_atom_tree() : protocols::protein_interface_design::movers::SetAtomTree
• create_atom_type_from_database() : core::chemical::AtomTypeSet
• create_atom_type_set() : core::chemical::ChemicalManager
• create_atomvdw_instance() : core::scoring::ScoringManager
• create_attach_nmr_data_to_pose() : core::scoring::nmr::NMRDataFactory
• create_background_edge() : core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• create_background_node() : core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• create_bb_angle_constraint() : protocols::fldsgn::SheetConstraintGenerator
• create_bb_angle_func() : protocols::fldsgn::SheetConstraintGenerator , protocols::fold_from_loops::constraint_generator::AutomaticSheetConstraintGenerator
• create_bb_cacb_dihedral_constraint() : protocols::fldsgn::SheetConstraintGenerator
• create_bb_dihedral_constraint() : protocols::fldsgn::SheetConstraintGenerator
• create_bb_dihedral_func() : protocols::fldsgn::SheetConstraintGenerator , protocols::fold_from_loops::constraint_generator::AutomaticSheetConstraintGenerator
• create_bb_moves() : protocols::abinitio::KinematicAbinitio
• create_bump_grid_for_bb() : protocols::match::BumpGrid
• create_ca_ca_atom_pair_constraint() : protocols::fldsgn::SheetConstraintGenerator
• create_caca_atom_pair_func() : protocols::fldsgn::SheetConstraintGenerator
• create_cacb_dihedral_func() : protocols::fldsgn::SheetConstraintGenerator
• create_calculator_from_file() : protocols::helical_bundle_predict::HBPHelixParameters
• create_carbon_hbond_potential_instance() : core::scoring::ScoringManager
• create_cenhbpotential_instance() : core::scoring::ScoringManager
• create_cenrotenvpair_instance() : core::scoring::ScoringManager
• create_centroid_disulfide_potential_instance() : core::scoring::ScoringManager
• create_centroid_move_generator() : protocols::helical_bundle_predict::HelicalBundlePredictApplication
• create_centroid_rotamer_libraries_from_ASCII() : core::pack::dunbrack::cenrot::CenrotLibrary
• create_centroid_scorefunction() : protocols::helical_bundle_predict::HelicalBundlePredictApplication
• create_chi_energy_function_instance() : core::scoring::ScoringManager
• create_chimera_segment() : protocols::legacy_sewing::Assembly
• create_collcheck_ordering() : protocols::toolbox::match_enzdes_util::LigandConformer
• create_comparer() : protocols::rotamer_recovery::RRComparerAutomorphicRMSDCreator , protocols::rotamer_recovery::RRComparerChiDiffCreator , protocols::rotamer_recovery::RRComparerCreator , protocols::rotamer_recovery::RRComparerElecDensDiffCreator , protocols::rotamer_recovery::RRComparerRotBinsCreator
• create_complex_type_generator() : protocols::task_operations::RestrictConservedLowDdgOperation , protocols::task_operations::SeqprofConsensusOperation
• create_consensus_design_task() : protocols::calc_taskop_movers::ConsensusDesignMover
• create_constraint() : core::pack::dunbrack::DunbrackConstraintCreator , core::scoring::constraints::AmbiguousConstraintCreator , core::scoring::constraints::AmbiguousNMRConstraintCreator , core::scoring::constraints::AmbiguousNMRDistanceConstraintCreator , core::scoring::constraints::AngleConstraintCreator , core::scoring::constraints::AtomPairConstraintCreator , core::scoring::constraints::BasePairConstraintCreator , core::scoring::constraints::BigBinConstraintCreator , core::scoring::constraints::ConstraintCreator , core::scoring::constraints::CoordinateConstraintCreator , core::scoring::constraints::DihedralConstraintCreator , core::scoring::constraints::DihedralPairConstraintCreator , core::scoring::constraints::FabConstraintCreator , core::scoring::constraints::KofNConstraintCreator , core::scoring::constraints::LocalCoordinateConstraintCreator , core::scoring::constraints::MultiConstraintCreator , core::scoring::constraints::NamedAngleConstraintCreator , core::scoring::constraints::NamedAtomPairConstraintCreator , core::scoring::constraints::SequenceProfileConstraintCreator , core::scoring::constraints::SiteConstraintCreator , core::scoring::constraints::SiteConstraintResiduesCreator , protocols::constraint_generator::DistanceConstraintGenerator , protocols::constraints_additional::BindingSiteConstraintCreator , protocols::constraints_additional::NamedAtomPairConstraintCreator , protocols::constraints_additional::SequenceCoupling1BDConstraintCreator , protocols::constraints_additional::SequenceCouplingConstraintCreator , protocols::noesy_assign::PeakAssignment , protocols::pockets::PocketConstraintCreator
• create_constraint_from_file() : protocols::aa_composition::AddCompositionConstraintMover , protocols::aa_composition::AddMHCEpitopeConstraintMover , protocols::aa_composition::AddNetChargeConstraintMover
• create_constraint_from_file_contents() : protocols::aa_composition::AddCompositionConstraintMover , protocols::aa_composition::AddMHCEpitopeConstraintMover , protocols::aa_composition::AddNetChargeConstraintMover
• create_constraint_generator() : protocols::constraint_generator::AtomPairConstraintGeneratorCreator , protocols::constraint_generator::ConstraintGeneratorCreator , protocols::constraint_generator::CoordinateConstraintGeneratorCreator , protocols::constraint_generator::DihedralConstraintGeneratorCreator , protocols::constraint_generator::DistanceConstraintGeneratorCreator , protocols::constraint_generator::HydrogenBondConstraintGeneratorCreator , protocols::constraint_generator::MembraneSpanConstraintGeneratorCreator , protocols::constraint_generator::MetalContactsConstraintGeneratorCreator , protocols::constraint_generator::ResidueTypeConstraintGeneratorCreator , protocols::constraint_generator::TerminiConstraintGeneratorCreator , protocols::denovo_design::constraints::FileConstraintGeneratorCreator , protocols::fldsgn::SheetConstraintGeneratorCreator , protocols::fold_from_loops::constraint_generator::AutomaticSheetConstraintGeneratorCreator , protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGeneratorCreator
• create_constraint_generators() : protocols::denovo_design::movers::BuildDeNovoBackboneMover
• create_constraints() : protocols::cluster::ClusterBase
• create_context_graph() : core::scoring::ContextGraphFactory
• create_coordinate_constraint() : protocols::constraint_generator::CoordinateConstraintGenerator
• create_coordinate_constraint_atom_id_map() : protocols::stepwise::modeler::align::StepWisePoseAligner
• create_coordinate_constraints() : protocols::stepwise::modeler::align::StepWisePoseAligner
• create_corresponding_mress_for_mres() : core::pack::annealer::SequenceSymmetricAnnealer
• create_count_pair_function() : core::scoring::etable::count_pair::CountPairFactory
• create_count_pair_function_and_invoke() : core::scoring::etable::count_pair::CountPairFactory
• create_data() : protocols::abinitio::abscript::JumpSampleDataCreator , protocols::denovo_design::components::StructureDataCreator , protocols::environment::AutoCutDataCreator
• create_database_occsolene_instance() : core::scoring::ScoringManager
• create_database_session() : protocols::antibody::AntibodyDatabaseManager
• create_db() : protocols::loophash::LoopHashLibrary
• create_db_ : protocols::loophash::LoopHashLibrary
• create_ddp_lookup_instance() : core::scoring::ScoringManager
• create_default_movemap() : protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover
• create_default_task_factory() : protocols::denovo_design::movers::FastDesign
• create_dense_pdig_from_rot_to_pack() : protocols::pack_daemon::DenseIGRepacker , protocols::pack_daemon::DoubleDenseIGRepacker
• create_directed_dependency() : protocols::fldsgn::BluePrintBDR , protocols::forge::build::BuildManager , protocols::forge::components::BDR
• create_dist_constraints() : protocols::toolbox::DecoySetEvaluation
• create_dist_constraints_median() : protocols::toolbox::DecoySetEvaluation
• create_disulfide_matching_potential_instance() : core::scoring::ScoringManager
• create_dna_bform_potential_instance() : core::scoring::ScoringManager
• create_dna_dihedralpotential_instance() : core::scoring::ScoringManager
• create_dna_directreadoutpotential_instance() : core::scoring::ScoringManager
• create_dna_envpairpotential_instance() : core::scoring::ScoringManager
• create_dna_torsion_potential_instance() : core::scoring::ScoringManager
• create_dnabase_potential_instance() : core::scoring::ScoringManager
• create_docking_high_res_mover() : protocols::docking::DockingHighResFactory
• create_ds_builder() : protocols::match::Matcher
• create_dummy_atom() : core::chemical::sdf::MolFileIOMolecule
• create_element_set() : core::chemical::ChemicalManager
• create_embedding_virtual() : protocols::membrane::visualize::VisualizeEmbeddingMover
• create_empty_map() : protocols::frag_picker::scores::FragmentScoreManager
• create_energy_map_instance() : protocols::relax::RelaxScriptManager
• create_energy_method() : core::energy_methods::DEEREnergyCreator , core::pack::dunbrack::cenrot::CenRotDunEnergyCreator , core::pack::dunbrack::DunbrackEnergyCreator , core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenaltyCreator , core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenaltyCreator , core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergyCreator , core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyEnergyCreator , core::pack::interaction_graph::HPatchEnergyCreator , core::pack::interaction_graph::SurfaceEnergyCreator , core::scoring::aa_composition_energy::AACompositionEnergyCreator , core::scoring::aa_repeat_energy::AARepeatEnergyCreator , core::scoring::carbon_hbonds::CarbonHBondEnergyCreator , core::scoring::constraints::ConstraintsEnergyCreator , core::scoring::cryst::XtalMLEnergyCreator , core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergyCreator , core::scoring::disulfides::CentroidDisulfideEnergyCreator , core::scoring::disulfides::DisulfideMatchingEnergyCreator , core::scoring::disulfides::FullatomDisulfideEnergyCreator , core::scoring::dna::DNAChiEnergyCreator , core::scoring::dna::DNATorsionEnergyCreator , core::scoring::elec::FA_ElecEnergyAroAllCreator , core::scoring::elec::FA_ElecEnergyAroAroCreator , core::scoring::elec::FA_ElecEnergyCreator , core::scoring::elec::FA_GrpElecEnergyCreator , core::scoring::elec::RNA_FA_ElecEnergyCreator , core::scoring::electron_density::ElecDensAllAtomCenEnergyCreator , core::scoring::electron_density::ElecDensCenEnergyCreator , core::scoring::electron_density::ElecDensEnergyCreator , core::scoring::electron_density::FastDensEnergyCreator , core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergyCreator , core::scoring::etable::EtableClassicIntraEnergyCreator , core::scoring::etable::EtableEnergyCreator , core::scoring::fiber_diffraction::FiberDiffractionEnergyCreator , core::scoring::fiber_diffraction::FiberDiffractionEnergyDensCreator , core::scoring::geometric_solvation::ContextDependentGeometricSolEnergyCreator , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergyCreator , core::scoring::geometric_solvation::ExactOccludedHbondSolEnergyCreator , core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebodyCreator , core::scoring::geometric_solvation::OccludedHbondSolEnergyCreator , core::scoring::hackaro::HackAroEnergyCreator , core::scoring::hbonds::HBondEnergyCreator , core::scoring::hbonds::NPDHBondEnergyCreator , core::scoring::interface_::DDPscoreCreator , core::scoring::lkball::LK_BallEnergyCreator , core::scoring::loop_graph::LoopCloseEnergyCreator , core::scoring::magnesium::MgEnergyCreator , core::scoring::magnesium::RNA_MgPointEnergyCreator , core::scoring::membrane::FaMPEnvEnergyCreator , core::scoring::membrane::FaMPEnvSmoothEnergyCreator , core::scoring::membrane::FaMPSolvEnergyCreator , core::scoring::membrane::MPCbetaEnergyCreator , core::scoring::membrane::MPEnvEnergyCreator , core::scoring::membrane::MPHelicalityEnergyCreator , core::scoring::membrane::MPNonHelixPenaltyCreator , core::scoring::membrane::MPPairEnergyCreator , core::scoring::membrane::MPResidueLipophilicityEnergyCreator , core::scoring::membrane::MPSpanAngleEnergyCreator , core::scoring::membrane::MPSpanInsertionEnergyCreator , core::scoring::membrane::MPTerminiPenaltyCreator , core::scoring::membrane::MPTMProjPenaltyCreator , core::scoring::methods::AbegoEnergyCreator , core::scoring::methods::ArgCationPiEnergyCreator , core::scoring::methods::AromaticBackboneRestraintEnergyCreator , core::scoring::methods::AspartimidePenaltyEnergyCreator , core::scoring::methods::BranchEnergyCreator , core::scoring::methods::Burial_v2EnergyCreator , core::scoring::methods::BurialEnergyCreator , core::scoring::methods::carbohydrates::SugarBackboneEnergyCreator , core::scoring::methods::CartesianBondedEnergyCreator , core::scoring::methods::CenHBEnergyCreator , core::scoring::methods::CenPairEnergyCreator , core::scoring::methods::CenPairMotifDegreeEnergyCreator , core::scoring::methods::CenPairMotifEnergyCreator , core::scoring::methods::CenRotEnvEnergyCreator , core::scoring::methods::CenRotPairEnergyCreator , core::scoring::methods::ChainbreakEnergyCreator , core::scoring::methods::ChemicalShiftAnisotropyEnergyCreator , core::scoring::methods::ContactOrderEnergyCreator , core::scoring::methods::CovalentLabelingEnergyCreator , core::scoring::methods::CovalentLabelingFAEnergyCreator , core::scoring::methods::CustomAtomPairEnergyCreator , core::scoring::methods::D2H_SA_EnergyCreator , core::scoring::methods::dfire::DFIRE_EnergyCreator , core::scoring::methods::DipolarCouplingEnergyCreator , core::scoring::methods::DirectReadoutEnergyCreator , core::scoring::methods::DistanceChainbreakEnergyCreator , core::scoring::methods::DNA_BaseEnergyCreator , core::scoring::methods::DNA_DihedralEnergyCreator , core::scoring::methods::DNA_EnvPairEnergyCreator , core::scoring::methods::DNA_ReferenceEnergyCreator , core::scoring::methods::EnergyMethodCreator , core::scoring::methods::EnvEnergyCreator , core::scoring::methods::EnvSmoothEnergyCreator , core::scoring::methods::Fa_MbenvEnergyCreator , core::scoring::methods::Fa_MbsolvEnergyCreator , core::scoring::methods::FACTSEnergyCreator , core::scoring::methods::FreeDOF_EnergyCreator , core::scoring::methods::GaussianOverlapEnergyCreator , core::scoring::methods::GenBornEnergyCreator , core::scoring::methods::GenericBondedEnergyCreator , core::scoring::methods::GoapEnergyCreator , core::scoring::methods::HRF_MSLabelingEnergyCreator , core::scoring::methods::HRFDynamicsEnergyCreator , core::scoring::methods::HybridVDW_EnergyCreator , core::scoring::methods::HydroxylTorsionEnergyCreator , core::scoring::methods::IntermolEnergyCreator , core::scoring::methods::LinearBranchEnergyCreator , core::scoring::methods::LinearChainbreakEnergyCreator , core::scoring::methods::LK_hackCreator , core::scoring::methods::LK_PolarNonPolarEnergyCreator , core::scoring::methods::MembraneCbetaEnergyCreator , core::scoring::methods::MembraneCenPairEnergyCreator , core::scoring::methods::MembraneEnvEnergyCreator , core::scoring::methods::MembraneEnvPenaltiesCreator , core::scoring::methods::MembraneEnvSmoothEnergyCreator , core::scoring::methods::MembraneLipoCreator , core::scoring::methods::MissingEnergyCreator , core::scoring::methods::MMBondAngleEnergyCreator , core::scoring::methods::MMBondLengthEnergyCreator , core::scoring::methods::MMLJEnergyInterCreator , core::scoring::methods::MMLJEnergyIntraCreator , core::scoring::methods::MMTorsionEnergyCreator , core::scoring::methods::MotifDockEnergyCreator , core::scoring::methods::MultipoleElecEnergyCreator , core::scoring::methods::NMerPSSMEnergyCreator , core::scoring::methods::NMerRefEnergyCreator , core::scoring::methods::NMerSVMEnergyCreator , core::scoring::methods::OmegaTetherEnergyCreator , core::scoring::methods::OtherPoseEnergyCreator , core::scoring::methods::P_AA_EnergyCreator , core::scoring::methods::P_AA_pp_EnergyCreator , core::scoring::methods::P_AA_ss_EnergyCreator , core::scoring::methods::PackStatEnergyCreator , core::scoring::methods::PairEnergyCreator , core::scoring::methods::PeptideBondEnergyCreator , core::scoring::methods::pHEnergyCreator , core::scoring::methods::PointWaterEnergyCreator , core::scoring::methods::PoissonBoltzmannEnergyCreator , core::scoring::methods::ProClosureEnergyCreator , core::scoring::methods::ProQ_EnergyCreator , core::scoring::methods::RamachandranEnergy2BCreator , core::scoring::methods::RamachandranEnergyCreator , core::scoring::methods::RamaPreProEnergyCreator , core::scoring::methods::ReferenceEnergyCreator , core::scoring::methods::ReferenceEnergyNoncanonicalCreator , core::scoring::methods::ResidualDipolarCouplingEnergy_RohlCreator , core::scoring::methods::ResidualDipolarCouplingEnergyCreator , core::scoring::methods::RG_Energy_FastCreator , core::scoring::methods::RG_LocalEnergyCreator , core::scoring::methods::RingClosureEnergyCreator , core::scoring::methods::RMS_EnergyCreator , core::scoring::methods::SA_EnergyCreator , core::scoring::methods::SASAEnergyCreator , core::scoring::methods::SecondaryStructureEnergyCreator , core::scoring::methods::SequenceDependentRefEnergyCreator , core::scoring::methods::SmoothCenPairEnergyCreator , core::scoring::methods::SmoothEnvEnergyCreator , core::scoring::methods::SplitUnfoldedTwoBodyEnergyCreator , core::scoring::methods::SSElementMotifContactEnergyCreator , core::scoring::methods::SuckerEnergyCreator , core::scoring::methods::SymmetricLigandEnergyCreator , core::scoring::methods::UnfoldedStateEnergyCreator , core::scoring::methods::VdWTinkerEnergyCreator , core::scoring::methods::WaterAdductHBondEnergyCreator , core::scoring::methods::WaterAdductIntraEnergyCreator , core::scoring::methods::WaterSpecificEnergyCreator , core::scoring::methods::YHHPlanarityEnergyCreator , core::scoring::mhc_epitope_energy::MHCEpitopeEnergyCreator , core::scoring::netcharge_energy::NetChargeEnergyCreator , core::scoring::nv::NVscoreCreator , core::scoring::orbitals::OrbitalsScoreCreator , core::scoring::packing::HolesEnergyCreator , core::scoring::packing::SurfEnergyCreator , core::scoring::packing::SurfVolEnergyCreator , core::scoring::rna::chemical_shift::RNA_ChemicalShiftEnergyCreator , core::scoring::rna::data::RNA_ChemicalMappingEnergyCreator , core::scoring::rna::data::RNA_DataBackboneEnergyCreator , core::scoring::rna::RG_Energy_RNACreator , core::scoring::rna::RNA_BulgeEnergyCreator , core::scoring::rna::RNA_FullAtomStackingEnergyCreator , core::scoring::rna::RNA_FullAtomVDW_BasePhosphateCreator , core::scoring::rna::RNA_JR_SuiteEnergyCreator , core::scoring::rna::RNA_LJ_BaseEnergyCreator , core::scoring::rna::RNA_LowResolutionPotentialCreator , core::scoring::rna::RNA_PairwiseLowResolutionEnergyCreator , core::scoring::rna::RNA_PartitionEnergyCreator , core::scoring::rna::RNA_StubCoordinateEnergyCreator , core::scoring::rna::RNA_SugarCloseEnergyCreator , core::scoring::rna::RNA_SuiteEnergyCreator , core::scoring::rna::RNA_TorsionEnergyCreator , core::scoring::rna::RNA_VDW_EnergyCreator , core::scoring::rna::RNP_LowResEnergyCreator , core::scoring::rna::RNP_LowResPairDistEnergyCreator , core::scoring::rna::RNP_LowResStackEnergyCreator , core::scoring::rna::StackElecEnergyCreator , core::scoring::rna::TNA_SuiteEnergyCreator , core::scoring::saxs::FastSAXSEnergyCreator , core::scoring::saxs::SAXSEnergy , core::scoring::saxs::SAXSEnergyCreator , core::scoring::saxs::SAXSEnergyCreatorCEN , core::scoring::saxs::SAXSEnergyCreatorFA , core::scoring::sym_e::symECreator , core::scoring::util_methods::DumpTrajectoryEnergyCreator , core::scoring::vdwaals::VDW_EnergyCreator , protocols::fldsgn::potentials::AACompositionEnergyCreator , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergyCreator , protocols::membrane::scoring::FaWaterToBilayerEnergyCreator , protocols::nmr::pcs::PCSEnergyCreator , protocols::nmr::pre::PREEnergyCreator , protocols::nmr::rdc::RDCEnergyCreator , protocols::rna::AlignmentEnergyCreator , protocols::scoring::methods::EnsembleEnergyCreator , protocols::scoring::methods::InterchainEnvEnergyCreator , protocols::scoring::methods::InterchainPairEnergyCreator , protocols::scoring::methods::pcs2::PcsEnergyCreator , protocols::scoring::methods::pcs::PseudocontactShiftEnergyCreator , protocols::scoring::methods::pcsTs1::PseudocontactShiftEnergyCreator_Ts1 , protocols::scoring::methods::pcsTs2::PseudocontactShiftEnergyCreator_Ts2 , protocols::scoring::methods::pcsTs3::PseudocontactShiftEnergyCreator_Ts3 , protocols::scoring::methods::pcsTs4::PseudocontactShiftEnergyCreator_Ts4 , protocols::scoring::methods::ResidualDipolarCouplingEnergyRigidSegmentsCreator , protocols::scoring::methods::saxs::PDDFEnergy , protocols::scoring::methods::saxs::PDDFEnergyCreator , protocols::scoring::methods::SpecialRotamerEnergyCreator , protocols::scoring::methods::TargetClashEnergyCreator , protocols::scoring::VDW_GridEnergyCreator
• create_ensemble() : protocols::simple_moves::ShakeStructureMover
• create_envpairpotential_instance() : core::scoring::ScoringManager
• create_enzdes_movemap() : protocols::enzdes::EnzdesBaseProtocol
• create_enzdes_pack_task() : protocols::enzdes::EnzdesBaseProtocol
• create_etable_instance() : core::scoring::ScoringManager
• create_evaluator() : protocols::match::output::ProcessorFactory
• create_excl_info() : core::scoring::ResidueExclParams
• create_exgs() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• create_fa_and_cen_constraint() : protocols::noesy_assign::CrossPeak
• create_fa_dunbrack_libraries() : core::pack::dunbrack::RotamerLibrary
• create_fa_dunbrack_libraries_02_from_ASCII() : core::pack::dunbrack::RotamerLibrary
• create_fa_dunbrack_libraries_02_from_binary() : core::pack::dunbrack::RotamerLibrary
• create_fa_dunbrack_libraries_10_from_ASCII() : core::pack::dunbrack::RotamerLibrary
• create_fa_dunbrack_libraries_10_from_binary() : core::pack::dunbrack::RotamerLibrary
• create_fa_dunbrack_libraries_from_ASCII() : core::pack::dunbrack::RotamerLibrary
• create_fa_dunbrack_libraries_from_binary() : core::pack::dunbrack::RotamerLibrary
• create_facts_potential_instance() : core::scoring::ScoringManager
• create_false_movemap() : protocols::denovo_design::components::RemodelLoopMoverPoseFolder
• create_fasta_file() : core::io::external::PsiPredInterface
• create_faster_ig_from_rot_to_pack() : protocols::pack_daemon::FASTER_IG_Repacker
• create_features_reporter() : protocols::antibody::AntibodyFeaturesCreator , protocols::antibody::clusters::CDRClusterFeaturesCreator , protocols::features::AtomAtomPairFeaturesCreator , protocols::features::AtomInResidueAtomInResiduePairFeaturesCreator , protocols::features::AtomTypesFeaturesCreator , protocols::features::BetaTurnDetectionFeaturesCreator , protocols::features::ChargeChargeFeaturesCreator , protocols::features::DdGFeaturesCreator , protocols::features::FeaturesReporterCreator , protocols::features::GeometricSolvationFeaturesCreator , protocols::features::HBondFeaturesCreator , protocols::features::HBondParameterFeaturesCreator , protocols::features::helixAssembly::ConcurrencyTestCreator , protocols::features::helixAssembly::HelixBundleFeaturesCreator , protocols::features::HelixCapFeaturesCreator , protocols::features::InterfaceFeaturesCreator , protocols::features::JobDataFeaturesCreator , protocols::features::LoopAnchorFeaturesCreator , protocols::features::ModelFeaturesCreator , protocols::features::OrbitalsFeaturesCreator , protocols::features::PairFeaturesCreator , protocols::features::PdbDataFeaturesCreator , protocols::features::PoseCommentsFeaturesCreator , protocols::features::PoseConformationFeaturesCreator , protocols::features::ProteinBackboneAtomAtomPairFeaturesCreator , protocols::features::ProteinBackboneTorsionAngleFeaturesCreator , protocols::features::ProteinBondGeometryFeaturesCreator , protocols::features::ProteinResidueConformationFeaturesCreator , protocols::features::ProteinRMSDFeaturesCreator , protocols::features::ProteinRMSDNoSuperpositionFeaturesCreator , protocols::features::RadiusOfGyrationFeaturesCreator , protocols::features::ResidueBurialFeaturesCreator , protocols::features::ResidueConformationFeaturesCreator , protocols::features::ResidueFeaturesCreator , protocols::features::ResidueGridScoresFeaturesCreator , protocols::features::ResidueScoresFeaturesCreator , protocols::features::ResidueSecondaryStructureFeaturesCreator , protocols::features::ResidueTotalScoresFeaturesCreator , protocols::features::ResidueTypesFeaturesCreator , protocols::features::RotamerBoltzmannWeightFeaturesCreator , protocols::features::RotamerFeaturesCreator , protocols::features::RotamerRecoveryFeaturesCreator , protocols::features::RuntimeFeaturesCreator , protocols::features::SaltBridgeFeaturesCreator , protocols::features::ScoreFunctionFeaturesCreator , protocols::features::ScoreTypeFeaturesCreator , protocols::features::ScreeningFeaturesCreator , protocols::features::SecondaryStructureSegmentFeaturesCreator , protocols::features::SimpleMetricFeaturesCreator , protocols::features::SmotifFeaturesCreator , protocols::features::strand_assembly::SandwichFeaturesCreator , protocols::features::strand_assembly::StrandBundleFeaturesCreator , protocols::features::StructureFeaturesCreator , protocols::features::StructureScoresFeaturesCreator , protocols::features::TaskOperationFeaturesCreator , protocols::features::TotalScoreFeaturesCreator , protocols::features::TrajectoryMapFeaturesCreator , protocols::features::UnrecognizedAtomFeaturesCreator , protocols::features::WaterFeaturesCreator
• create_file_contents_instance() : core::scoring::ScoringManager
• create_filter() : protocols::calc_taskop_filters::ConservedPosMutationFilterCreator , protocols::calc_taskop_filters::MultipleSigmoidsFilterCreator , protocols::calc_taskop_filters::OperatorFilterCreator , protocols::calc_taskop_filters::RelativePoseFilterCreator , protocols::calc_taskop_filters::RotamerBoltzmannWeight2Creator , protocols::calc_taskop_filters::RotamerBoltzmannWeightFilterCreator , protocols::calc_taskop_filters::SigmoidFilterCreator , protocols::constraint_filters::ConstraintScoreCutoffFilterCreator , protocols::constraint_filters::ConstraintScoreFilterCreator , protocols::constraint_filters::SavePoseConstraintToFileFilterCreator , protocols::constraint_filters::ShowConstraintsFilterCreator , protocols::cyclic_peptide::CycpepSymmetryFilterCreator , protocols::cyclic_peptide::OversaturatedHbondAcceptorFilterCreator , protocols::cyclic_peptide::PeptideInternalHbondsFilterCreator , protocols::denovo_design::filters::CavityVolumeFilterCreator , protocols::denovo_design::filters::ExposedHydrophobicsFilterCreator , protocols::denovo_design::filters::PreProlineFilterCreator , protocols::denovo_design::filters::SSPredictionFilterCreator , protocols::denovo_design::filters::SSShapeComplementarityFilterCreator , protocols::dna_dock::DNAClashCheckFilterCreator , protocols::dna_dock::PropagateClashCheckFilterCreator , protocols::enzdes::DiffAtomSasaFilterCreator , protocols::enzdes::EnzdesScorefileFilterCreator , protocols::enzdes::EnzScoreFilterCreator , protocols::enzdes::LigBurialFilterCreator , protocols::enzdes::LigDSasaFilterCreator , protocols::enzdes::LigInterfaceEnergyFilterCreator , protocols::enzdes::RemoveLigandFilterCreator , protocols::enzdes::RepackWithoutLigandFilterCreator , protocols::enzdes::ResidueConformerFilterCreator , protocols::evolution::AASynthesisFitnessCostFilterCreator , protocols::evolution::AlignmentAAFinderFilterCreator , protocols::evolution::AlignmentGapInserterFilterCreator , protocols::filters::CalculatorFilterCreator , protocols::filters::CombinedFilterCreator , protocols::filters::CompoundFilterCreator , protocols::filters::ContingentFilterCreator , protocols::filters::FalseFilterCreator , protocols::filters::FilterCreator , protocols::filters::IfThenFilterCreator , protocols::filters::MoveBeforeFilterCreator , protocols::filters::ReplicateFilterCreator , protocols::filters::StochasticFilterCreator , protocols::filters::TimeFilterCreator , protocols::filters::TrueFilterCreator , protocols::fldsgn::filters::CoreDunbrackFilterCreator , protocols::fldsgn::filters::FragQualFilterCreator , protocols::fldsgn::filters::HelixBendFilterCreator , protocols::fldsgn::filters::HelixKinkFilterCreator , protocols::fldsgn::filters::HelixPairingFilterCreator , protocols::fldsgn::filters::HSSTripletFilterCreator , protocols::fldsgn::filters::InterlockingAromaFilterCreator , protocols::fldsgn::filters::NcontactsFilterCreator , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilterCreator , protocols::fldsgn::filters::SecondaryStructureCountFilterCreator , protocols::fldsgn::filters::SecondaryStructureFilterCreator , protocols::fldsgn::filters::SecondaryStructureHasResidueFilterCreator , protocols::fldsgn::filters::SheetTopologyFilterCreator , protocols::fldsgn::filters::StrandCurvatureByLevelsCreator , protocols::fldsgn::filters::StrandHelixGeometryFilterCreator , protocols::fold_from_loops::filters::ConstraintFulfilmentFilterCreator , protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilterCreator , protocols::fold_from_loops::filters::ScorePoseSegmentFromResidueSelectorFilterCreator , protocols::frag_picker::FragmentScoreFilterCreator , protocols::hbnet::HBNetScoreFilterCreator , protocols::helical_bundle::BundleReporterFilterCreator , protocols::indexed_structure_store::filters::FragmentLookupFilterCreator , protocols::ligand_docking::AtomCountFilterCreator , protocols::ligand_docking::ChainExistsFilterCreator , protocols::ligand_docking::CompleteConnectionsFilterCreator , protocols::ligand_docking::HBondAcceptorFilterCreator , protocols::ligand_docking::HBondDonorFilterCreator , protocols::ligand_docking::HeavyAtomFilterCreator , protocols::ligand_docking::MolarMassFilterCreator , protocols::ligand_docking::MolecularMassFilterCreator , protocols::loops::filters::LoopAnalyzerFilterCreator , protocols::matdes::ClashCheckFilterCreator , protocols::matdes::GetRBDOFValuesCreator , protocols::matdes::InterfacePackingFilterCreator , protocols::matdes::OligomericAverageDegreeFilterCreator , protocols::matdes::SymUnsatHbondFilterCreator , protocols::peptide_deriver::PeptideDeriverFilterCreator , protocols::protein_interface_design::filters::AtomicContactCountFilterCreator , protocols::protein_interface_design::filters::AverageDegreeFilterCreator , protocols::protein_interface_design::filters::BindingStrainFilterCreator , protocols::protein_interface_design::filters::BoltzmannFilterCreator , protocols::protein_interface_design::filters::ClashWithTargetFilterCreator , protocols::protein_interface_design::filters::DesignableResiduesFilterCreator , protocols::protein_interface_design::filters::DisulfideFilterCreator , protocols::protein_interface_design::filters::FilterScanFilterCreator , protocols::protein_interface_design::filters::FNatFilterCreator , protocols::protein_interface_design::filters::HbondsToAtomFilterCreator , protocols::protein_interface_design::filters::HbondsToResidueFilterCreator , protocols::protein_interface_design::filters::InterfaceHolesFilterCreator , protocols::protein_interface_design::filters::IRmsdFilterCreator , protocols::protein_interface_design::filters::LRmsdFilterCreator , protocols::protein_interface_design::filters::RelativeSegmentFilterCreator , protocols::protein_interface_design::filters::RmsdFilterCreator , protocols::protein_interface_design::filters::RmsdSimpleFilterCreator , protocols::protein_interface_design::filters::SequenceRecoveryFilterCreator , protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilterCreator , protocols::protein_interface_design::filters::SSamountFilterCreator , protocols::protein_interface_design::filters::StubScoreFilterCreator , protocols::protein_interface_design::filters::StubScoreLoopsFilterCreator , protocols::protein_interface_design::filters::TorsionCreator , protocols::recon_design::FitnessFilterCreator , protocols::score_filters::GeometryFilterCreator , protocols::score_filters::ScoreCutoffFilterCreator , protocols::score_filters::ScoreTypeFilterCreator , protocols::simple_ddg::AlaScanFilterCreator , protocols::simple_ddg::DdgFilterCreator , protocols::simple_ddg::DdGScanCreator , protocols::simple_ddg::InterfaceBindingEnergyDensityFilterCreator , protocols::simple_ddg::SSElementBisectddGFilterCreator , protocols::simple_filters::AngleToVectorFilterCreator , protocols::simple_filters::AtomicContactFilterCreator , protocols::simple_filters::AtomicDistanceFilterCreator , protocols::simple_filters::AveragePathLengthFilterCreator , protocols::simple_filters::BuriedSurfaceAreaFilterCreator , protocols::simple_filters::BuriedUnsatHbondFilterCreator , protocols::simple_filters::ChainBreakFilterCreator , protocols::simple_filters::ChainCountFilterCreator , protocols::simple_filters::ContactMolecularSurfaceFilterCreator , protocols::simple_filters::DeltaFilterCreator , protocols::simple_filters::DisulfideEntropyFilterCreator , protocols::simple_filters::EnergyPerResidueFilterCreator , protocols::simple_filters::ExpiryFilterCreator , protocols::simple_filters::FileExistFilterCreator , protocols::simple_filters::FileRemoveFilterCreator , protocols::simple_filters::HelixHelixAngleFilterCreator , protocols::simple_filters::HolesFilterCreator , protocols::simple_filters::InterfaceHbondsFilterCreator , protocols::simple_filters::InterfaceHydrophobicResidueContactsFilterCreator , protocols::simple_filters::InterfaceSasaFilterCreator , protocols::simple_filters::InterRepeatContactFilterCreator , protocols::simple_filters::IntraRepeatContactFilterCreator , protocols::simple_filters::LeastNativeLike9merFilterCreator , protocols::simple_filters::LongestContinuousApolarSegmentFilterCreator , protocols::simple_filters::LongestContinuousPolarSegmentFilterCreator , protocols::simple_filters::MembAccesResidueLipophilicityFilterCreator , protocols::simple_filters::MotifScoreFilterCreator , protocols::simple_filters::MPSpanAngleFilterCreator , protocols::simple_filters::MutationsFilterCreator , protocols::simple_filters::NeighborTypeFilterCreator , protocols::simple_filters::NetChargeFilterCreator , protocols::simple_filters::NMerPSSMEnergyFilterCreator , protocols::simple_filters::NMerSVMEnergyFilterCreator , protocols::simple_filters::NonSequentialNeighborsFilterCreator , protocols::simple_filters::PackStatFilterCreator , protocols::simple_filters::PoseCommentFilterCreator , protocols::simple_filters::PoseInfoFilterCreator , protocols::simple_filters::RangeFilterCreator , protocols::simple_filters::ReadPoseExtraScoreFilterCreator , protocols::simple_filters::RepeatParameterFilterCreator , protocols::simple_filters::ReportFilterCreator , protocols::simple_filters::ResidueBurialFilterCreator , protocols::simple_filters::ResidueChiralityFilterCreator , protocols::simple_filters::ResidueCountFilterCreator , protocols::simple_filters::ResidueDepthFilterCreator , protocols::simple_filters::ResidueDistanceFilterCreator , protocols::simple_filters::ResidueIEFilterCreator , protocols::simple_filters::ResidueLipophilicityFilterCreator , protocols::simple_filters::ResidueSelectionDistanceFilterCreator , protocols::simple_filters::ResidueSetChainEnergyFilterCreator , protocols::simple_filters::ResiduesInInterfaceFilterCreator , protocols::simple_filters::SaveResfileToDiskFilterCreator , protocols::simple_filters::SecretionPredictionFilterCreator , protocols::simple_filters::SequenceDistanceFilterCreator , protocols::simple_filters::ShapeComplementarityFilterCreator , protocols::simple_filters::SidechainRmsdFilterCreator , protocols::simple_filters::SimpleHbondsToAtomFilterCreator , protocols::simple_filters::SimpleMetricFilterCreator , protocols::simple_filters::SpanTopologyMatchPoseFilterCreator , protocols::simple_filters::SSElementLengthFilterCreator , protocols::simple_filters::SSElementMotifContactFilterCreator , protocols::simple_filters::SSMotifFinderFilterCreator , protocols::simple_filters::StemFinderFilterCreator , protocols::simple_filters::SymmetricMotifFilterCreator , protocols::simple_filters::TaskAwareSASAFilterCreator , protocols::simple_filters::TaskAwareScoreTypeFilterCreator , protocols::simple_filters::TerminusDistanceFilterCreator , protocols::simple_filters::TMsAACompFilterCreator , protocols::simple_filters::TMsSpanMembraneFilterCreator , protocols::simple_filters::TotalSasaFilterCreator
• create_filters() : protocols::match::output::ProcessorFactory
• create_final_fullatom_refinement_move_generator() : protocols::helical_bundle_predict::HelicalBundlePredictApplication
• create_flexbb_interaction_graph() : protocols::flexpack::interaction_graph::FlexbbIGFactory
• create_float_constraint() : protocols::noesy_assign::PeakAssignment
• create_fold_tree_with_cutpoints() : protocols::ligand_docking::MinimizeBackbone
• create_fold_tree_with_ligand_jumps_from_attach_pts() : protocols::ligand_docking::MinimizeBackbone
• create_fragment_and_rigid_mover() : protocols::medal::MedalMover
• create_fragment_mover() : protocols::medal::MedalMover
• create_fragment_movers() : protocols::forge::remodel::RemodelLoopMover
• create_fragment_movers_limit_size() : protocols::forge::remodel::RemodelLoopMover
• create_fresh_packer_neighbor_graph() : protocols::minimization_packing::GreenPacker
• create_fresh_rotamers() : protocols::minimization_packing::GreenPacker
• create_fresh_task() : protocols::minimization_packing::GreenPacker
• create_from_cacheable_data() : protocols::denovo_design::components::StructureDataFactory
• create_from_file() : protocols::rosetta_scripts::XmlObjects
• create_from_motifs() : protocols::denovo_design::components::StructureDataFactory
• create_from_pose() : protocols::denovo_design::components::StructureDataFactory , protocols::toolbox::ResidueNetwork
• create_from_remarks() : protocols::denovo_design::components::StructureDataFactory
• create_from_spanfile() : core::conformation::membrane::SpanningTopology
• create_from_string() : protocols::rosetta_scripts::XmlObjects
• create_from_structure() : core::conformation::membrane::SpanningTopology
• create_from_tag() : protocols::denovo_design::architects::DeNovoArchitectFactory
• create_from_xml() : protocols::denovo_design::components::StructureDataFactory
• create_fullatom_disulfide_potential_instance() : core::scoring::ScoringManager
• create_fullatom_scorefunction() : protocols::helical_bundle_predict::HelicalBundlePredictApplication
• create_function() : protocols::constraint_generator::CoordinateConstraintGenerator
• create_genborn_instance() : core::scoring::ScoringManager
• create_generic_bonded_potential_instance() : core::scoring::ScoringManager
• create_grid() : protocols::magnesium::SampleGrid , protocols::qsar::scoring_grid::AtrGridCreator , protocols::qsar::scoring_grid::ChargeGridCreator , protocols::qsar::scoring_grid::ClassicGridCreator , protocols::qsar::scoring_grid::GridCreator , protocols::qsar::scoring_grid::HbaGridCreator , protocols::qsar::scoring_grid::HbdGridCreator , protocols::qsar::scoring_grid::LigandPropertyScoreCreator , protocols::qsar::scoring_grid::PCSMultiGridCreator , protocols::qsar::scoring_grid::PCSSingleGridCreator , protocols::qsar::scoring_grid::RepGridCreator , protocols::qsar::scoring_grid::ShapeGridCreator , protocols::qsar::scoring_grid::SiteGridCreator , protocols::qsar::scoring_grid::SolvationGridCreator , protocols::qsar::scoring_grid::SolvationMetaGridCreator , protocols::qsar::scoring_grid::VdwGridCreator
• create_grid_for_bb() : protocols::match::Bool3DGrid
• create_grid_for_sphere() : protocols::match::Bool3DGrid
• create_grouper() : protocols::match::output::ProcessorFactory
• create_hotspot_after_pose() : protocols::hotspot_hashing::HotspotStubSet
• create_hts_for_chi() : protocols::match::upstream::FullChiSampleSet
• create_hxl_potential_instance() : core::scoring::ScoringManager
• create_ideal_bond_length_set() : core::chemical::ChemicalManager
• create_info() : core::scoring::FACTSRsdTypeInfo
• create_initial_job_dag() : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::JobQueen , protocols::jd3::standard::StandardJobQueen , protocols::multistage_rosetta_scripts::MRSJobQueen , protocols::multistage_rosetta_scripts::MRSJobQueenChecker , protocols::rosetta_scripts::RosettaScriptsJobQueen
• create_inner_cycle() : protocols::loops::loop_mover::refine::LoopRefineInnerCycleFactory
• create_inner_larval_job() : protocols::jd3::standard::StandardJobQueen
• create_inputter() : protocols::jd3::chunk_library_inputters::ChunkLibraryInputterCreator , protocols::jd3::chunk_library_inputters::PDBChunkLibraryInputterCreator , protocols::jd3::full_model_inputters::FullModelInputterCreator , protocols::jd3::full_model_inputters::PDBFullModelInputterCreator , protocols::jd3::full_model_inputters::SilentFileFullModelInputterCreator , protocols::jd3::pose_inputters::PDBPoseInputterCreator , protocols::jd3::pose_inputters::PoseInputterCreator , protocols::jd3::pose_inputters::SilentFilePoseInputterCreator
• create_instance() : protocols::denovo_design::architects::DeNovoArchitectFactory
• create_interaction_graph() : core::pack::interaction_graph::InteractionGraphFactory
• create_intrares_count_pair_function() : core::scoring::etable::count_pair::CountPairFactory
• create_job_distributor() : protocols::jd2::JobDistributorFactory , protocols::jd3::JobDistributorFactory
• create_job_inputter() : protocols::jd2::JobDistributorFactory
• create_job_outputter() : protocols::jd2::JobDistributorFactory
• create_job_result() : protocols::jd3::chunk_library::MoverAndChunkLibraryJob , protocols::jd3::jobs::MoverJob
• create_job_summary() : protocols::jd3::chunk_library::MoverAndChunkLibraryJob , protocols::jd3::jobs::MoverJob
• create_JobInputter() : protocols::comparative_modeling::GenericJobInputterCreator , protocols::comparative_modeling::ThreadingJobInputterCreator , protocols::enzdes::EnzdesJobInputterCreator , protocols::features::DatabaseJobInputterCreator , protocols::jd2::AtomTreeDiffJobInputterCreator , protocols::jd2::EmptyPoseJobInputterCreator , protocols::jd2::EnsembleJobInputterCreator , protocols::jd2::JobInputterCreator , protocols::jd2::LargeNstructJobInputterCreator , protocols::jd2::LazySilentFileJobInputterCreator , protocols::jd2::PDBJobInputterCreator , protocols::jd2::PoseInputStreamJobInputterCreator , protocols::jd2::ScreeningJobInputterCreator , protocols::jd2::SerializedPoseJobInputterCreator , protocols::jd2::SilentFileJobInputterCreator , protocols::make_rot_lib::MakeRotLibJobInputterCreator , protocols::protein_interface_design::ParserJobInputterCreator
• create_JobOutputter() : protocols::enzdes::EnzdesJobOutputterCreator , protocols::features::DatabaseJobOutputterCreator , protocols::jd2::AtomTreeDiffJobOutputterCreator , protocols::jd2::JobOutputterCreator , protocols::jd2::mmCIFJobOutputterCreator , protocols::jd2::mmtfJobOutputterCreator , protocols::jd2::NoOutputJobOutputterCreator , protocols::jd2::PDBJobOutputterCreator , protocols::jd2::RNA_DeNovoJobOutputterCreator , protocols::jd2::ScoreOnlyJobOutputterCreator , protocols::jd2::SerializedPoseJobOutputterCreator , protocols::jd2::SilentFileJobOutputterCreator
• create_jump_def() : protocols::abinitio::Templates
• create_jump_fragments() : protocols::jumping::BasePairingLibrary , protocols::jumping::DisulfPairingLibrary , protocols::jumping::PairingLibrary
• create_jump_moves() : protocols::abinitio::KinematicAbinitio
• create_jump_sample() : protocols::abinitio::FixTemplateJumpSetup , protocols::abinitio::TemplateJumpSetup , protocols::jumping::BaseJumpSetup , protocols::jumping::JumpSelector , protocols::jumping::JumpSetup , protocols::jumping::JumpsFromAllPairings , protocols::jumping::ResiduePairJumpSetup , protocols::jumping::SheetBuilder
• create_jump_selector() : core::select::jump_selector::AndJumpSelectorCreator , core::select::jump_selector::InterchainJumpSelectorCreator , core::select::jump_selector::JumpIndexSelectorCreator , core::select::jump_selector::JumpSelectorCreator , core::select::jump_selector::NotJumpSelectorCreator , core::select::jump_selector::OrJumpSelectorCreator
• create_key() : protocols::frag_picker::VallChunk
• create_large_cluster_centers_member_list() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• create_larval_job() : protocols::jd3::standard::StandardJobQueen
• create_loader() : protocols::ligand_docking::InterfaceBuilderLoaderCreator , protocols::ligand_docking::LigandAreaLoaderCreator , protocols::ligand_docking::MoveMapBuilderLoaderCreator , protocols::loops::loops_definers::LoopsDefinerLoaderCreator , protocols::parser::ConstraintGeneratorLoaderCreator , protocols::parser::DatabaseSessionLoaderCreator , protocols::parser::DataLoaderCreator , protocols::parser::FragSetLoaderCreator , protocols::parser::JumpSelectorLoaderCreator , protocols::parser::MonteCarloLoaderCreator , protocols::parser::MoveMapFactoryLoaderCreator , protocols::parser::PackerPaletteLoaderCreator , protocols::parser::ResidueSelectorLoaderCreator , protocols::parser::ResLvlTaskOperationLoaderCreator , protocols::parser::ScoreFunctionLoaderCreator , protocols::parser::SimpleMetricLoaderCreator , protocols::parser::TaskOperationLoaderCreator , protocols::qsar::scoring_grid::ScoringGridLoaderCreator
• create_loop_mover() : protocols::loops::LoopMoverFactory
• create_loophash_WUs() : protocols::loophash::MPI_LoopHashRefine_Master
• create_loops() : protocols::denovo_design::components::FoldGraph , protocols::denovo_design::movers::BuildDeNovoBackboneMover
• create_loops_definer() : protocols::loops::loops_definers::LoopsDatabaseDefinerCreator , protocols::loops::loops_definers::LoopsDefinerCreator , protocols::loops::loops_definers::LoopsDefinerFactory , protocols::loops::loops_definers::LoopsExplicitDefinerCreator , protocols::loops::loops_definers::LoopsFileDefinerCreator , protocols::loops::loops_definers::LoopsStringDefinerCreator
• create_loops_dfs() : protocols::denovo_design::components::FoldGraph
• create_mainchain_scoretable_instance() : core::scoring::ScoringManager
• create_map_helix_pairings() : protocols::fldsgn::topology::HelixPairingSet
• create_match_score_writer() : protocols::match::output::ProcessorFactory
• create_maximum_length_pose() : protocols::pose_length_moves::NearNativeLoopCloser
• create_mean_field() : protocols::mean_field::MeanFieldFactory
• create_memb_etable_instance() : core::scoring::ScoringManager
• create_memb_etable_instance_silly() : core::scoring::ScoringManager
• create_membrane_data_instance() : core::scoring::ScoringManager
• create_membrane_fa_potential_instance() : core::scoring::ScoringManager
• create_membrane_potential_instance() : core::scoring::ScoringManager
• create_membrane_virtual() : protocols::membrane::visualize::VisualizeMembraneMover
• create_metric() : protocols::multistage_rosetta_scripts::cluster::ClusterMetricCreator , protocols::multistage_rosetta_scripts::cluster::metrics::JumpMetricCreator , protocols::multistage_rosetta_scripts::cluster::metrics::SequenceMetricCreator
• create_mhc_csv_contents() : core::scoring::ScoringManager
• create_mhc_epitope_energy_setup_instance() : core::scoring::ScoringManager
• create_mhc_map_from_db() : core::scoring::ScoringManager
• create_mhc_matrix_contents() : core::scoring::ScoringManager
• create_mm_atom_type_set() : core::chemical::ChemicalManager
• create_mm_bondangle_library_instance() : core::scoring::ScoringManager
• create_mm_bondlength_library_instance() : core::scoring::ScoringManager
• create_mm_lj_energy_table_instance() : core::scoring::ScoringManager
• create_mm_lj_library_instance() : core::scoring::ScoringManager
• create_mm_torsion_library_instance() : core::scoring::ScoringManager
• create_motif() : protocols::denovo_design::architects::StrandArchitect
• create_movemap_from_pose() : core::select::movemap::MoveMapFactory
• create_mover() : protocols::aa_composition::AddCompositionConstraintMoverCreator , protocols::aa_composition::AddHelixSequenceConstraintsMoverCreator , protocols::aa_composition::AddMHCEpitopeConstraintMoverCreator , protocols::aa_composition::AddNetChargeConstraintMoverCreator , protocols::aa_composition::ClearCompositionConstraintsMoverCreator , protocols::abinitio::abscript::AbscriptLoopCloserCMCreator , protocols::abinitio::abscript::AbscriptMoverCreator , protocols::abinitio::abscript::ConstraintPreparerCreator , protocols::abinitio::abscript::FragmentCMCreator , protocols::abinitio::abscript::FragmentJumpCMCreator , protocols::abinitio::abscript::RigidChunkCMCreator , protocols::abinitio::abscript::StructPerturberCMCreator , protocols::abinitio::DomainAssemblyCreator , protocols::analysis::GlycanInfoMoverCreator , protocols::analysis::InterfaceAnalyzerMoverCreator , protocols::analysis::LoopAnalyzerMoverCreator , protocols::analysis::simple_metrics::RunSimpleMetricsMoverCreator , protocols::antibody::AntibodyCDRGrafterCreator , protocols::antibody::AntibodyNumberingConverterMoverCreator , protocols::antibody::constraints::CDRDihedralConstraintMoverCreator , protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMoverCreator , protocols::antibody::constraints::ParatopeSiteConstraintMoverCreator , protocols::antibody::design::AntibodyDesignMoverCreator , protocols::antibody::design::MutateFrameworkForClusterCreator , protocols::antibody::snugdock::SnugDockCreator , protocols::backbone_moves::local_backbone_mover::LocalBackboneMoverCreator , protocols::backbone_moves::RandomizeBBByRamaPreProCreator , protocols::backrub::BackrubMoverCreator , protocols::backrub::BackrubProtocolCreator , protocols::backrub::BackrubSidechainMoverCreator , protocols::calc_taskop_movers::ConsensusDesignMoverCreator , protocols::calc_taskop_movers::CreateSequenceMotifMoverCreator , protocols::calc_taskop_movers::ForceDisulfidesMoverCreator , protocols::canonical_sampling::DbTrajectoryRecorderCreator , protocols::canonical_sampling::HamiltonianExchangeCreator , protocols::canonical_sampling::MetricRecorderCreator , protocols::canonical_sampling::MetropolisHastingsMoverCreator , protocols::canonical_sampling::ParallelTemperingCreator , protocols::canonical_sampling::PDBTrajectoryRecorderCreator , protocols::canonical_sampling::ProgressBarObserverCreator , protocols::canonical_sampling::SidechainMetropolisHastingsMoverCreator , protocols::canonical_sampling::SilentTrajectoryRecorderCreator , protocols::canonical_sampling::SimulatedTemperingCreator , protocols::canonical_sampling::TrialCounterObserverCreator , protocols::carbohydrates::CreateGlycanSequonMoverCreator , protocols::carbohydrates::GlycanSamplerCreator , protocols::carbohydrates::GlycanTreeMinMoverCreator , protocols::carbohydrates::GlycanTreeModelerCreator , protocols::carbohydrates::IdealizeAnomericHydrogensCreator , protocols::carbohydrates::LinkageConformerMoverCreator , protocols::carbohydrates::RingPlaneFlipMoverCreator , protocols::carbohydrates::SimpleGlycosylateMoverCreator , protocols::carbohydrates::TautomerizeAnomerMoverCreator , protocols::chemically_conjugated_docking::UBQ_GTPaseMoverCreator , protocols::comparative_modeling::LoopRelaxMoverCreator , protocols::constraint_generator::AddConstraintsCreator , protocols::constraint_generator::RemoveConstraintsCreator , protocols::constraint_movers::AddConstraintsToCurrentConformationMoverCreator , protocols::constraint_movers::ClearConstraintsMoverCreator , protocols::constraint_movers::ConstraintSetMoverCreator , protocols::constraint_movers::CstInfoMoverCreator , protocols::constraint_movers::ResidueTypeConstraintMoverCreator , protocols::contact_map::ContactMapCreator , protocols::coupled_moves::CoupledMovesProtocolCreator , protocols::cryst::CrystRMSCreator , protocols::cryst::DockLatticeMoverCreator , protocols::cryst::FitBfactorsMoverCreator , protocols::cryst::LoadDensityMapMoverCreator , protocols::cryst::MakeLatticeMoverCreator , protocols::cryst::MakeLayerMoverCreator , protocols::cryst::RecomputeDensityMapMoverCreator , protocols::cryst::ReportGradientsMoverCreator , protocols::cryst::SetCrystWeightMoverCreator , protocols::cryst::SetRefinementOptionsMoverCreator , protocols::cryst::TagPoseWithRefinementStatsMoverCreator , protocols::cryst::UpdateCrystInfoCreator , protocols::cryst::UpdateSolventMoverCreator , protocols::cutoutdomain::CutOutDomainCreator , protocols::cyclic_peptide::CreateAngleConstraintCreator , protocols::cyclic_peptide::CreateDistanceConstraintCreator , protocols::cyclic_peptide::CreateTorsionConstraintCreator , protocols::cyclic_peptide::CrosslinkerMoverCreator , protocols::cyclic_peptide::DeclareBondCreator , protocols::cyclic_peptide::FlipChiralityMoverCreator , protocols::cyclic_peptide::PeptideCyclizeMoverCreator , protocols::cyclic_peptide::PeptideStubMoverCreator , protocols::cyclic_peptide::SymmetricCycpepAlignCreator , protocols::cyclic_peptide::TryDisulfPermutationsCreator , protocols::denovo_design::DisulfidizeMoverCreator , protocols::denovo_design::movers::AddSegmentDataMoverCreator , protocols::denovo_design::movers::AlignResiduesMoverCreator , protocols::denovo_design::movers::BridgeChainsCreator , protocols::denovo_design::movers::BridgeChainsMoverCreator , protocols::denovo_design::movers::BuildDeNovoBackboneMoverCreator , protocols::denovo_design::movers::DeclareStructureDataCovalentBondMoverCreator , protocols::denovo_design::movers::ExtendChainMoverCreator , protocols::denovo_design::movers::FastDesignCreator , protocols::denovo_design::movers::FoldTreeFromFoldGraphMoverCreator , protocols::denovo_design::movers::MakeAsymmetricStructureDataMoverCreator , protocols::denovo_design::movers::RotateSegmentMoverCreator , protocols::denovo_design::movers::SealFoldTreeMoverCreator , protocols::denovo_design::movers::SetResidueAliasMoverCreator , protocols::design_opt::GreedyOptMutationMoverCreator , protocols::dna::DesignProteinBackboneAroundDNACreator , protocols::dna::DnaInterfaceMinMoverCreator , protocols::dna::DnaInterfaceMultiStateDesignCreator , protocols::dna::DnaInterfacePackerCreator , protocols::dna::SeparateDnaFromNonDnaCreator , protocols::docking::ConformerSwitchMoverCreator , protocols::docking::DockingHighResLegacyCreator , protocols::docking::DockingInitialPerturbationCreator , protocols::docking::DockingPrepackProtocolCreator , protocols::docking::DockingProtocolCreator , protocols::docking::DockingSlideIntoContactCreator , protocols::docking::DockMCMProtocolCreator , protocols::docking::DockMinMoverCreator , protocols::docking::DockSetupMoverCreator , protocols::docking::membrane::MPDockingMoverCreator , protocols::docking::membrane::MPDockingSetupMoverCreator , protocols::docking::membrane::MPFindInterfaceMoverCreator , protocols::docking::membrane::QuickRelaxPartnersSeparatelyCreator , protocols::docking::TemperedDockingCreator , protocols::electron_density::BfactorFittingMoverCreator , protocols::electron_density::ReportFSCCreator , protocols::electron_density::ScaleMapIntensitiesCreator , protocols::electron_density::SetupForDensityScoringMoverCreator , protocols::electron_density::VoxelSpacingRefinementMoverCreator , protocols::environment::CoMTrackerCMCreator , protocols::environment::EnvMoverCreator , protocols::environment::ScriptCMCreator , protocols::enzdes::AddOrRemoveMatchCstsCreator , protocols::enzdes::BackboneSamplerCreator , protocols::enzdes::EnzRepackMinimizeCreator , protocols::enzdes::PackRotamersMoverPartGreedyCreator , protocols::enzdes::PredesignPerturbMoverCreator , protocols::enzdes::UpdateEnzdesHeaderMoverCreator , protocols::enzymatic_movers::DNAMethyltransferaseMoverCreator , protocols::enzymatic_movers::GlycosyltransferaseMoverCreator , protocols::enzymatic_movers::KinaseMoverCreator , protocols::enzymatic_movers::NTerminalAcetyltransferaseMoverCreator , protocols::evolution::EvolutionaryDynamicsMoverCreator , protocols::evolution::NucleotideMutationCreator , protocols::farnesyl::InstallFarnesylMoverCreator , protocols::farnesyl::SampleFarnesylMoverCreator , protocols::features::InterfaceDdGMoverCreator , protocols::features::ReportToDBCreator , protocols::features::TrajectoryReportToDBCreator , protocols::fldsgn::BluePrintBDRCreator , protocols::fldsgn::CircularPermutationCreator , protocols::fldsgn::MatchResiduesMoverCreator , protocols::fldsgn::potentials::SetAACompositionPotentialCreator , protocols::fldsgn::potentials::SetSecStructEnergiesCreator , protocols::fldsgn::SheetRemodelConstraintGeneratorCreator , protocols::flexpep_docking::FlexPepDockingProtocolCreator , protocols::flxbb::FlxbbDesignCreator , protocols::flxbb::InterlockAromaCreator , protocols::fold_from_loops::movers::AlignByResidueSelectorMoverCreator , protocols::fold_from_loops::movers::DisplayPoseLabelsMoverCreator , protocols::fold_from_loops::movers::LabelPoseFromResidueSelectorMoverCreator , protocols::fold_from_loops::movers::MoveMapFactoryToNamedMoveMapMoverCreator , protocols::fold_from_loops::movers::NubInitioLoopClosureMoverCreator , protocols::fold_from_loops::movers::ReleaseConstraintFromResidueMoverCreator , protocols::fold_from_loops::movers::ResidueLabelsToPymolSelectionMoverCreator , protocols::fold_from_loops::movers::SavePDBInfoMoverCreator , protocols::fold_from_loops::movers::SplitAndMixPoseMoverCreator , protocols::fold_from_loops::NubInitioMoverCreator , protocols::forge::constraints::InverseRotamersCstGeneratorCreator , protocols::forge::constraints::InvrotTreeCstGeneratorCreator , protocols::forge::constraints::NtoCConstraintGeneratorCreator , protocols::forge::constraints::RemoveRemodelCstsCreator , protocols::forge::remodel::RemodelMoverCreator , protocols::forge::remodel::ResidueVicinityCstGeneratorCreator , protocols::generalized_kinematic_closure::GeneralizedKICCreator , protocols::grafting::AnchoredGraftMoverCreator , protocols::grafting::CCDEndsGraftMoverCreator , protocols::grafting::simple_movers::DeleteRegionMoverCreator , protocols::grafting::simple_movers::InsertPoseIntoPoseMoverCreator , protocols::grafting::simple_movers::KeepRegionMoverCreator , protocols::grafting::simple_movers::ReplaceRegionMoverCreator , protocols::hbnet::HBNetCreator , protocols::hbnet::HBNetStapleInterfaceCreator , protocols::helical_bundle::BackboneGridSamplerCreator , protocols::helical_bundle::BundleGridSamplerCreator , protocols::helical_bundle::FitSimpleHelixCreator , protocols::helical_bundle::MakeBundleCreator , protocols::helical_bundle::MakeBundleHelixCreator , protocols::helical_bundle::PerturbBundleCreator , protocols::helical_bundle::PerturbBundleHelixCreator , protocols::hotspot_hashing::movers::PlaceSurfaceProbeCreator , protocols::hybridization::BackboneTorsionPerturbationCreator , protocols::hybridization::BackboneTorsionSamplerCreator , protocols::hybridization::CartesianSamplerCreator , protocols::hybridization::HybridizeProtocolCreator , protocols::idealize::IdealizeMoverCreator , protocols::indexed_structure_store::movers::DirectSegmentLookupMoverCreator , protocols::indexed_structure_store::movers::SegmentSequenceProfileMoverCreator , protocols::kinematic_closure::KicMoverCreator , protocols::legacy_sewing::LegacyAddStartnodeFragmentsCreator , protocols::legacy_sewing::LegacyAppendAssemblyMoverCreator , protocols::legacy_sewing::LegacyAssemblyConstraintsMoverCreator , protocols::legacy_sewing::LegacyEnumerateAssemblyMoverCreator , protocols::legacy_sewing::LegacyGivenPathAssemblyMoverCreator , protocols::legacy_sewing::LegacyGreedyAssemblyMoverCreator , protocols::legacy_sewing::LegacyMonteCarloAssemblyMoverCreator , protocols::legacy_sewing::LegacyRepeatAssemblyMoverCreator , protocols::ligand_docking::AddHydrogensCreator , protocols::ligand_docking::CompoundTranslateCreator , protocols::ligand_docking::ComputeLigandRDFCreator , protocols::ligand_docking::FinalMinimizerCreator , protocols::ligand_docking::ga_ligand_dock::GALigandDockCreator , protocols::ligand_docking::GrowLigandCreator , protocols::ligand_docking::HighResDockerCreator , protocols::ligand_docking::HighResEnsembleCreator , protocols::ligand_docking::InterfaceScoreCalculatorCreator , protocols::ligand_docking::LigandDesignCreator , protocols::ligand_docking::MinimizeBackboneCreator , protocols::ligand_docking::ProtLigEnsembleCreator , protocols::ligand_docking::RandomConformersCreator , protocols::ligand_docking::RotateCreator , protocols::ligand_docking::RotatesCreator , protocols::ligand_docking::SlideTogetherCreator , protocols::ligand_docking::StartFromCreator , protocols::ligand_docking::TransformCreator , protocols::ligand_docking::TransformEnsembleCreator , protocols::ligand_docking::TranslateCreator , protocols::ligand_docking::WriteLigandMolFileCreator , protocols::loop_build::LoopmodelWrapperCreator , protocols::loop_build::LoopMover_SlidingWindowCreator , protocols::loop_grower::FragmentExtensionCreator , protocols::loop_modeler::LoopModelerCreator , protocols::loop_modeling::LoopBuilderCreator , protocols::loop_modeling::LoopProtocolCreator , protocols::loop_modeling::refiners::MinimizationRefinerCreator , protocols::loop_modeling::refiners::RepackingRefinerCreator , protocols::loop_modeling::refiners::RotamerTrialsRefinerCreator , protocols::loop_modeling::samplers::LegacyKicSamplerCreator , protocols::loop_modeling::utilities::PrepareForCentroidCreator , protocols::loop_modeling::utilities::PrepareForFullatomCreator , protocols::loophash::LoopHashDiversifierCreator , protocols::loophash::LoopHashMoverWrapperCreator , protocols::loops::FoldTreeFromLoopsCreator , protocols::loops::loop_closure::ccd::CCDLoopClosureMoverCreator , protocols::loops::loop_closure::jacobi::JacobiLoopClosureMoverCreator , protocols::loops::loop_mover::LoopCMCreator , protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCDCreator , protocols::loops::loop_mover::perturb::LoopMover_Perturb_KICCreator , protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_MovesCreator , protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCDCreator , protocols::loops::loop_mover::refine::LoopMover_Refine_BackrubCreator , protocols::loops::loop_mover::refine::LoopMover_Refine_CCDCreator , protocols::loops::loop_mover::refine::LoopMover_Refine_KICCreator , protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainerCreator , protocols::loops::loop_mover::refine::RepackTrialCreator , protocols::loops::loop_mover::refine::ShearMinCCDTrialCreator , protocols::loops::loop_mover::refine::SmallMinCCDTrialCreator , protocols::match::MatcherMoverCreator , protocols::matdes::ExtractSubposeMoverCreator , protocols::matdes::MatDesGreedyOptMutationMoverCreator , protocols::matdes::SchemePlaceMotifsMoverCreator , protocols::matdes::SymDofMoverCreator , protocols::md::CartesianMDCreator , protocols::mean_field::GenMeanFieldMoverCreator , protocols::membrane::AddMembraneMoverCreator , protocols::membrane::AddMembraneSpanConstraintCreator , protocols::membrane::AddMembraneSpanTermZConstraintCreator , protocols::membrane::AddMPLigandMoverCreator , protocols::membrane::AqueousPoreFinderCreator , protocols::membrane::benchmark::MakeCanonicalHelixCreator , protocols::membrane::benchmark::SampleTiltAnglesCreator , protocols::membrane::FlipMoverCreator , protocols::membrane::HelixFromSequenceCreator , protocols::membrane::MembranePositionFromTopologyMoverCreator , protocols::membrane::MPLipidAccessibilityCreator , protocols::membrane::MPMutateRelaxMoverCreator , protocols::membrane::MPQuickRelaxMoverCreator , protocols::membrane::OptimizeMembranePositionMoverCreator , protocols::membrane::OptimizeProteinEmbeddingMoverCreator , protocols::membrane::RotationMoverCreator , protocols::membrane::SetMembraneCenterMoverCreator , protocols::membrane::SetMembraneNormalMoverCreator , protocols::membrane::SetMembranePositionMoverCreator , protocols::membrane::SpinAroundPartnerMoverCreator , protocols::membrane::symmetry::SymmetricAddMembraneMoverCreator , protocols::membrane::TiltMoverCreator , protocols::membrane::TransformIntoMembraneMoverCreator , protocols::membrane::TranslationMoverCreator , protocols::membrane::TranslationRotationMoverCreator , protocols::membrane::visualize::VisualizeEmbeddingMoverCreator , protocols::membrane::visualize::VisualizeMembraneMoverCreator , protocols::membrane_benchmark::MembraneEnergyLandscapeSamplerCreator , protocols::membrane_benchmark::PeptideOrientationMoverCreator , protocols::minimization_packing::BoltzmannRotamerMoverCreator , protocols::minimization_packing::DisulfideOptimizationMoverCreator , protocols::minimization_packing::MinMoverCreator , protocols::minimization_packing::MinPackMoverCreator , protocols::minimization_packing::PackRotamersMoverCreator , protocols::minimization_packing::PertMinMoverCreator , protocols::minimization_packing::RepackSidechainsMoverCreator , protocols::minimization_packing::RotamerTrialsMinMoverCreator , protocols::minimization_packing::RotamerTrialsMoverCreator , protocols::minimization_packing::SaneMinMoverCreator , protocols::minimization_packing::symmetry::SymMinMoverCreator , protocols::minimization_packing::symmetry::SymPackRotamersMoverCreator , protocols::minimization_packing::symmetry::SymRotamerTrialsMoverCreator , protocols::minimization_packing::symmetry::TaskAwareSymMinMoverCreator , protocols::minimization_packing::TaskAwareMinMoverCreator , protocols::monte_carlo::GenericMonteCarloMoverCreator , protocols::monte_carlo::GenericSimulatedAnnealerCreator , protocols::monte_carlo::MonteCarloRecoverCreator , protocols::monte_carlo::MonteCarloResetCreator , protocols::monte_carlo::MonteCarloTestCreator , protocols::monte_carlo::ResetBaselineMoverCreator , protocols::motif_grafting::movers::MotifGraftCreator , protocols::motifs::MotifDnaPackerCreator , protocols::moves::DsspMoverCreator , protocols::moves::FilterReportAsPoseExtraScoresMoverCreator , protocols::moves::IfMoverCreator , protocols::moves::IteratedConvergenceMoverCreator , protocols::moves::MoverCreator , protocols::moves::PyMOLMoverCreator , protocols::moves::RampingMoverCreator , protocols::moves::RandomMoverCreator , protocols::moves::SwitchMoverCreator , protocols::ncbb::NcbbDockDesignProtocolCreator , protocols::ncbb::oop::OopCreatorMoverCreator , protocols::ncbb::oop::OopDockDesignProtocolCreator , protocols::ncbb::ResidueReplacementRebuildMoverCreator , protocols::ncbb::SecStructFinderCreator , protocols::ncbb::SecStructMinimizeMoverCreator , protocols::nmr::ParaNMRScoreMoverCreator , protocols::nmr::pcs::PCSLigandTransformMoverCreator , protocols::nmr::pre::PREMoverCreator , protocols::nonlocal::SingleFragmentMoverCreator , protocols::normalmode::NormalModeMinimizerCreator , protocols::normalmode::NormalModeRelaxMoverCreator , protocols::pb_potential::SetupPoissonBoltzmannPotentialCreator , protocols::pdbinfo_manipulations::AlignPDBInfoToSequencesCreator , protocols::pose_creation::ExtendedPoseMoverCreator , protocols::pose_creation::MakeJunctionsMoverCreator , protocols::pose_creation::MakePolyXMoverCreator , protocols::pose_creation::MergePDBatOverlapMoverCreator , protocols::pose_creation::MergePDBMoverCreator , protocols::pose_creation::PoseFromSequenceMoverCreator , protocols::pose_creation::SliceToMiniProteinMoverCreator , protocols::pose_length_moves::AnalyzeLoopModelingCreator , protocols::pose_length_moves::ConnectChainsMoverCreator , protocols::pose_length_moves::FixAllLoopsMoverCreator , protocols::pose_length_moves::InsertResMoverCreator , protocols::pose_length_moves::NearNativeLoopCloserCreator , protocols::protein_interface_design::movers::AddChainBreakCreator , protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspotsCreator , protocols::protein_interface_design::movers::BackrubDDMoverCreator , protocols::protein_interface_design::movers::BestHotspotCstMoverCreator , protocols::protein_interface_design::movers::BuildAlaPoseCreator , protocols::protein_interface_design::movers::DesignMinimizeHbondsCreator , protocols::protein_interface_design::movers::DisulfideMoverCreator , protocols::protein_interface_design::movers::DockAndRetrieveSidechainsCreator , protocols::protein_interface_design::movers::DockWithHotspotMoverCreator , protocols::protein_interface_design::movers::FavorNativeResiduePreCycleCreator , protocols::protein_interface_design::movers::FavorNonNativeResiduePreCycleCreator , protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMoverCreator , protocols::protein_interface_design::movers::HotspotHasherMoverCreator , protocols::protein_interface_design::movers::InterfaceRecapitulationMoverCreator , protocols::protein_interface_design::movers::LoopFinderCreator , protocols::protein_interface_design::movers::LoopLengthChangeCreator , protocols::protein_interface_design::movers::LoopMoverFromCommandLineCreator , protocols::protein_interface_design::movers::LoopOverCreator , protocols::protein_interface_design::movers::LoopRemodelCreator , protocols::protein_interface_design::movers::MapHotspotCreator , protocols::protein_interface_design::movers::PatchdockTransformCreator , protocols::protein_interface_design::movers::PeptideStapleDesignMoverCreator , protocols::protein_interface_design::movers::PlacementAuctionMoverCreator , protocols::protein_interface_design::movers::PlacementMinimizationMoverCreator , protocols::protein_interface_design::movers::PlaceOnLoopCreator , protocols::protein_interface_design::movers::PlaceSimultaneouslyMoverCreator , protocols::protein_interface_design::movers::PlaceStubMoverCreator , protocols::protein_interface_design::movers::PrepackMoverCreator , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMoverCreator , protocols::protein_interface_design::movers::RandomMutationCreator , protocols::protein_interface_design::movers::RepackMinimizeCreator , protocols::protein_interface_design::movers::SaveAndRetrieveSidechainsCreator , protocols::protein_interface_design::movers::SetAtomTreeCreator , protocols::protein_interface_design::movers::SetTemperatureFactorCreator , protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMoverCreator , protocols::protein_interface_design::movers::SetupHotspotConstraintsMoverCreator , protocols::protein_interface_design::movers::ShoveResidueMoverCreator , protocols::protein_interface_design::movers::SpinMoverCreator , protocols::protein_interface_design::movers::SubroutineMoverCreator , protocols::protein_interface_design::movers::TaskAwareCstsCreator , protocols::protein_interface_design::movers::TopologyBrokerMoverCreator , protocols::protein_interface_design::movers::TryRotamersCreator , protocols::protein_interface_design::movers::VLBCreator , protocols::qsar::qsarCreator , protocols::qsar::RenderGridsToKinemageCreator , protocols::quantum_annealing::ExternalPackerResultLoaderCreator , protocols::rbsegment_relax::IdealizeHelicesMoverCreator , protocols::rbsegment_relax::MakeStarTopologyMoverCreator , protocols::rbsegment_relax::OptimizeThreadingMoverCreator , protocols::recces::scratch::ThermalMinimizerCreator , protocols::recces::scratch::ThermalSamplingMoverCreator , protocols::recon_design::FindConsensusSequenceCreator , protocols::recon_design::MSDMoverCreator , protocols::relax::AcceptToBestMoverCreator , protocols::relax::AtomCoordinateCstMoverCreator , protocols::relax::ClassicRelaxCreator , protocols::relax::FastRelaxCreator , protocols::relax::LocalRelaxCreator , protocols::relax::membrane::MPFastRelaxMoverCreator , protocols::relax::RepeatProteinRelaxCreator , protocols::residue_selectors::StoreResidueSubsetMoverCreator , protocols::rigid::RigidBodyPerturbNoCenterMoverCreator , protocols::rigid::RigidBodyTiltMoverCreator , protocols::rigid::RigidBodyTransMoverCreator , protocols::rigid::RollMoverCreator , protocols::rigid::UniformRigidBodyCMCreator , protocols::rigid::UniformRigidBodyMoverCreator , protocols::rna::denovo::movers::RNA_DeNovoProtocolMoverCreator , protocols::rna::denovo::RNA_DeNovoProtocolCreator , protocols::rna::movers::ERRASER2ProtocolCreator , protocols::rna::movers::ErraserMinimizerMoverCreator , protocols::rna::movers::RNAIdealizeMoverCreator , protocols::rna::movers::RNAThreadAndMinimizeMoverCreator , protocols::rosetta_scripts::AdditionalOutputWrapperCreator , protocols::rosetta_scripts::MultipleOutputWrapperCreator , protocols::rosetta_scripts::MultiplePoseMoverCreator , protocols::rosetta_scripts::ParsedProtocolCreator , protocols::rosetta_scripts::SavePoseMoverCreator , protocols::rotamer_recovery::RotamerRecoveryMoverCreator , protocols::seeded_abinitio::CAcstGeneratorCreator , protocols::seeded_abinitio::CloseFoldCreator , protocols::seeded_abinitio::CoordinateCstCreator , protocols::seeded_abinitio::DefineMovableLoopsCreator , protocols::seeded_abinitio::GrowPeptidesCreator , protocols::seeded_abinitio::SeedFoldTreeCreator , protocols::seeded_abinitio::SeedSetupMoverCreator , protocols::seeded_abinitio::SegmentHybridizerCreator , protocols::seeded_abinitio::SwapSegmentCreator , protocols::sewing::hashing::AlignmentFileGeneratorMoverCreator , protocols::sewing::movers::AppendAssemblyMoverCreator , protocols::sewing::movers::AssemblyMoverCreator , protocols::sewing::movers::LigandBindingAssemblyMoverCreator , protocols::simple_ddg::ddGCreator , protocols::simple_moves::AddChainMoverCreator , protocols::simple_moves::AddJobPairDataCreator , protocols::simple_moves::AddPDBInfoMoverCreator , protocols::simple_moves::AddResidueCouplingConstraintCreator , protocols::simple_moves::AddResidueLabelMoverCreator , protocols::simple_moves::AlignChainMoverCreator , protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockMoveRbJumpMoverCreator , protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockRbTrialMoverCreator , protocols::simple_moves::BBDihedralSamplerMoverCreator , protocols::simple_moves::BBGaussianMoverCreator , protocols::simple_moves::bin_transitions::InitializeByBinsCreator , protocols::simple_moves::bin_transitions::PerturbByBinsCreator , protocols::simple_moves::ChangeAndResetFoldTreeMoverCreator , protocols::simple_moves::ConcatenatePosesMoverCreator , protocols::simple_moves::ContingentAcceptMoverCreator , protocols::simple_moves::ConvertRealToVirtualMoverCreator , protocols::simple_moves::ConvertVirtualToRealMoverCreator , protocols::simple_moves::CopyRotamerMoverCreator , protocols::simple_moves::CoupledMoverCreator , protocols::simple_moves::CutChainMoverCreator , protocols::simple_moves::DeleteChainMoverCreator , protocols::simple_moves::DeleteChainsMoverCreator , protocols::simple_moves::DisulfideInsertionMoverCreator , protocols::simple_moves::DumpPdbCreator , protocols::simple_moves::DumpSingleResidueRotamersCreator , protocols::simple_moves::ExplicitWaterMoverCreator , protocols::simple_moves::FavorSequenceProfileCreator , protocols::simple_moves::FavorSymmetricSequenceCreator , protocols::simple_moves::FoldTreeFromMotifCreator , protocols::simple_moves::LoadPDBMoverCreator , protocols::simple_moves::LoadUnboundRotMoverCreator , protocols::simple_moves::MembraneTopologyCreator , protocols::simple_moves::ModifyVariantTypeMoverCreator , protocols::simple_moves::MutateResidueCreator , protocols::simple_moves::PDBReloadMoverCreator , protocols::simple_moves::PeriodicBoxMoverCreator , protocols::simple_moves::PoseFromPoseResourceMoverCreator , protocols::simple_moves::PSSM2BfactorMoverCreator , protocols::simple_moves::RandomOmegaFlipMoverCreator , protocols::simple_moves::RandomTorsionMoverCreator , protocols::simple_moves::RepeatPropagationMoverCreator , protocols::simple_moves::ReportEffectivePKACreator , protocols::simple_moves::ReportXYZCreator , protocols::simple_moves::ResetFoldTreeCreator , protocols::simple_moves::ResetFullModelInfoMoverCreator , protocols::simple_moves::RingConformationMoverCreator , protocols::simple_moves::SaveSequenceToCommentsMoverCreator , protocols::simple_moves::ScoreMoverCreator , protocols::simple_moves::SequenceProfileMoverCreator , protocols::simple_moves::SetTorsionCreator , protocols::simple_moves::SetupMetalsMoverCreator , protocols::simple_moves::ShearMoverCreator , protocols::simple_moves::ShortBackrubMoverCreator , protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMoverCreator , protocols::simple_moves::sidechain_moves::PerturbChiSidechainMoverCreator , protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMoverCreator , protocols::simple_moves::sidechain_moves::SetChiMoverCreator , protocols::simple_moves::sidechain_moves::SidechainMCMoverCreator , protocols::simple_moves::sidechain_moves::SidechainMoverCreator , protocols::simple_moves::SimpleThreadingMoverCreator , protocols::simple_moves::SmallMoverCreator , protocols::simple_moves::StorePoseSnapshotCreator , protocols::simple_moves::StructProfileMoverCreator , protocols::simple_moves::SuperimposeMoverCreator , protocols::simple_moves::SwitchChainOrderMoverCreator , protocols::simple_moves::SwitchResidueTypeSetMoverCreator , protocols::simple_moves::TumbleCreator , protocols::simple_moves::VirtualRootMoverCreator , protocols::simple_moves::WriteFiltersToPoseCreator , protocols::simple_moves::WriteSSEMoverCreator , protocols::splice::AlignEndsMoverCreator , protocols::splice::RBInMoverCreator , protocols::splice::RBOutMoverCreator , protocols::splice::RotLibOutCreator , protocols::splice::SpliceCreator , protocols::splice::SpliceInAntibodyCreator , protocols::splice::SpliceInCreator , protocols::splice::SpliceInTailCreator , protocols::splice::SpliceOutAntibodyCreator , protocols::splice::SpliceOutCreator , protocols::splice::SpliceOutTailCreator , protocols::splice::TailSegmentMoverCreator , protocols::stepwise::monte_carlo::mover::AddMoverCreator , protocols::stepwise::monte_carlo::mover::DeleteMoverCreator , protocols::stepwise::monte_carlo::mover::FromScratchMoverCreator , protocols::stepwise::monte_carlo::mover::ResampleMoverCreator , protocols::struct_fragment::StructFragmentMoverCreator , protocols::switches::GraftSwitchMoverCreator , protocols::symmetric_docking::membrane::MPSymDockMoverCreator , protocols::symmetric_docking::SymDockProtocolCreator , protocols::symmetric_docking::SymFoldandDockMoveRbJumpMoverCreator , protocols::symmetric_docking::SymFoldandDockRbTrialMoverCreator , protocols::symmetric_docking::SymFoldandDockSlideTrialMoverCreator , protocols::symmetry::DetectSymmetryMoverCreator , protocols::symmetry::ExtractAsymmetricPoseMoverCreator , protocols::symmetry::ExtractAsymmetricUnitMoverCreator , protocols::symmetry::SetupForSequenceSymmetryMoverCreator , protocols::symmetry::SetupForSymmetryMoverCreator , protocols::symmetry::SetupNCSMoverCreator , protocols::task_operations::StoreCombinedStoredTasksMoverCreator , protocols::task_operations::StoreCompoundTaskMoverCreator , protocols::task_operations::StoreTaskMoverCreator , protocols::testing::BenchmarkBuildRotamersMoverCreator , protocols::vardist_solaccess::LoadVarSolDistSasaCalculatorMoverCreator
• create_multipole_elec_instance() : core::scoring::ScoringManager
• create_netcharge_energy_setup_instance() : core::scoring::ScoringManager
• create_new_bump_grid_for_bb() : protocols::match::BumpGrid
• create_new_edge() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph , core::pack::hbonds::HBondGraphInitializerIG , core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > , core::pack::interaction_graph::NPDHBSimpleInteractionGraph , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::SimpleInteractionGraph , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistInteractionGraph , core::scoring::constraints::ConstraintGraph , core::scoring::EnergyGraph , core::scoring::MinimizationGraph , core::scoring::TenANeighborGraph , core::scoring::TwelveANeighborGraph , protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph , protocols::jd3::JobDigraph , protocols::legacy_sewing::SewGraph
• create_new_node() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph , core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > , core::pack::interaction_graph::NPDHBSimpleInteractionGraph , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::SimpleInteractionGraph , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistInteractionGraph , core::scoring::constraints::ConstraintGraph , core::scoring::EnergyGraph , core::scoring::MinimizationGraph , core::scoring::TenANeighborGraph , core::scoring::TwelveANeighborGraph , protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph , protocols::jd3::JobDigraph , protocols::legacy_sewing::SewGraph
• create_new_parameters_set() : core::conformation::Conformation
• create_new_random_topol() : protocols::jumping::RandomSheetBuilder , protocols::jumping::SheetBuilder
• create_new_submotif() : protocols::stepwise::monte_carlo::submotif::SubMotifLibrary
• create_nmer_pssm() : core::scoring::ScoringManager
• create_nmer_svm_aa_matrix() : core::scoring::ScoringManager
• create_nmer_svm_rank() : core::scoring::ScoringManager
• create_nvlookup_instance() : core::scoring::ScoringManager
• create_omega_preferences_function_instance() : core::scoring::ScoringManager
• create_omegatether_instance() : core::scoring::ScoringManager
• create_orbital_type_set() : core::chemical::ChemicalManager
• create_orbitals_lookup_instance() : core::scoring::ScoringManager
• create_orthogonal() : core::kinematics::Stub
• create_output_specification() : protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputter , protocols::jd3::pose_outputters::mmTFPoseOutputter , protocols::jd3::pose_outputters::PDBPoseOutputter , protocols::jd3::pose_outputters::PoseOutputter , protocols::jd3::pose_outputters::ScoreFileOutputter , protocols::jd3::pose_outputters::SilentFilePoseOutputter
• create_output_specification_for_job_result() : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::standard::StandardJobQueen
• create_output_upstream_pose() : protocols::match::output::PDBWriter
• create_output_writer() : protocols::match::output::ProcessorFactory
• create_outputter() : protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputterCreator , protocols::jd3::pose_outputters::mmTFPoseOutputterCreator , protocols::jd3::pose_outputters::PDBPoseOutputterCreator , protocols::jd3::pose_outputters::PoseOutputterCreator , protocols::jd3::pose_outputters::ScoreFileOutputterCreator , protocols::jd3::pose_outputters::SecondaryPoseOutputterCreator , protocols::jd3::pose_outputters::SilentFilePoseOutputterCreator
• create_overlap_constraint_generator() : protocols::denovo_design::movers::BuildDeNovoBackboneMover
• create_p_aa_abego3_instance() : core::scoring::ScoringManager
• create_p_aa_instance() : core::scoring::ScoringManager
• create_p_aa_ss_instance() : core::scoring::ScoringManager
• create_packer_data() : protocols::multistate_design::PackingState
• create_packer_palette() : core::pack::palette::CustomBaseTypePackerPaletteCreator , core::pack::palette::DefaultPackerPaletteCreator , core::pack::palette::NCAADefaultPackerPaletteCreator , core::pack::palette::NoDesignPackerPaletteCreator , core::pack::palette::PackerPaletteCreator
• create_packer_palette_from_global_defaults() : core::pack::palette::PackerPaletteFactory
• create_packer_task() : core::pack::task::TaskFactory
• create_pairE_potential_instance() : core::scoring::ScoringManager
• create_para_ion_from_string() : core::scoring::nmr::pre::PREMultiSet
• create_parameters_for_restype() : core::scoring::methods::IdealParametersDatabase
• create_parser() : protocols::jd2::JobDistributorFactory
• create_partitioned_search_pattern() : protocols::hotspot_hashing::movers::PlaceProbeMover , protocols::hotspot_hashing::movers::PlaceSurfaceProbe
• create_pddf() : protocols::scoring::methods::saxs::PDDFEnergy
• create_per_loop_fragment_movers() : protocols::forge::remodel::RemodelLoopMover
• create_point_water_potential_instance() : core::scoring::ScoringManager
• create_poisson_boltzmann_potential_instance() : core::scoring::ScoringManager
• create_pose_from_input_poses() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• create_pose_reference() : protocols::simple_moves::ConstrainToIdealMover
• create_position_data() : protocols::optimize_weights::OptEPositionDataFactory
• create_potential_loops() : protocols::pose_length_moves::NearNativeLoopCloser
• create_processor() : protocols::match::output::ProcessorFactory
• create_proq_potential_instance() : core::scoring::ScoringManager
• create_protocol() : protocols::rotamer_recovery::RRProtocolCreator , protocols::rotamer_recovery::RRProtocolMinPackCreator , protocols::rotamer_recovery::RRProtocolMoverCreator , protocols::rotamer_recovery::RRProtocolPackRotamersCreator , protocols::rotamer_recovery::RRProtocolReferenceStructureCreator , protocols::rotamer_recovery::RRProtocolRelaxCreator , protocols::rotamer_recovery::RRProtocolRotamerTrialsCreator , protocols::rotamer_recovery::RRProtocolRTMinCreator
• create_ptask() : protocols::enzdes::EnzRepackMinimize , protocols::hbnet::HBNet
• create_rama2b_instance() : core::scoring::ScoringManager
• create_rama_instance() : core::scoring::ScoringManager
• create_ramapp_instance() : core::scoring::ScoringManager
• create_random_fragments() : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover
• create_random_rotation() : protocols::ligand_docking::Rotate
• create_random_rotations() : protocols::ligand_docking::Rotate
• create_rdf_function() : protocols::ligand_docking::rdf::RDFBinaryHbondCreator , protocols::ligand_docking::rdf::RDFBinaryOrbitalFunctionCreator , protocols::ligand_docking::rdf::RDFChargeCreator , protocols::ligand_docking::rdf::RDFElecCreator , protocols::ligand_docking::rdf::RDFEtableCreator , protocols::ligand_docking::rdf::RDFFunctionCreator , protocols::ligand_docking::rdf::RDFHbondCreator , protocols::ligand_docking::rdf::RDFOrbitalFunctionCreator
• create_reference_data_ : protocols::minimization_packing::GreenPacker
• create_reference_packer_neighbor_graph() : protocols::minimization_packing::GreenPacker
• create_reference_packer_task() : protocols::minimization_packing::GreenPacker
• create_reference_rotamers() : protocols::minimization_packing::GreenPacker
• create_refinement_packing_task() : protocols::hotspot_hashing::movers::PlaceProbeMover
• create_refinement_pattern() : protocols::hotspot_hashing::movers::PlaceProbeMover , protocols::hotspot_hashing::movers::PlaceSurfaceProbe
• create_relax_script_instance() : protocols::relax::RelaxScriptManager
• create_remodel_loop_mover() : protocols::denovo_design::components::RemodelLoopMoverPoseFolder
• create_reporter() : protocols::pose_reporters::EnergyReporterCreator , protocols::pose_reporters::FilterReporterCreator , protocols::pose_reporters::RMSDReporterCreator , protocols::rosetta_scripts::PosePropertyReporterCreator , protocols::rotamer_recovery::RRReporterCreator , protocols::rotamer_recovery::RRReporterHumanCreator , protocols::rotamer_recovery::RRReporterSimpleCreator , protocols::rotamer_recovery::RRReporterSQLiteCreator
• create_requirement() : protocols::legacy_sewing::sampling::requirements::LegacyGlobalLengthRequirementCreator , protocols::legacy_sewing::sampling::requirements::LegacyGlobalRequirementCreator , protocols::legacy_sewing::sampling::requirements::LegacyIntraSegmentRequirementCreator , protocols::legacy_sewing::sampling::requirements::LegacyResidueRetentionRequirementCreator , protocols::legacy_sewing::sampling::requirements::LegacySegmentDsspRequirementCreator , protocols::legacy_sewing::sampling::requirements::LegacySegmentLengthRequirementCreator , protocols::sewing::requirements::AssemblyRequirementCreator , protocols::sewing::requirements::ClashRequirementCreator , protocols::sewing::requirements::DsspSpecificLengthRequirementCreator , protocols::sewing::requirements::KeepLigandContactsRequirementCreator , protocols::sewing::requirements::LengthInResiduesRequirementCreator , protocols::sewing::requirements::LigandClashRequirementCreator , protocols::sewing::requirements::NonTerminalStartingSegmentRequirementCreator , protocols::sewing::requirements::SizeInSegmentsRequirementCreator
• create_res_filter() : core::pack::task::operation::AllResFilterCreator , core::pack::task::operation::AnyResFilterCreator , core::pack::task::operation::ChainIsCreator , core::pack::task::operation::ChainIsntCreator , core::pack::task::operation::NoResFilterCreator , core::pack::task::operation::ResFilterCreator , core::pack::task::operation::ResidueHasPropertyCreator , core::pack::task::operation::ResidueIndexIsCreator , core::pack::task::operation::ResidueIndexIsntCreator , core::pack::task::operation::ResidueLacksPropertyCreator , core::pack::task::operation::ResidueName3IsCreator , core::pack::task::operation::ResidueName3IsntCreator , core::pack::task::operation::ResiduePDBIndexIsCreator , core::pack::task::operation::ResiduePDBIndexIsntCreator , core::pack::task::operation::ResiduePDBInfoHasLabelCreator , core::pack::task::operation::ResiduePDBInfoLacksLabelCreator , core::pack::task::operation::ResidueTypeFilterCreator , protocols::task_operations::ProteinCoreFilterCreator
• create_res_level_task_operation() : core::pack::task::operation::AddBehaviorRLTCreator , core::pack::task::operation::DisallowIfNonnativeRLTCreator , core::pack::task::operation::ExtraChiCutoffRLTCreator , core::pack::task::operation::ExtraRotamersGenericRLTCreator , core::pack::task::operation::IncludeCurrentRLTCreator , core::pack::task::operation::PreserveCBetaRLTCreator , core::pack::task::operation::PreventRepackingRLTCreator , core::pack::task::operation::ResLvlTaskOperationCreator , core::pack::task::operation::RestrictAbsentCanonicalAASExceptNativeRLTCreator , core::pack::task::operation::RestrictAbsentCanonicalAASRLTCreator , core::pack::task::operation::RestrictToRepackingRLTCreator
• create_residue() : core::conformation::Residue , core::conformation::ResidueFactory , protocols::constraint_generator::HydrogenBondInfo
• create_residue_constraint() : protocols::constraint_generator::HydrogenBondConstraintGenerator
• create_residue_constraints() : protocols::constraint_generator::CoordinateConstraintGenerator
• create_residue_selector() : core::pack::task::residue_selector::ClashBasedShellSelectorCreator , core::select::residue_selector::AndResidueSelectorCreator , core::select::residue_selector::AsymmetricUnitSelectorCreator , core::select::residue_selector::BinSelectorCreator , core::select::residue_selector::BondedResidueSelectorCreator , core::select::residue_selector::ChainSelectorCreator , core::select::residue_selector::CloseContactResidueSelectorCreator , core::select::residue_selector::DensityFitResidueSelectorCreator , core::select::residue_selector::FalseResidueSelectorCreator , core::select::residue_selector::GlycanLayerSelectorCreator , core::select::residue_selector::GlycanPositionSelectorCreator , core::select::residue_selector::GlycanResidueSelectorCreator , core::select::residue_selector::GlycanSequonsSelectorCreator , core::select::residue_selector::InterGroupInterfaceByVectorSelectorCreator , core::select::residue_selector::JumpDownstreamSelectorCreator , core::select::residue_selector::JumpUpstreamSelectorCreator , core::select::residue_selector::LayerSelectorCreator , core::select::residue_selector::NeighborhoodResidueSelectorCreator , core::select::residue_selector::NotResidueSelectorCreator , core::select::residue_selector::NumNeighborsSelectorCreator , core::select::residue_selector::OrResidueSelectorCreator , core::select::residue_selector::PhiSelectorCreator , core::select::residue_selector::PrimarySequenceNeighborhoodSelectorCreator , core::select::residue_selector::RandomGlycanFoliageSelectorCreator , core::select::residue_selector::RandomResidueSelectorCreator , core::select::residue_selector::ResidueIndexSelectorCreator , core::select::residue_selector::ResidueInMembraneSelectorCreator , core::select::residue_selector::ResidueInSequenceMotifSelectorCreator , core::select::residue_selector::ResidueNameSelectorCreator , core::select::residue_selector::ResiduePDBInfoHasLabelSelectorCreator , core::select::residue_selector::ResiduePropertySelectorCreator , core::select::residue_selector::ResidueSelectorCreator , core::select::residue_selector::ResidueSpanSelectorCreator , core::select::residue_selector::ScoreTermValueBasedSelectorCreator , core::select::residue_selector::SecondaryStructureSelectorCreator , core::select::residue_selector::SliceResidueSelectorCreator , core::select::residue_selector::SSElementSelectorCreator , core::select::residue_selector::SymmetricalResidueSelectorCreator , core::select::residue_selector::TrueResidueSelectorCreator , protocols::antibody::residue_selector::AntibodyRegionSelectorCreator , protocols::antibody::residue_selector::CDRResidueSelectorCreator , protocols::cyclic_peptide::RamaMutationSelectorCreator , protocols::denovo_design::residue_selectors::NamedSegmentSelectorCreator , protocols::denovo_design::residue_selectors::PairedSheetResidueSelectorCreator , protocols::fold_from_loops::selectors::ConstraintResidueSelectorCreator , protocols::fold_from_loops::selectors::CutpointResidueSelectorCreator , protocols::fold_from_loops::selectors::ProteinResidueSelectorCreator , protocols::hbnet::UnsatSelectorCreator , protocols::residue_selectors::HBondSelectorCreator , protocols::residue_selectors::LigandMetalContactSelectorCreator , protocols::residue_selectors::NativeSelectorCreator , protocols::residue_selectors::StoredResidueSubsetSelectorCreator , protocols::residue_selectors::TaskSelectorCreator
• create_residue_to_add() : protocols::stepwise::monte_carlo::mover::AddMover
• create_residue_type_set() : core::chemical::ChemicalManager
• create_resource() : core::conformation::symmetry::SymmDataLoader , core::fragment::FragmentSetLoader , core::import_pose::PoseResourceLoader , protocols::loophash::LoopHashLibraryLoader , protocols::loops::LoopsFileLoader , protocols::surface_docking::SurfaceVectorLoader
• create_resource_loader() : core::conformation::symmetry::SymmDataLoaderCreator , core::fragment::FragmentSetLoaderCreator , core::import_pose::PoseResourceLoaderCreator , protocols::loophash::LoopHashLibraryLoaderCreator , protocols::loops::LoopsFileLoaderCreator , protocols::surface_docking::SurfaceVectorLoaderCreator
• create_rigid_body_movers() : protocols::ligand_docking::HighResDocker
• create_rna_atomvdw_instance() : core::scoring::ScoringManager
• create_rna_chemshiftpotential_instance() : core::scoring::ScoringManager
• create_rna_dms_lowrespotential_instance() : core::scoring::ScoringManager
• create_rna_dms_potential_instance() : core::scoring::ScoringManager
• create_rna_lowresolutionpotential_instance() : core::scoring::ScoringManager
• create_rna_suitepotential_instance() : core::scoring::ScoringManager
• create_rnp_lowrespairdistpotential_instance() : core::scoring::ScoringManager
• create_rnp_lowrespotential_instance() : core::scoring::ScoringManager
• create_rnp_lowresstackdata_instance() : core::scoring::ScoringManager
• create_rotamer() : core::conformation::Residue
• create_rotamer_set() : core::pack::rotamer_set::RotamerSetFactory , protocols::pose_metric_calculators::RotamerBoltzCalculator , protocols::protein_interface_design::movers::MapHotspot
• create_rotamer_sets() : core::pack::rotamer_set::RotamerSetsFactory
• create_rotamer_subsets_from_rot_to_pack() : protocols::pack_daemon::RotamerSubsetRepacker
• create_rotamer_trie() : core::scoring::elec::FA_ElecEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::hbonds::HBondEnergy , core::scoring::lkball::LK_BallEnergy , core::scoring::methods::MMLJEnergyInter , core::scoring::vdwaals::VDW_Energy
• create_rotamer_trie_1() : core::scoring::etable::BaseEtableEnergy< Derived >
• create_rotamer_trie_2() : core::scoring::etable::BaseEtableEnergy< Derived >
• create_rotameric_dunlib() : core::pack::dunbrack::RotamerLibrary
• create_rotamers_from_chisets() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >
• create_sample_vector() : protocols::toolbox::match_enzdes_util::GeomSampleInfo
• create_sasa_potential_instance() : core::scoring::ScoringManager
• create_scalar_and_vector_expression_variable_expressions() : protocols::pack_daemon::DynamicAggregateFunction
• create_score_function() : core::scoring::ScoreFunctionFactory
• create_scorefxn() : protocols::denovo_design::components::RemodelLoopMoverPoseFolder
• create_scorefxn_from_tag() : protocols::parser::ScoreFunctionLoader
• create_scores() : protocols::frag_picker::FragmentPicker , protocols::frag_picker::scores::FragmentScoreManager
• create_scoring_method() : protocols::frag_picker::scores::FragmentScoreManager
• create_search_pattern() : protocols::hotspot_hashing::movers::PlaceProbeMover , protocols::hotspot_hashing::movers::PlaceSurfaceProbe
• create_SecMatchResiduePairEvaluatorOP() : protocols::match::downstream::SecMatchEvaluatorFactory
• create_secondarystructurepotential_instance() : core::scoring::ScoringManager
• create_segment() : protocols::denovo_design::movers::AddSegmentDataMover
• create_selector() : core::select::residue_selector::SelectorLogicParser , protocols::pose_selectors::AndSelectorCreator , protocols::pose_selectors::ClusterPoseSelectorCreator , protocols::pose_selectors::FilterCreator , protocols::pose_selectors::OrSelectorCreator , protocols::pose_selectors::TopNByPropertyCreator , protocols::rosetta_scripts::PoseSelectorCreator
• create_semaphore() : protocols::boinc::Boinc
• create_semi_rotameric_dunlib() : core::pack::dunbrack::RotamerLibrary
• create_sequence() : core::sequence::ChemicalShiftSequenceCreator , core::sequence::CompositeSequenceCreator , core::sequence::SequenceCouplingCreator , core::sequence::SequenceCreator , core::sequence::SequenceProfileCreator , core::sequence::SimpleSequenceCreator
• create_sequence_mapping() : protocols::constraint_generator::AtomPairConstraintGenerator
• create_sequence_match_fragments() : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover
• create_sequence_profile_constraints() : protocols::calc_taskop_movers::ConsensusDesignMover
• create_silent_file_and_tag_list() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• create_silent_struct() : core::import_pose::PDBSilentStructCreator , core::io::silent::BinarySilentStructCreator , core::io::silent::ProteinSilentStruct_SinglePrecCreator , core::io::silent::ProteinSilentStructCreator , core::io::silent::RigidBodySilentStructCreator , core::io::silent::RNA_SilentStructCreator , core::io::silent::ScoreFileSilentStructCreator , core::io::silent::ScoreJumpFileSilentStructCreator , core::io::silent::SilentStructCreator
• create_SilentStructOP() : core::io::silent::SilentFileData
• create_simple_metric() : core::simple_metrics::composite_metrics::CompositeEnergyMetricCreator , core::simple_metrics::composite_metrics::ElectrostaticComplementarityMetricCreator , core::simple_metrics::composite_metrics::ProtocolSettingsMetricCreator , core::simple_metrics::metrics::CalculatorMetricCreator , core::simple_metrics::metrics::DihedralDistanceMetricCreator , core::simple_metrics::metrics::InteractionEnergyMetricCreator , core::simple_metrics::metrics::ResidueSummaryMetricCreator , core::simple_metrics::metrics::RMSDMetricCreator , core::simple_metrics::metrics::SasaMetricCreator , core::simple_metrics::metrics::SecondaryStructureMetricCreator , core::simple_metrics::metrics::SelectedResidueCountMetricCreator , core::simple_metrics::metrics::SelectedResiduesMetricCreator , core::simple_metrics::metrics::SelectedResiduesPyMOLMetricCreator , core::simple_metrics::metrics::SequenceMetricCreator , core::simple_metrics::metrics::SequenceSimilarityMetricCreator , core::simple_metrics::metrics::TimingProfileMetricCreator , core::simple_metrics::metrics::TotalEnergyMetricCreator , core::simple_metrics::per_residue_metrics::HbondMetricCreator , core::simple_metrics::per_residue_metrics::PerResidueClashMetricCreator , core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetricCreator , core::simple_metrics::per_residue_metrics::PerResidueEnergyMetricCreator , core::simple_metrics::per_residue_metrics::PerResidueGlycanLayerMetricCreator , core::simple_metrics::per_residue_metrics::PerResidueRMSDMetricCreator , core::simple_metrics::per_residue_metrics::PerResidueSasaMetricCreator , core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetricCreator , core::simple_metrics::SimpleMetricCreator , core::simple_metrics::TestCompositeRealMetricCreator , core::simple_metrics::TestCompositeStringMetricCreator , core::simple_metrics::TestPerResidueRealMetricCreator , core::simple_metrics::TestPerResidueStringMetricCreator , core::simple_metrics::TestRealMetricCreator , core::simple_metrics::TestStringMetricCreator , protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetricCreator , protocols::analysis::simple_metrics::SequenceRecoveryMetricCreator , protocols::cyclic_peptide::PeptideInternalHbondsMetricCreator , protocols::filters::FilterValueMetricCreator , protocols::quantum_annealing::InteractionGraphSummaryMetricCreator
• create_singleton_instance() : protocols::indexed_structure_store::SSHashedFragmentStore , protocols::jd2::JobDistributor , protocols::noesy_assign::PeakAssignmentParameters
• create_sixdtransrotpotential_instance() : core::scoring::ScoringManager
• create_sliced_pose() : protocols::stepwise::legacy::modeler::rna::SlicedPoseWorkingParameters
• create_small_mover() : protocols::medal::MedalMover
• create_smoothenvpair_instance() : core::scoring::ScoringManager
• create_split_unfolded_2body_potential_instance() : core::scoring::ScoringManager
• create_srdl() : core::pack::dunbrack::RotamerLibrary
• create_starting_pose() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• create_state_variable_expressions() : protocols::pack_daemon::DynamicAggregateFunction
• create_sub_to_full_map() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• create_subpose() : protocols::simple_moves::CutChainMover
• create_surface_packer_task() : protocols::surface_docking::SurfaceDockingProtocol
• create_surface_params() : protocols::surface_docking::SurfaceVectorLoader
• create_svm_rosetta() : core::scoring::ScoringManager
• create_tag() : protocols::monte_carlo::GenericSimulatedAnnealer
• create_tag_from_xml() : protocols::rosetta_scripts::RosettaScriptsParser
• create_tag_from_xml_string() : protocols::rosetta_scripts::RosettaScriptsParser
• create_tags_map() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• create_task_and_apply_taskoperations() : core::pack::task::TaskFactory
• create_task_for_allhotspot_packing() : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• create_task_for_hotspot_packing() : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• create_task_operation() : core::pack::task::operation::AppendResidueRotamerSetCreator , core::pack::task::operation::AppendRotamerCreator , core::pack::task::operation::AppendRotamerSetCreator , core::pack::task::operation::ClashBasedRepackShellCreator , core::pack::task::operation::DesignRestrictionsCreator , core::pack::task::operation::DisallowIfNonnativeCreator , core::pack::task::operation::EnableMultiCoolAnnealerCreator , core::pack::task::operation::EnableSmartAnnealerCreator , core::pack::task::operation::ExtraChiCutoffCreator , core::pack::task::operation::ExtraRotamersCreator , core::pack::task::operation::ExtraRotamersGenericCreator , core::pack::task::operation::FillAUTOTaskOperationCreator , core::pack::task::operation::IncludeCurrentCreator , core::pack::task::operation::InitializeExtraRotsFromCommandlineCreator , core::pack::task::operation::InitializeFromCommandlineCreator , core::pack::task::operation::InitializeFromOptionCollectionCreator , core::pack::task::operation::KeepSequenceSymmetryCreator , core::pack::task::operation::NoRepackDisulfidesCreator , core::pack::task::operation::OperateOnCertainResiduesCreator , core::pack::task::operation::OperateOnResidueSubsetCreator , core::pack::task::operation::OptCysHGCreator , core::pack::task::operation::OptHCreator , core::pack::task::operation::PreserveCBetaCreator , core::pack::task::operation::PreventRepackingCreator , core::pack::task::operation::ProhibitResiduePropertiesCreator , core::pack::task::operation::ProhibitSpecifiedBaseResidueTypesCreator , core::pack::task::operation::ReadResfileAndObeyLengthEventsCreator , core::pack::task::operation::ReadResfileCreator , core::pack::task::operation::RestrictAbsentCanonicalAASCreator , core::pack::task::operation::RestrictInteractionGraphThreadsOperationCreator , core::pack::task::operation::RestrictResidueToRepackingCreator , core::pack::task::operation::RestrictToRepackingCreator , core::pack::task::operation::RestrictToResiduePropertiesCreator , core::pack::task::operation::RestrictToSpecifiedBaseResidueTypesCreator , core::pack::task::operation::RestrictYSDesignCreator , core::pack::task::operation::RotamerExplosionCreator , core::pack::task::operation::SetRotamerCouplingsCreator , core::pack::task::operation::SetRotamerLinksCreator , core::pack::task::operation::TaskOperationCreator , core::pack::task::operation::UseMultiCoolAnnealerCreator , protocols::antibody::task_operations::AddCDRProfileSetsOperationCreator , protocols::antibody::task_operations::AddCDRProfilesOperationCreator , protocols::antibody::task_operations::DisableAntibodyRegionOperationCreator , protocols::antibody::task_operations::DisableCDRsOperationCreator , protocols::antibody::task_operations::RestrictToCDRsAndNeighborsCreator , protocols::denovo_design::task_operations::ConsensusLoopDesignOperationCreator , protocols::dna::RestrictDesignToProteinDNAInterfaceCreator , protocols::dna::WatsonCrickRotamerCouplingsCreator , protocols::enzdes::AddLigandMotifRotamersOperationCreator , protocols::enzdes::AddRigidBodyLigandConfsCreator , protocols::enzdes::DetectProteinLigandInterfaceOperationCreator , protocols::enzdes::ProteinLigandInterfaceUpweighterOperationCreator , protocols::enzdes::SetCatalyticResPackBehaviorCreator , protocols::flxbb::LayerDesignOperationCreator , protocols::forge::remodel::RemodelRotamerLinksCreator , protocols::hbnet::ConstrainHBondNetworkCreator , protocols::legacy_sewing::LegacyReadNativeRotamersFileCreator , protocols::legacy_sewing::LegacyReadRepeatNativeRotamersFileCreator , protocols::matdes::BuildingBlockInterfaceOperationCreator , protocols::pack_interface::ProteinProteinInterfaceUpweighterTaskOperationCreator , protocols::simple_task_operations::RestrictToInterfaceCreator , protocols::simple_task_operations::RestrictToLoopsAndNeighborsCreator , protocols::simple_task_operations::RestrictToLoopsCreator , protocols::splice::DesignInterfacesOperationCreator , protocols::splice::FindEndpointsOperationCreator , protocols::splice::SampleRotamersFromPDBCreator , protocols::task_operations::AlignedThreadOperationCreator , protocols::task_operations::ConservativeDesignOperationCreator , protocols::task_operations::CrystalContactsOperationCreator , protocols::task_operations::DatabaseThreadCreator , protocols::task_operations::DesignAroundOperationCreator , protocols::task_operations::DsspDesignOperationCreator , protocols::task_operations::ImportUnboundRotamersOperationCreator , protocols::task_operations::InteractingRotamerExplosionCreator , protocols::task_operations::JointSequenceOperationCreator , protocols::task_operations::LimitAromaChi2OperationCreator , protocols::task_operations::LinkResiduesCreator , protocols::task_operations::ModifyAnnealerCreator , protocols::task_operations::pHVariantTaskOperationCreator , protocols::task_operations::PreventChainFromRepackingOperationCreator , protocols::task_operations::PreventResiduesFromRepackingOperationCreator , protocols::task_operations::ProteinInterfaceDesignOperationCreator , protocols::task_operations::PruneBuriedUnsatsOperationCreator , protocols::task_operations::ReadResfileFromDBCreator , protocols::task_operations::ResfileCommandOperationCreator , protocols::task_operations::ResidueProbDesignOperationCreator , protocols::task_operations::RestrictByCalculatorsOperationCreator , protocols::task_operations::RestrictChainToRepackingOperationCreator , protocols::task_operations::RestrictConservedLowDdgOperationCreator , protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperationCreator , protocols::task_operations::RestrictIdentitiesOperationCreator , protocols::task_operations::RestrictInterGroupVectorOperationCreator , protocols::task_operations::RestrictNativeResiduesOperationCreator , protocols::task_operations::RestrictNonSurfaceToRepackingOperationCreator , protocols::task_operations::RestrictResiduesToRepackingOperationCreator , protocols::task_operations::RestrictToAlignedSegmentsOperationCreator , protocols::task_operations::RestrictToCDRH3LoopCreator , protocols::task_operations::RestrictToInterfaceOperationCreator , protocols::task_operations::RestrictToInterfaceVectorOperationCreator , protocols::task_operations::RestrictToNeighborhoodOperationCreator , protocols::task_operations::RestrictToTerminiOperationCreator , protocols::task_operations::RetrieveStoredTaskOperationCreator , protocols::task_operations::SelectByDeltaScoreOperationCreator , protocols::task_operations::SelectByDensityFitOperationCreator , protocols::task_operations::SelectBySASAOperationCreator , protocols::task_operations::SelectResiduesWithinChainOperationCreator , protocols::task_operations::SeqprofConsensusOperationCreator , protocols::task_operations::SequenceMotifTaskOperationCreator , protocols::task_operations::SetIGTypeOperationCreator , protocols::task_operations::ThreadSequenceOperationCreator
• create_template_pose() : protocols::denovo_design::components::ExtendedPoseBuilder
• create_tna_suitepotential_instance() : core::scoring::ScoringManager
• create_unfolded_state_potential_instance() : core::scoring::ScoringManager
• create_unique_id() : protocols::wum::WorkUnitBase
• create_unweighted_scorefunction() : protocols::optimize_weights::IterativeOptEDriver
• create_updated_span() : core::scoring::membrane::MPSpanInsertionEnergy
• create_variable_vector_expressions() : protocols::pack_daemon::DynamicAggregateFunction
• create_VDW_rep_screen_pose() : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• create_VDW_screen_bin() : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• create_vdw_tinker_potential_instance() : core::scoring::ScoringManager
• create_vrt_if_necessary() : protocols::environment::claims::JumpClaim
• create_vrt_p1_ : protocols::environment::claims::JumpClaim
• create_vrt_p2_ : protocols::environment::claims::JumpClaim
• create_water_adduct_hbond_potential_instance() : core::scoring::ScoringManager
• create_weighted_scorefunction() : protocols::optimize_weights::IterativeOptEDriver
• create_WUs() : protocols::mpi_refinement::MPI_Refine_Master
• create_xyz_constraints_median() : protocols::toolbox::DecoySetEvaluation
• CreateAngleConstraint() : protocols::cyclic_peptide::CreateAngleConstraint
• createAngleList() : protocols::cartesian::MolecularDynamics
• CreateAtomicEnvironmentToTypesMap() : core::chemical::gasteiger::PossibleAtomTypesForAtom
• createBondList() : protocols::cartesian::MolecularDynamics
• createCartesianArray() : protocols::cartesian::MolecularDynamics
• createCartesianDerivatives() : protocols::cartesian::MolecularDynamics
• createConstraints() : protocols::cluster::EnsembleConstraints , protocols::cluster::EnsembleConstraints_Simple
• createDihedral() : protocols::cartesian::MolecularDynamics
• createDihedralList() : protocols::cartesian::MolecularDynamics
• CreateDistanceConstraint() : protocols::cyclic_peptide::CreateDistanceConstraint
• CreateGlycanSequonMover() : protocols::carbohydrates::CreateGlycanSequonMover
• creates_undefined_backbone() : protocols::forge::build::Bridge , protocols::forge::build::BuildInstruction , protocols::forge::build::ConnectRight , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap
• CreateSequenceMotifMover() : protocols::calc_taskop_movers::CreateSequenceMotifMover
• CreateTorsionConstraint() : protocols::cyclic_peptide::CreateTorsionConstraint
• creator_list_ : protocols::jd3::chunk_library_inputters::ChunkLibraryInputterFactory , protocols::jd3::full_model_inputters::FullModelInputterFactory , protocols::jd3::pose_inputters::PoseInputterFactory , protocols::jd3::pose_outputters::PoseOutputterFactory
• creator_map() : core::pack::task::operation::TaskOperationFactory , core::select::jump_selector::JumpSelectorFactory , core::select::residue_selector::ResidueSelectorFactory , protocols::multistage_rosetta_scripts::cluster::ClusterMetricFactory
• creator_map_ : core::chemical::rotamers::RotamerLibrarySpecificationFactory , core::pack::rotamers::SingleResidueRotamerLibraryFactory , core::select::jump_selector::JumpSelectorFactory , core::select::residue_selector::ResidueSelectorFactory , core::simple_metrics::SimpleMetricFactory , protocols::constraint_generator::ConstraintGeneratorFactory , protocols::multistage_rosetta_scripts::cluster::ClusterMetricFactory
• CreatorList : protocols::jd3::chunk_library_inputters::ChunkLibraryInputterFactory , protocols::jd3::full_model_inputters::FullModelInputterFactory , protocols::jd3::pose_inputters::PoseInputterFactory , protocols::jd3::pose_outputters::PoseOutputterFactory
• CreatorMap : core::chemical::rotamers::RotamerLibrarySpecificationFactory , core::pack::rotamers::SingleResidueRotamerLibraryFactory , core::simple_metrics::SimpleMetricFactory , protocols::constraint_generator::ConstraintGeneratorFactory
• creators_ : protocols::denovo_design::architects::DeNovoArchitectFactory
• crick_params_filename() : protocols::helical_bundle_predict::HBPHelix
• crick_params_filename_ : protocols::helical_bundle_predict::HBPHelix
• criteria_match_i() : core::scoring::bin_transitions::BinTransitionData
• criteria_match_iplus1() : core::scoring::bin_transitions::BinTransitionData
• cross_angle() : protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::topology::HelixPairing
• cross_angle_ : protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential , protocols::fldsgn::topology::HelixPairing
• CROSS_CHAIN_ALL : protocols::protein_interface_design::filters::AtomicContactCountFilter
• cross_chain_bonus() : core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::HBondBonusOptions
• cross_chain_bonus_ : core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::HBondBonusOptions
• cross_chain_boundaries_ : core::select::residue_selector::PrimarySequenceNeighborhoodSelector
• CROSS_CHAIN_DETECTED : protocols::protein_interface_design::filters::AtomicContactCountFilter
• CROSS_JUMP : protocols::protein_interface_design::filters::AtomicContactCountFilter
• cross_over() : core::optimization::GA_Minimizer , protocols::fldsgn::topology::BetaAlphaBetaMotif
• cross_over_ : protocols::fldsgn::topology::BetaAlphaBetaMotif
• cross_peaks_ : protocols::noesy_assign::DistanceScoreMover
• cross_product_helper() : core::chemical::orbitals::AssignOrbitals
• cross_val_ : core::scoring::ProQPotential
• crossing_angle : protocols::features::helixAssembly::FragmentPair
• CrosslinkerMover() : protocols::cyclic_peptide::CrosslinkerMover
• CrosslinkerMoverHelper() : protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper
• crossover() : core::scoring::etable::etrie::TrieCountPairGeneric , protocols::genetic_algorithm::EntityRandomizer , protocols::ligand_docking::ga_ligand_dock::LigandConformer
• crossover_ : core::scoring::etable::count_pair::CountPairGeneric , core::scoring::etable::etrie::TrieCountPairGeneric
• crossover_ft : protocols::ligand_docking::ga_ligand_dock::LigandConformer
• CrossPeak() : protocols::noesy_assign::CrossPeak
• crosspeak() : protocols::noesy_assign::PeakAssignment
• CrossPeak3D() : protocols::noesy_assign::CrossPeak3D
• CrossPeak4D() : protocols::noesy_assign::CrossPeak4D
• crosspeak_ : protocols::noesy_assign::PeakAssignment
• CrossPeakInfo() : protocols::noesy_assign::CrossPeakInfo
• CrossPeakList() : protocols::noesy_assign::CrossPeakList
• CrossPeaks : protocols::noesy_assign::CrossPeakList
• crosspeaks() : protocols::noesy_assign::NoesyModule
• crosspeaks_ : protocols::noesy_assign::NoesyModule
• crossterm_interface_energy : protocols::analysis::InterfaceData
• crossterm_interface_energy_dSASA_ratio : protocols::analysis::InterfaceData
• cryst1_ : protocols::symmetry::SetupForSymmetryMover
• CrystalContactsOperation() : protocols::task_operations::CrystalContactsOperation
• CrystInfo() : core::io::CrystInfo
• crystinfo() : core::io::StructFileRep
• CrystInfo : core::pose::PDBInfo
• crystinfo() : core::pose::PDBInfo
• crystinfo_ : core::io::StructFileRep , core::pose::PDBInfo
• CrystRMS() : protocols::cryst::CrystRMS
• CS2ndShift() : protocols::frag_picker::CS2ndShift
• CS_RAD_params_ : core::scoring::rna::chemical_shift::RNA_CS_parameters
• CS_RCY_params_ : core::scoring::rna::chemical_shift::RNA_CS_parameters
• cs_resnum : core::enzymes::EnzymeData
• CS_RGU_params_ : core::scoring::rna::chemical_shift::RNA_CS_parameters
• cs_type : core::enzymes::EnzymeData
• CS_URA_params_ : core::scoring::rna::chemical_shift::RNA_CS_parameters
• cs_verbose_mode_ : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• CSA() : core::scoring::CSA
• csa_bank_size_ : protocols::rna::setup::RNA_CSA_JobDistributor
• csa_from_pose() : core::scoring::methods::ChemicalShiftAnisotropyEnergy
• CSA_lines : core::scoring::ChemicalShiftAnisotropy
• csa_rmsd_ : protocols::rna::setup::RNA_CSA_JobDistributor
• csa_score_ : core::scoring::methods::ChemicalShiftAnisotropyEnergy
• CSAcomputed() : core::scoring::CSA
• CSAerr() : core::scoring::CSA
• CSAerr_ : core::scoring::CSA
• CSAval() : core::scoring::CSA
• CSAval_ : core::scoring::CSA
• CSAval_computed_ : core::scoring::CSA
• csblast_ : protocols::frag_picker::FragmentScoreFilter
• csequence_ : protocols::seeded_abinitio::GrowPeptides
• csf_cbang1_ : core::scoring::disulfides::CB_Angle_Func , core::scoring::disulfides::CBSG_Dihedral_Func
• csf_cbang1a_ : core::scoring::disulfides::SGSG_Dihedral_Func
• csf_cbang1b_ : core::scoring::disulfides::SGSG_Dihedral_Func
• csf_cbang2_ : core::scoring::disulfides::CB_Angle_Func , core::scoring::disulfides::CBSG_Dihedral_Func
• csf_cbang2a_ : core::scoring::disulfides::SGSG_Dihedral_Func
• csf_cbang2b_ : core::scoring::disulfides::SGSG_Dihedral_Func
• csf_cbang3_ : core::scoring::disulfides::CBSG_Dihedral_Func
• CSP_ : protocols::ub_e2c::ubi_e2c_modeler
• CSP_fraction() : protocols::ub_e2c::ubi_e2c_modeler
• CSP_swap_trim_ : protocols::ub_e2c::ubi_e2c_modeler
• CSP_trim_ : protocols::ub_e2c::ubi_e2c_modeler
• CSScore() : protocols::frag_picker::scores::CSScore
• cst : protocols::ligand_docking::ga_ligand_dock::StructInfo
• cst_ : core::scoring::constraints::Obsolet_NamedAtomPairConstraint , protocols::md::Rattle
• cst_action_ : protocols::enzdes::AddOrRemoveMatchCsts
• cst_block() : protocols::toolbox::match_enzdes_util::CstResInteractions , protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• cst_block_ : protocols::toolbox::match_enzdes_util::CstResInteractions , protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• cst_cache() : protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver
• cst_cache_ : protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver
• cst_cleanup() : protocols::protein_interface_design::movers::PlaceStubMover
• cst_conformers_ : protocols::jumping::ResiduePairJump
• cst_cutoff_ : protocols::score_filters::GeometryFilter
• cst_data_ : protocols::abinitio::IterativeBase
• cst_fa_data_ : protocols::abinitio::IterativeBase
• cst_fa_file_ : protocols::constraint_movers::ConstraintSetMover , protocols::ligand_docking::Transform
• cst_fa_weight_ : protocols::docking::DockingProtocol , protocols::ligand_docking::Transform
• cst_file() : protocols::abinitio::abscript::ConstraintPreparer , protocols::constraint_movers::CstInfoMover
• cst_file_ : protocols::constraint_movers::ConstraintSetMover , protocols::constraint_movers::CstInfoMover , protocols::hybridization::FoldTreeHybridize , protocols::membrane::MPQuickRelaxMover , protocols::relax::RangeRelaxMover , protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• cst_file_name_ : protocols::simple_moves::SequenceProfileMover
• cst_file_written : protocols::hbnet::HBondNetStruct
• cst_filename_ : protocols::topology_broker::ConstraintClaimer , protocols::topology_broker::CoordConstraintClaimer
• cst_files() : protocols::relax::RelaxProtocolBase
• cst_files_ : protocols::energy_based_clustering::EnergyBasedClusteringOptions , protocols::relax::RelaxProtocolBase
• cst_func_ : protocols::cyclic_peptide::CreateAngleConstraint , protocols::cyclic_peptide::CreateDistanceConstraint , protocols::cyclic_peptide::CreateTorsionConstraint , protocols::topology_broker::CoordConstraintClaimer
• cst_func_angle2_ : protocols::cyclic_peptide::PeptideCyclizeMover
• cst_func_angle_ : protocols::cyclic_peptide::PeptideCyclizeMover
• cst_func_dist_ : protocols::cyclic_peptide::PeptideCyclizeMover
• cst_func_torsion_ : protocols::cyclic_peptide::PeptideCyclizeMover
• cst_gap() : core::import_pose::options::RNA_DeNovoProtocolOptions
• cst_gap_ : core::import_pose::options::RNA_DeNovoProtocolOptions
• cst_gen_loader_ct_namer() : protocols::parser::ConstraintGeneratorLoader
• cst_graph_ : core::scoring::constraints::CstEnergyContainer
• cst_in_ : protocols::hybridization::FoldTreeHybridize
• cst_interactions() : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• cst_io() : protocols::match::output::OutputWriter
• cst_io_ : protocols::match::output::OutputWriter
• cst_jumps_ : protocols::jumping::ResiduePairJump
• cst_lib_ : protocols::constraints_additional::CombinedConstraintEvaluator
• cst_map_ : protocols::constraint_generator::ConstraintsMap , protocols::forge::remodel::RemodelConstraintGenerator
• cst_max_seq_sep() : core::scoring::methods::EnergyMethodOptions
• cst_max_seq_sep_ : core::scoring::methods::EnergyMethodOptions
• cst_minimize() : protocols::enzdes::EnzdesBaseProtocol
• cst_on_pose_dynamic() : protocols::md::CartesianMD
• cst_on_pose_simple() : protocols::md::CartesianMD
• cst_opt_ : protocols::enzdes::EnzRepackMinimize
• cst_pairs_ : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• cst_params : protocols::relax::CentroidRelax::parameters
• cst_pose_ : protocols::topology_broker::CoordConstraintClaimer
• cst_score_types_ : core::scoring::constraints::AmbiguousConstraint , core::scoring::constraints::KofNConstraint
• cst_sd() : protocols::relax::AtomCoordinateCstMover
• cst_sd_ : protocols::relax::AtomCoordinateCstMover
• cst_sdev() : protocols::md::MDBase , protocols::normalmode::NormalModeRelaxMover
• cst_sdev_ : protocols::md::MDBase , protocols::normalmode::NormalModeRelaxMover
• cst_selector_name_ : core::scoring::mhc_epitope_energy::MHCEpitopeConstraint
• cst_seqwidth_ : protocols::rbsegment_relax::RBSegmentRelax
• cst_set() : core::pose::full_model_info::FullModelParameters
• cst_set_ : core::pose::full_model_info::FullModelParameters , protocols::ddg::ddGMover , protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::modeler::StepWiseModeler
• cst_set_revision_id_ : core::scoring::constraints::CstEnergyContainer
• cst_sfx_ : protocols::forge::remodel::RemodelLigandHandler
• cst_sidechain() : protocols::relax::AtomCoordinateCstMover
• cst_sidechain_ : protocols::relax::AtomCoordinateCstMover
• cst_source_ : protocols::constraints_additional::ConstraintEvaluator
• cst_stdev_ : protocols::rbsegment_relax::RBSegmentRelax
• cst_strength_ : protocols::noesy_assign::PeakAssignmentParameters
• cst_string() : core::pose::full_model_info::FullModelParameters
• cst_string_ : core::pose::full_model_info::FullModelParameters
• cst_to_native_ : protocols::relax::RangeRelaxMover
• cst_to_start_ : protocols::relax::RangeRelaxMover
• cst_type() : protocols::protein_interface_design::movers::TaskAwareCsts
• cst_type_ : protocols::protein_interface_design::movers::TaskAwareCsts
• cst_types_ : core::scoring::constraints::ConstraintFactory
• cst_weight() : protocols::constraint_movers::AddConstraintsToCurrentConformationMover , protocols::simple_moves::ShakeStructureMover
• cst_weight_ : core::scoring::mhc_epitope_energy::MHCEpitopeConstraint , protocols::antibody::AntibodyModelerProtocol , protocols::antibody::GraftCDRLoopsProtocol , protocols::antibody_legacy::AntibodyModeler , protocols::constraint_movers::AddConstraintsToCurrentConformationMover , protocols::docking::DockingProtocol , protocols::membrane::MPQuickRelaxMover , protocols::rbsegment_relax::IdealizeHelicesMover , protocols::rbsegment_relax::RBSegmentRelax , protocols::relax::RangeRelaxMover
• cst_width() : protocols::relax::AtomCoordinateCstMover
• cst_width_ : protocols::rbsegment_relax::IdealizeHelicesMover , protocols::rbsegment_relax::RBSegmentRelax , protocols::relax::AtomCoordinateCstMover
• cst_wtd_ : protocols::ligand_docking::ga_ligand_dock::ReweightableRepEnergy
• CSTalosIO() : protocols::frag_picker::CSTalosIO
• cstAtoms() : protocols::jumping::ResiduePairJump , protocols::jumping::ResiduePairJumpSingle
• cstAtoms_ : protocols::jumping::ResiduePairJumpSingle
• cstAtoms_defined() : protocols::jumping::ResiduePairJump , protocols::jumping::ResiduePairJumpSingle
• cstblocksize_ : protocols::forge::remodel::RemodelEnzdesCstModule
• CstEnergyContainer() : core::scoring::constraints::CstEnergyContainer
• cstfile() : protocols::enzdes::AddOrRemoveMatchCsts
• cstfile_ : protocols::abinitio::Template , protocols::enzdes::AddOrRemoveMatchCsts , protocols::forge::remodel::RemodelMover::instruction_flags
• cstfile_map_ : protocols::enzdes::AddOrRemoveMatchCsts
• cstfile_name() : protocols::match::MatcherTask , protocols::match::output::PDBWriter
• cstfile_name_ : protocols::match::MatcherTask , protocols::match::output::PDBWriter
• cstid_ : protocols::enzdes::EnzScoreFilter
• cstid_list_ : protocols::enzdes::DetectProteinLigandInterface , protocols::enzdes::PackRotamersMoverPartGreedy , protocols::enzdes::RepackWithoutLigandFilter
• cstInfoMap : protocols::jumping::ResiduePairJump
• cstInfoMap_ : protocols::jumping::ResiduePairJump
• cstInfoMap_defined() : protocols::jumping::ResiduePairJump
• cstInfoMapIterator : protocols::jumping::ResiduePairJump
• CstInfoMover() : protocols::constraint_movers::CstInfoMover
• CstMinimizationData() : core::scoring::constraints::CstMinimizationData
• cstres_interactions_ : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• CstResInteractions() : protocols::toolbox::match_enzdes_util::CstResInteractions
• CstResNeighbConstIterator() : core::scoring::constraints::CstResNeighbConstIterator
• CstResNeighbIterator() : core::scoring::constraints::CstResNeighbIterator
• csts_ : protocols::forge::remodel::RemodelConstraintGenerator , protocols::sic_dock::ConstraintSetScore
• csts_from_frags_ : protocols::hybridization::HybridizeProtocol
• cstset_ : protocols::abinitio::AbrelaxApplication , protocols::abinitio::Template
• cstw : protocols::mpi_refinement::MethodParams
• cstyle_A_ : protocols::scoring::methods::pcs2::PcsDataLanthanide
• cstyle_b_ : protocols::scoring::methods::pcs2::PcsDataLanthanide
• cstyle_b_individual_scale_ : protocols::scoring::methods::pcs2::PcsDataLanthanide
• ct_ : protocols::abinitio::hConvergenceCheck , protocols::hybridization::hConvergenceCheck
• ctab_mode_ : core::chemical::sdf::MolWriter
• CtabMode : core::chemical::sdf::MolWriter
• CtabParserBase() : core::chemical::sdf::CtabParserBase
• Cter_insert_flexibility() : protocols::grafting::AnchoredGraftMover
• Cter_insert_flexibility_ : protocols::grafting::AnchoredGraftMover
• Cter_loop_end() : protocols::grafting::AnchoredGraftMover
• Cter_loop_end_ : protocols::grafting::AnchoredGraftMover
• Cter_loop_start() : protocols::grafting::AnchoredGraftMover
• Cter_loop_start_ : protocols::grafting::AnchoredGraftMover
• cter_overhang_ : protocols::antibody::AntibodyCDRGrafter , protocols::grafting::simple_movers::DeleteRegionMover , protocols::grafting::simple_movers::KeepRegionMover , protocols::tcr::TCRmodel
• Cter_overhang_length() : protocols::grafting::GraftMoverBase
• Cter_overhang_length_ : protocols::grafting::GraftMoverBase
• Cter_scaffold_flexibility() : protocols::grafting::AnchoredGraftMover
• Cter_scaffold_flexibility_ : protocols::grafting::AnchoredGraftMover
• cTerm_cap_size_ : protocols::simple_moves::RepeatPropagationMover
• cterm_included() : protocols::denovo_design::components::Segment
• cterm_included_ : protocols::denovo_design::components::Segment
• cterm_length_ : protocols::match::RemoveNorCTermMPM
• Cterm_offset() : protocols::splice::FindEndpointsOperation
• Cterm_offset_ : protocols::splice::FindEndpointsOperation
• cterm_rsd_num_ : protocols::simple_moves::CyclizationMover
• ctor() : protocols::loops::loop_closure::kinematic_closure::KinematicWrapper
• ctrl_strength() : protocols::environment::claims::TorsionClaim , protocols::environment::claims::XYZClaim
• cube_dim_ : protocols::scoring::ImplicitFastClashCheck
• cube_dim_ca_ : protocols::scoring::ImplicitFastClashCheck
• cubes : core::scoring::packstat::Octree2D
• cubes_ : protocols::scoring::ImplicitFastClashCheck
• cubes_ca_ : protocols::scoring::ImplicitFastClashCheck
• cubic_interpolation() : core::optimization::LineMinimizationAlgorithm
• cull_list_ : protocols::abinitio::Templates
• cull_mutatable_residues() : protocols::vip::VIP_Mover
• cull_violators() : protocols::abinitio::Template
• cum_dist6_ : protocols::noesy_assign::FragsToAtomDist::DistanceRecord
• cum_dist_ : protocols::noesy_assign::FragsToAtomDist::DistanceRecord
• cummulative_time() : protocols::md::MDBase
• cummulative_time_ : protocols::md::MDBase
• cumulate_jobs() : protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::TrajectoryRecorder
• cumulate_jobs_ : protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::TrajectoryRecorder
• cumulate_prob_ : protocols::hybridization::CartesianSampler
• cumulate_probability() : protocols::hybridization::FragmentBiasAssigner
• cumulate_replicas() : protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::TrajectoryRecorder
• cumulate_replicas_ : protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::TrajectoryRecorder
• cumulated_jobs_ : protocols::jd2::MPIFileBufJobDistributor
• cumulated_runtime_ : protocols::jd2::MPIFileBufJobDistributor
• cumulative_ : protocols::hybridization::FragmentBiasAssigner
• cumulative_peak_volume() : protocols::noesy_assign::CrossPeak
• cumulative_peak_volume_ : protocols::noesy_assign::CrossPeak
• cumulative_sums_ : protocols::frag_picker::scores::AdaptiveScoreHistogram
• cur_energy() : protocols::flexpack::interaction_graph::FlexbbEdge
• cur_energy_ : protocols::flexpack::interaction_graph::FlexbbEdge
• cur_indices_ : protocols::helical_bundle::BackboneGridSamplerHelper , protocols::helical_bundle::BundleGridSamplerHelper
• cur_ncluster_ : protocols::toolbox::KMedoid
• curr_ : core::chemical::AutomorphismIterator
• curr_aa() : protocols::mean_field::AAMatrix
• curr_aa_ : protocols::mean_field::AAMatrix
• curr_aa_prob() : protocols::mean_field::AAMatrix
• curr_atom_hbonds_ : core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G > , core::pack::interaction_graph::NPDHBondNode< V, E, G > , core::pack::interaction_graph::NPDHBSimpleNode
• curr_bb() : protocols::flexpack::interaction_graph::FlexbbNode
• curr_bg_bg_exhpobeolap_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• curr_bin_ : protocols::match::VoxelSetIterator
• curr_coordinate_constraints_ : protocols::protein_interface_design::movers::PlaceStubMover
• curr_dots_cache_ : core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G >
• curr_exemplar : protocols::cluster::DataPoint
• curr_gen_entities_ : protocols::genetic_algorithm::GeneticAlgorithmBase
• curr_gen_entity() : protocols::genetic_algorithm::GeneticAlgorithmBase
• curr_hbonds_ : core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G > , core::pack::interaction_graph::NPDHBondNode< V, E, G > , core::pack::interaction_graph::NPDHBSimpleNode
• curr_id() : protocols::recces::sampler::MC_Any
• curr_id_ : protocols::recces::sampler::MC_Any
• curr_idx_ : core::scoring::PolymerBondedNeighborConstIterator , core::scoring::PolymerBondedNeighborIterator
• curr_in_recent_history_ : core::pack::annealer::FASTERAnnealer
• curr_inner_larval_job_index_ : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::standard::StandardJobQueen
• curr_jobid_ : protocols::jobdist::BaseJobDistributor
• curr_loop_end_ : protocols::protein_interface_design::movers::PlaceOnLoop
• curr_memory_for_rpes_ : core::pack::interaction_graph::DoubleLazyInteractionGraph
• curr_min_bb_ : protocols::calc_taskop_movers::DesignRepackMover
• curr_min_rb_ : protocols::calc_taskop_movers::DesignRepackMover
• curr_min_sc_ : protocols::calc_taskop_movers::DesignRepackMover
• curr_mut_filename : protocols::ddG::ddGData
• curr_mut_read : protocols::ddG::ddGData
• curr_pos_ : protocols::match::VoxelSetIterator
• curr_pose_ : protocols::seeded_abinitio::CAcstGenerator
• curr_rot() : protocols::mean_field::RotMatrix
• curr_rot_ : protocols::mean_field::RotMatrix
• curr_rot_2_orig_rot_ : protocols::minimization_packing::GreenPacker
• curr_rot_prob() : protocols::mean_field::RotMatrix
• curr_rotamers_with_correspondence_ : protocols::minimization_packing::GreenPacker
• curr_rotamers_without_correspondence_ : protocols::minimization_packing::GreenPacker
• curr_sc_centroid() : core::pack::interaction_graph::SimpleNode
• curr_sc_centroid_ : core::pack::interaction_graph::SimpleNode
• curr_sc_radius() : core::pack::interaction_graph::SimpleNode
• curr_sc_radius_ : core::pack::interaction_graph::SimpleNode
• curr_score_log : protocols::relax::SRelaxPose
• curr_state_ : protocols::stepwise::sampler::StepWiseSamplerSizedAny
• curr_state_energy() : core::pack::interaction_graph::SymmMinimalistEdge
• curr_state_energy_ : core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmMinimalistEdge
• curr_state_exolap_hphobes_ : core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G > , core::pack::interaction_graph::HPatchEdge< V, E, G >
• curr_state_exp_hphobes() : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G >
• curr_state_exp_hphobes_ : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G >
• curr_state_hphobes() : core::pack::interaction_graph::HPatchNode< V, E, G >
• curr_state_inv_dots() : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G >
• curr_state_inv_dots_ : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G >
• curr_state_one_body_energy() : protocols::flexpack::interaction_graph::FlexbbNode
• curr_state_one_body_energy_ : 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
• curr_state_rotamer() : core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::NPDHBondNode< V, E, G >
• curr_state_rotamer_op() : core::pack::interaction_graph::NPDHBondNode< V, E, G >
• curr_state_sparse_mat_info_ : core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode
• curr_state_total_energy() : protocols::flexpack::interaction_graph::FlexbbNode
• curr_state_total_energy_ : 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
• curr_state_total_hASA_ : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G >
• curr_state_two_body_energies() : protocols::flexpack::interaction_graph::FlexbbNode
• curr_state_two_body_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
• curr_wt_filename : protocols::ddG::ddGData
• curr_wt_read : protocols::ddG::ddGData
• current_ : core::scoring::nmr::NMRGridSearch , protocols::simple_moves::sidechain_moves::SidechainMCMover
• current_acceptance_ratio() : protocols::jd2::archive::ArchiveBase
• current_add_probability_ : protocols::sewing::movers::AssemblyMover
• current_angles_ : protocols::matdes::SymDofMoverSampler
• current_basis_pair_ : protocols::sewing::data_storage::SmartAssembly
• current_batch_ : protocols::jd2::BatchJobInputter
• current_batch_id() : protocols::jd2::JobDistributor
• current_batch_id_ : protocols::jd2::JobDistributor
• current_binary_format_version_id_02() : core::pack::dunbrack::RotamerLibrary
• current_binary_format_version_id_10() : core::pack::dunbrack::RotamerLibrary
• current_chain_pair_pose_ : protocols::peptide_deriver::PeptideDeriverPoseOutputter
• current_claims_ : protocols::topology_broker::TopologyBroker , protocols::topology_broker::TopologyClaimer
• current_clashes_ : protocols::sewing::requirements::ClashRequirement , protocols::sewing::requirements::LigandClashRequirement
• current_conformer_ensemble1_ : protocols::docking::DockingLowResEnsemble
• current_conformer_ensemble2_ : protocols::docking::DockingLowResEnsemble
• current_contacts_ : protocols::sewing::data_storage::LigandResidue
• current_cycle_ : protocols::features::TrajectoryMapFeatures
• current_cycle_number() : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• current_cycle_number_ : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• current_dbase_entry_ : protocols::splice::Splice , protocols::splice::SpliceIn
• current_digraph_node_ : protocols::jd3::job_distributors::JobExtractor
• current_dna_design_string() : protocols::dna::DnaInterfacePacker
• current_embedding_ : protocols::membrane::TransformIntoMembraneMover
• current_end : protocols::antibody_legacy::Antibody
• current_energy_ : core::pack::interaction_graph::ResidueArrayAnnealingEvaluator , core::pack::interaction_graph::SimpleEdge , protocols::simple_moves::sidechain_moves::SidechainMCMover
• current_entry_ : protocols::splice::RBInMover
• current_exchange_schedule_ : protocols::canonical_sampling::HamiltonianExchange
• current_filename_ : core::import_pose::pose_stream::LazySilentFilePoseInputStream
• current_func_ : protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover , protocols::antibody::constraints::ParatopeSiteConstraintMover
• current_generation() : protocols::genetic_algorithm::GeneticAlgorithmBase
• current_generation_ : protocols::genetic_algorithm::GeneticAlgorithmBase
• current_generation_begin() : protocols::genetic_algorithm::GeneticAlgorithmBase
• current_generation_complete() : protocols::genetic_algorithm::GeneticAlgorithmBase
• current_generation_end() : protocols::genetic_algorithm::GeneticAlgorithmBase
• current_global_job_index_ : protocols::jd3::JobTracker
• current_hbs() : core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G > , core::pack::interaction_graph::NPDHBondNode< V, E, G >
• current_helix_assignments_ : protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator
• current_idx_ : protocols::pdbinfo_manipulations::SequenceSpecification
• current_ig_ : protocols::minimization_packing::GreenPacker
• current_index_ : core::import_pose::pose_stream::MetaPoseInputStream
• current_inner_larval_job_for_stage_ : protocols::multistage_rosetta_scripts::MRSJobQueen
• current_input_name_ : protocols::constraint_movers::ConstraintSetMover
• current_input_stream_ : core::import_pose::pose_stream::MetaPoseInputStream
• current_inter_group_packer_neighbor_graph_ : protocols::minimization_packing::GreenPacker
• current_intra_group_packer_neighbor_graph_ : protocols::minimization_packing::GreenPacker
• current_jacobians_ : protocols::recces::sampler::rna::MC_RNA_KIC_Sampler
• current_job() : protocols::comparative_modeling::ThreadingJob , protocols::jd2::JobDistributor , protocols::jd2::VectorPoseJobDistributor , protocols::jobdist::BaseJobDistributor
• current_job_ : protocols::jd2::JobDistributor , protocols::jobdist::BaseJobDistributor , protocols::moves::Mover
• current_job_finished() : protocols::jd2::FileSystemJobDistributor , protocols::jd2::JobDistributor
• current_job_id() : protocols::jd2::JobDistributor
• current_job_id_ : protocols::jd2::JobDistributor , protocols::jd2::MPIWorkPoolJobDistributor
• current_job_index() : protocols::jd3::JobTracker , protocols::jd3::standard::StandardJobQueen
• current_jump_ : protocols::symmetry::SymmetrySlider
• current_jump_calculator_ : protocols::topology_broker::RigidChunkClaimer
• current_jumps_ : protocols::topology_broker::FragmentJumpClaimer , protocols::topology_broker::RigidChunkClaimer
• current_kinematics() : protocols::abinitio::KinematicTaskControl
• current_kinematics_ : protocols::abinitio::KinematicTaskControl
• current_loop_is_H3_ : protocols::antibody::H3PerturbCCD , protocols::antibody_legacy::CDRH3Modeler
• current_maximum_id_ : core::environment::EnvCore
• current_mode_ : protocols::hotspot_hashing::movers::PlaceProbeMover
• current_n_ : core::import_pose::pose_stream::ExtendedPoseInputStream
• current_noesy_sampling_file_ : protocols::abinitio::IterativeBase
• current_nstruct() : protocols::jobdist::BaseJobDistributor
• current_nstruct_ : protocols::jd2::VectorPoseJobDistributor , protocols::jobdist::BaseJobDistributor
• current_ntrial_ : protocols::simple_moves::sidechain_moves::SidechainMCMover
• current_one_body_energy() : core::pack::interaction_graph::SimpleNode
• current_one_body_energy_ : core::pack::interaction_graph::SimpleNode
• current_outer_cycle_ : protocols::docking::DockingLowResEnsemble
• current_output_name() : protocols::jd2::JobDistributor
• current_packer_neighbor_graph_ : protocols::minimization_packing::GreenPacker
• current_partner_chain_letter_ : protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter , protocols::peptide_deriver::PeptideDeriverPoseOutputter
• current_pep_length_ : protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter
• current_peptide_length_ : protocols::peptide_deriver::PeptideDeriverPoseOutputter
• current_phore_match_ : protocols::ligand_docking::ga_ligand_dock::ConstraintInfo
• current_pose() : protocols::topology_broker::TopologyBroker
• current_pose_ : protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::jd2::VectorPoseJobDistributor , protocols::recon_design::MSDMover , protocols::topology_broker::TMHTopologySamplerClaimer , protocols::topology_broker::TopologyBroker
• current_pose_buf : protocols::boinc::BoincSharedMemory
• current_pose_energy_ : protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
• current_pose_exists : protocols::boinc::BoincSharedMemory
• current_pose_ghost_buf : protocols::boinc::BoincSharedMemory
• current_pose_ghost_exists : protocols::boinc::BoincSharedMemory
• current_pose_landing_atom() : core::scoring::loop_graph::evaluator::LoopClosePotentialEvaluator
• current_pose_landing_atom_ : core::scoring::loop_graph::evaluator::LoopClosePotentialEvaluator
• current_pose_landing_xyz() : core::scoring::loop_graph::evaluator::LoopClosePotentialEvaluator
• current_pose_landing_xyz_ : core::scoring::loop_graph::evaluator::LoopClosePotentialEvaluator
• current_pose_loop_score_evaluators_ : core::scoring::loop_graph::LoopGraph
• current_pose_takeoff_atom() : core::scoring::loop_graph::evaluator::LoopClosePotentialEvaluator
• current_pose_takeoff_atom_ : core::scoring::loop_graph::evaluator::LoopClosePotentialEvaluator
• current_pose_takeoff_xyz() : core::scoring::loop_graph::evaluator::LoopClosePotentialEvaluator
• current_pose_takeoff_xyz_ : core::scoring::loop_graph::evaluator::LoopClosePotentialEvaluator
• current_position() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• current_position_ : core::import_pose::pose_stream::PDBPoseInputStream , core::import_pose::pose_stream::SilentFilePoseInputStream
• current_radial_disps_ : protocols::matdes::SymDofMoverSampler
• current_receptor_chain_letter_ : protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter , protocols::peptide_deriver::PeptideDeriverPoseOutputter
• current_residue_ : core::pack::interaction_graph::SimpleNode
• current_residues_ : core::pack::interaction_graph::ResidueArrayAnnealingEvaluator
• current_rigid_core_ : protocols::topology_broker::RigidChunkClaimer
• current_rot_index() : core::pack::annealer::SimAnnealerBase
• current_rot_index_ : core::pack::annealer::SimAnnealerBase
• current_rotamer() : core::pack::rotamers::SingleResidueRotamerLibrary
• current_rotamer_coords() : core::pack::rotamer_set::ContinuousRotamerSet
• current_rotamer_copy_ : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• current_rotamer_ids_ : core::pack::interaction_graph::ResidueArrayAnnealingEvaluator
• current_rotamer_sets_ : protocols::minimization_packing::GreenPacker
• current_rotamers_ : protocols::minimization_packing::GreenPacker
• current_round() : protocols::helical_bundle_predict::HBP_MoveGenerator , protocols::helical_bundle_predict::HBP_TemperatureScheduleGenerator
• current_round_ : protocols::helical_bundle_predict::HBP_MoveGenerator , protocols::helical_bundle_predict::HBP_TemperatureScheduleGenerator
• current_score() : protocols::monte_carlo::GenericMonteCarloMover , protocols::relax::SRelaxPose , protocols::stepwise::modeler::rna::output_data_struct
• current_score_ : protocols::monte_carlo::GenericMonteCarloMover
• current_score_cutoff_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection
• current_scorefxn() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• current_segment_ : protocols::sewing::requirements::DsspSpecificLengthRequirement
• current_segment_pos : protocols::splice::Splice
• current_sequence_ : protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter
• current_size() : protocols::frag_picker::quota::ABEGO_SS_Pool , protocols::frag_picker::quota::QuotaPool , protocols::frag_picker::quota::SecondaryStructurePool
• current_start : protocols::antibody_legacy::Antibody
• current_state() : protocols::flexpack::interaction_graph::FlexbbNode
• current_state_ : 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
• current_state_atom_atom_overlaps_ : core::pack::interaction_graph::HPatchEdge< V, E, G >
• current_state_info() : protocols::flexpack::interaction_graph::FlexbbNode
• current_state_info_ : protocols::flexpack::interaction_graph::FlexbbNode
• current_state_rotamer_dots_ : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G >
• current_struct : protocols::relax::SRelaxPose
• current_struct_ : core::import_pose::pose_stream::LazySilentFilePoseInputStream
• current_tag_ : protocols::moves::Mover
• current_tags_map_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• current_task_ : protocols::minimization_packing::GreenPacker
• current_temp() : protocols::canonical_sampling::TemperingBase
• current_temp_ : protocols::canonical_sampling::TemperingBase
• current_to_pick_ : core::pack::annealer::RotamerAssigningAnnealer
• current_total_isc_ : protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter
• current_transform_ : protocols::antibody::AntibodyInfo
• current_trial() : protocols::canonical_sampling::MetropolisHastingsMover , protocols::flxbb::FilterStructs
• current_trial_ : protocols::canonical_sampling::MetropolisHastingsMover , protocols::flxbb::FilterStructs , protocols::monte_carlo::GenericSimulatedAnnealer
• current_working_sequence() : protocols::dna::DnaInterfacePacker
• curstate_graph_ : core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty
• custom_angle() : protocols::backrub::BackrubMover
• custom_angle_ : protocols::backrub::BackrubMover
• custom_coords_ : core::scoring::epr_deer::EPRSpinLabel
• custom_electrons_ : core::scoring::epr_deer::EPRSpinLabel
• custom_properties_ : core::chemical::Selector_PROPERTY
• custom_rama_cdf() : core::scoring::Ramachandran
• custom_rama_map_ : protocols::simple_moves::SetTorsion
• custom_rama_probability_table() : core::scoring::Ramachandran
• custom_rama_table() : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• custom_rama_table_ : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• custom_rama_table_defined() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• custom_structure_input_tag_ : protocols::features::ReportToDB
• custom_structure_tag_ : protocols::features::ReportToDB
• custom_torsion_ : protocols::constraint_generator::DihedralConstraintGenerator
• custom_type_ : core::simple_metrics::SimpleMetric
• custom_types() : core::chemical::Patch
• custom_types_ : core::chemical::Patch
• custom_variant_types() : core::chemical::ResidueTypeBase
• custom_variant_types_ : core::chemical::ResidueProperties
• custom_variants_ : core::chemical::ResidueTypeFinder , core::chemical::Selector_VARIANT_TYPE
• CustomAtomPairEnergy() : core::scoring::methods::CustomAtomPairEnergy
• CustomBaseTypePackerPalette() : core::pack::palette::CustomBaseTypePackerPalette
• CustomScoreSelector() : protocols::frag_picker::CustomScoreSelector
• cut() : protocols::environment::claims::JumpClaim , protocols::loops::Loop , protocols::loops::SerializedLoop
• cut1_ : protocols::enzdes::DetectProteinLigandInterface , protocols::enzdes::SecondaryMatchProtocol
• cut2_ : protocols::enzdes::DetectProteinLigandInterface , protocols::enzdes::SecondaryMatchProtocol
• cut3_ : protocols::enzdes::DetectProteinLigandInterface , protocols::enzdes::SecondaryMatchProtocol
• cut4_ : protocols::enzdes::DetectProteinLigandInterface , protocols::enzdes::SecondaryMatchProtocol
• cut_ : protocols::environment::claims::JumpClaim , protocols::kinematic_closure::pivot_pickers::FixedPivots , protocols::loops::Loop , protocols::rbsegment_relax::CCDMoveWrapper
• cut_bias_ : protocols::topology_broker::CutBiasClaimer
• cut_bond() : core::chemical::Bond
• cut_bond_ : core::chemical::Bond
• cut_bond_neighbor() : core::chemical::ResidueType , core::conformation::Residue
• cut_bond_neighbor_indices_ : core::chemical::ResidueType
• cut_edge() : core::kinematics::FoldTree
• cut_point : protocols::stepwise::modeler::rna::Jump_point
• cut_points_ : protocols::seeded_abinitio::CAcstGenerator , protocols::seeded_abinitio::SeedFoldTree
• cut_prob_ : protocols::jumping::JumpsFromAllPairings
• cut_random_edge() : core::kinematics::FoldTree
• cut_reg_ : protocols::jumping::JumpSetup::JumpDef , protocols::jumping::ResiduePairJumpSetup::JumpDef
• cut_residue() : protocols::kinematic_closure::ClosureProblem
• cut_secondarystruc() : protocols::splice::Splice , protocols::splice::SpliceOut
• cut_secondarystruc_ : protocols::splice::Splice , protocols::splice::SpliceOut
• cut_site() : protocols::splice::ResidueBBDofs , protocols::splice::SpliceManager
• cut_site_ : protocols::splice::ResidueBBDofs , protocols::splice::SpliceManager
• CutAndJump() : protocols::denovo_design::movers::CutAndJump
• CutBiasClaim() : protocols::environment::claims::CutBiasClaim
• CutBiasClaimer() : protocols::topology_broker::CutBiasClaimer
• CutBiasElement() : protocols::environment::claims::CutBiasElement
• CutBiasElemVect : protocols::environment::EnvClaimBroker
• CutChainMover() : protocols::simple_moves::CutChainMover
• CutClaim() : protocols::topology_broker::claims::CutClaim
• CutElement() : protocols::environment::claims::CutElement
• CutElemVect : protocols::environment::EnvClaimBroker
• cutoff() : core::scoring::CenHBPotential , core::scoring::epr_deer::EPRSpinLabel , protocols::constraint_filters::ConstraintScoreCutoffFilter , protocols::score_filters::ScoreCutoffFilter , protocols::simple_filters::LongestContinuousPolarSegmentFilter , protocols::simple_filters::PDDFScoreFilter , protocols::simple_filters::SAXSScoreFilter , protocols::simple_moves::FragmentCost
• cutoff_ : core::pack::annealer::SmartFixbbSimAnnealer , core::scoring::epr_deer::EPRSpinLabel , core::simple_metrics::metrics::ResidueSummaryMetric , protocols::antibody::task_operations::AddCDRProfileSetsOperation , protocols::constraint_filters::ConstraintScoreCutoffFilter , protocols::enzdes::ValueEvaluator , protocols::frag_picker::DiversifyCrmsdSelector , protocols::frag_picker::DiversifyDihedralsSelector , protocols::frag_picker::SidechainContactDistCutoff , protocols::ligand_docking::LigandArea , protocols::qsar::qsarOptFunc , protocols::qsar::scoring_grid::VdwGrid , protocols::score_filters::ScoreCutoffFilter , protocols::simple_filters::LongestContinuousPolarSegmentFilter , protocols::simple_filters::PDDFScoreFilter , protocols::simple_filters::SAXSScoreFilter , protocols::simple_filters::SimpleMetricFilter , protocols::simple_moves::FragmentCost , protocols::task_operations::RestrictToMoveMapChiOperation
• cutoff_3_ : protocols::antibody::H3PerturbCCD , protocols::antibody_legacy::CDRH3Modeler
• cutoff_9_ : protocols::antibody::H3PerturbCCD , protocols::antibody_legacy::CDRH3Modeler
• cutoff_angle_ : protocols::sewing::scoring::LigandScorer
• cutoff_area_ : protocols::simple_filters::BuriedSurfaceAreaFilter
• cutoff_buried_surface_area() : protocols::simple_filters::BuriedSurfaceAreaFilter
• cutoff_cst_score_ : core::scoring::constraints::KofNConstraint
• cutoff_distance() : protocols::simple_task_operations::RestrictToLoopsAndNeighbors
• cutoff_distance_ : protocols::sewing::scoring::LigandScorer , protocols::simple_task_operations::RestrictToLoopsAndNeighbors
• cutoff_flag_ : protocols::match::downstream::ScoringSecMatchRPE
• cutoff_lower() : core::scoring::func::FadeFunc
• cutoff_lower_ : core::scoring::func::FadeFunc
• cutoff_lr_ : core::scoring::CenHBPotential
• cutoff_scoreType_flag_ : protocols::match::downstream::ScoringSecMatchRPE
• cutoff_squared_ : protocols::frag_picker::SidechainContactDistCutoff
• cutoff_sr_ : core::scoring::CenHBPotential
• cutoff_upper() : core::scoring::func::FadeFunc
• cutoff_upper_ : core::scoring::func::FadeFunc
• cutoffE_ : protocols::pose_metric_calculators::NonlocalContactsCalculator
• CutOutDomain() : protocols::cutoutdomain::CutOutDomain
• cutpoint() : core::kinematics::FoldTree , protocols::denovo_design::components::Segment , protocols::denovo_design::movers::CutAndJump
• cutpoint_ : core::kinematics::FoldTree , protocols::antibody::H3RefineCCD , protocols::denovo_design::components::Segment , protocols::loop_grower::LoopPartialSolutionStore , protocols::simple_moves::ChainSplitMover
• cutpoint_by_jump() : core::kinematics::FoldTree
• cutpoint_closed_ : core::import_pose::FullModelPoseBuilder , protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• cutpoint_closed_list() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• cutpoint_closed_list_ : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• cutpoint_handler_ : protocols::recces::sampler::rna::MC_RNA_KIC_Sampler
• cutpoint_list_ : protocols::rna::movers::ErraserMinimizerMover
• cutpoint_map() : core::kinematics::FoldTree
• cutpoint_map_ : core::kinematics::FoldTree
• cutpoint_open_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• cutpoint_open_in_full_model() : core::pose::full_model_info::FullModelInfo
• cutpoint_open_in_full_model_ : core::import_pose::FullModelPoseBuilder
• cutpoint_open_list() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• cutpoint_open_list_ : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• cutpoint_res() : protocols::loops::LoopFromFileData
• cutpoint_res_ : protocols::loops::LoopFromFileData
• cutpoint_segment() : protocols::denovo_design::components::Segment
• cutpoint_separation() : protocols::antibody_legacy::CDRH3Modeler
• cutpoint_suite_ : protocols::stepwise::monte_carlo::mover::TransientCutpointHandler
• CutpointResidueSelector() : protocols::fold_from_loops::selectors::CutpointResidueSelector
• cutpoints() : core::kinematics::FoldTree , protocols::denovo_design::components::StructureData , protocols::denovo_design::connection::ConnectionArchitect
• Cutpoints : protocols::denovo_design::movers::SealFoldTreeMover
• cutpoints() : protocols::star::Extender
• cutpoints_ : protocols::denovo_design::components::FoldGraph , protocols::denovo_design::movers::SealFoldTreeMover , protocols::ligand_docking::MinimizeBackbone , protocols::star::Extender
• cutpoints_closed() : core::import_pose::RNA_DeNovoParameters
• cutpoints_closed_ : core::import_pose::RNA_DeNovoParameters
• cutpoints_cyclize() : core::import_pose::RNA_DeNovoParameters
• cutpoints_cyclize_ : core::import_pose::RNA_DeNovoParameters
• cutpoints_open() : core::import_pose::RNA_DeNovoParameters
• cutpoints_open_ : core::import_pose::RNA_BasePairHandler , core::import_pose::RNA_DeNovoParameters
• cutpoints_separation() : protocols::antibody_legacy::CDRH3Modeler
• cutpos_ : protocols::rna::denovo::coarse::CoarseRNA_LoopCloser
• cutpos_list() : protocols::rna::denovo::coarse::CoarseRNA_LoopCloser
• cutpos_list_ : protocols::rna::denovo::coarse::CoarseRNA_LoopCloser
• cutradis_ : core::scoring::atomic_depth::AtomicDepth
• cuts() : protocols::environment::AutoCutData , protocols::jumping::JumpSample
• cuts_ : protocols::jumping::JumpSample , protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup , protocols::topology_broker::TMHTopologySamplerClaimer
• cuttable() : core::environment::FoldTreeSketch
• cw_angle : core::scoring::packstat::Event
• cyc_comment : protocols::peptide_deriver::CyclizedPeptideInfo
• cyc_info_set : protocols::peptide_deriver::DerivedPeptideEntry
• cyc_isc : protocols::peptide_deriver::CyclizedPeptideInfo
• cyc_pose : protocols::peptide_deriver::CyclizedPeptideInfo
• cyc_report_info_set_ : protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter
• cycle() : core::environment::FoldTreeSketch , core::scoring::loop_graph::cycle_printer
• cycle_counts_ : protocols::features::TrajectoryReportToDB
• cycle_printer() : core::scoring::loop_graph::cycle_printer
• cycle_selector_ : protocols::noesy_assign::PeakAssignmentParameters
• CycleMover() : protocols::moves::CycleMover
• cycles() : core::scoring::power_diagram::PDsphere , protocols::grafting::AnchoredGraftMover , protocols::ligand_docking::Rotate_info , protocols::ligand_docking::Transform_info , protocols::ligand_docking::TransformEnsemble_info , protocols::ligand_docking::Translate_info , protocols::magnesium::MgMonteCarlo , protocols::moves::IteratedConvergenceMover , protocols::rna::movers::RNA_DeNovoOptimizer , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• cycles_ : core::scoring::loop_graph::cycle_printer , core::scoring::power_diagram::PDsphere , protocols::abinitio::abscript::AbscriptStageMover , protocols::grafting::AnchoredGraftMover , protocols::legacy_sewing::LegacyGreedyAssemblyMover , protocols::legacy_sewing::LegacyMonteCarloAssemblyMover , protocols::loops::loop_closure::ccd::LoopClosure , protocols::magnesium::MgMonteCarlo , protocols::moves::IteratedConvergenceMover , protocols::protein_interface_design::movers::LoopRemodel , protocols::rbsegment_relax::RBSegmentRelax , protocols::relax::RangeRelaxMover , protocols::rna::movers::RNA_DeNovoOptimizer , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• cycles_adjust_ : protocols::abinitio::abscript::AbscriptStageMover
• cycles_inner_ : protocols::dna::DesignProteinBackboneAroundDNA
• cycles_outer_ : protocols::dna::DesignProteinBackboneAroundDNA
• cyclic_ : protocols::energy_based_clustering::EnergyBasedClusteringOptions
• cyclic_oxygen() : core::chemical::carbohydrates::CarbohydrateInfo
• cyclic_oxygen_ : core::chemical::carbohydrates::CarbohydrateInfo
• cyclic_oxygen_index() : core::chemical::carbohydrates::CarbohydrateInfo
• cyclic_oxygen_index_ : core::chemical::carbohydrates::CarbohydrateInfo
• cyclic_oxygen_name() : core::chemical::carbohydrates::CarbohydrateInfo
• cyclic_oxygen_name_ : core::chemical::carbohydrates::CarbohydrateInfo
• cyclic_peptide_encountered_for_current_pep_length : protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter::CyclizedReportInfo
• cyclic_peptides_ : protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter::CyclizedReportInfo
• cyclic_permutation_offset_ : protocols::energy_based_clustering::EnergyBasedClusteringOptions
• cyclic_permutations_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• cyclic_symmetry_ : protocols::energy_based_clustering::EnergyBasedClusteringOptions
• cyclic_symmetry_mirroring_ : protocols::energy_based_clustering::EnergyBasedClusteringOptions
• cyclic_symmetry_threshold_ : protocols::energy_based_clustering::EnergyBasedClusteringOptions
• cyclic_symmetry_threshold_specified_ : protocols::energy_based_clustering::EnergyBasedClusteringOptions
• CyclicMover() : protocols::moves::CyclicMover
• cyclization_type() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• cyclization_type_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• CyclizationMover() : protocols::simple_moves::CyclizationMover
• cyclize_res() : core::pose::full_model_info::FullModelInfo
• cyclize_res_ : core::import_pose::FullModelPoseBuilder
• CyclizedPeptideInfo() : protocols::peptide_deriver::CyclizedPeptideInfo
• CyclizedReportInfoCOP : protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter
• CyclizedReportInfoOP : protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter
• CycpepSymmetryFilter() : protocols::cyclic_peptide::CycpepSymmetryFilter
• cys_design_selector() : protocols::fold_from_loops::NubInitioMover