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

- h -

• H : protocols::ligand_docking::ga_ligand_dock::hbDon
• h : protocols::sic_dock::Rose
• h1() : protocols::fldsgn::topology::HelixPairing
• h1_ : protocols::fldsgn::topology::HelixPairing , protocols::sic_dock::SICFast
• H1_t_name_ : protocols::antibody::Ab_TemplateInfo
• H1_t_pose_ : protocols::antibody::Ab_TemplateInfo
• h2() : protocols::fldsgn::topology::HelixPairing
• h2_ : protocols::fldsgn::topology::HelixPairing , protocols::sic_dock::SICFast
• H2_t_name_ : protocols::antibody::Ab_TemplateInfo
• H2_t_pose_ : protocols::antibody::Ab_TemplateInfo
• h2o_hbond_score_1way() : core::scoring::WaterAdductHBondPotential
• H3_base_library : protocols::antibody_legacy::CDRH3Modeler
• H3_base_library_ : protocols::antibody::H3CterInsert , protocols::antibody_legacy::AntibodyModeler
• h3_base_type_enum_to_string() : protocols::antibody::AntibodyEnumManager
• h3_base_type_string_to_enum() : protocols::antibody::AntibodyEnumManager
• h3_base_type_to_enum_ : protocols::antibody::AntibodyEnumManager
• h3_base_type_to_string_ : protocols::antibody::AntibodyEnumManager
• H3_filter_ : protocols::antibody::H3PerturbCCD , protocols::antibody::H3RefineCCD , protocols::antibody_legacy::CDRH3Modeler
• h3_flank_ : protocols::antibody_legacy::CDRH3Modeler
• h3_fraction_ : protocols::antibody::H3PerturbCCD
• h3_loop_csts_hr_ : protocols::antibody::AntibodyModelerProtocol
• h3_loop_csts_lr_ : protocols::antibody::AntibodyModelerProtocol
• h3_no_stem_graft_ : protocols::antibody::GraftCDRLoopsProtocol
• h3_random_cut_ : protocols::antibody_legacy::CDRH3Modeler
• H3_t_name_ : protocols::antibody::Ab_TemplateInfo
• H3_t_pose_ : protocols::antibody::Ab_TemplateInfo
• H3_ter_library_filename_ : protocols::antibody::H3CterInsert
• H3CterInsert() : protocols::antibody::H3CterInsert
• H3PerturbCCD() : protocols::antibody::H3PerturbCCD
• H3RefineCCD() : protocols::antibody::H3RefineCCD
• H5_prime_mode_ : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• h_ : core::scoring::hbonds::SSWeightParameters , core::scoring::saxs::DistanceHistogram
• H_atom_id() : protocols::match::upstream::UpstreamResTypeGeometry
• H_atom_id_ : protocols::match::upstream::UpstreamResTypeGeometry
• H_chain_ : protocols::antibody::AntibodyInfo
• h_deriv : core::scoring::hbonds::HBondDerivs
• h_ind() : core::scoring::hbonds::HBDerivAssigner
• h_ind_ : core::scoring::hbonds::HBDerivAssigner
• H_mult_ : protocols::frag_picker::scores::TalosSSSimilarity
• H_pos() : protocols::match::upstream::ProteinBackboneBuildPoint
• H_pos_ : protocols::match::upstream::ProteinBackboneBuildPoint
• h_type : core::scoring::orbitals::OrbitalsLookup
• HA_atom_id() : protocols::match::upstream::UpstreamResTypeGeometry
• HA_atom_id_ : protocols::match::upstream::UpstreamResTypeGeometry
• HA_pos() : protocols::match::upstream::ProteinBackboneBuildPoint
• HA_pos_ : protocols::match::upstream::ProteinBackboneBuildPoint
• hack_assemble_next_loop_combination() : protocols::enzdes::EnzdesFlexBBProtocol
• hack_fillup_frag_designabilities() : protocols::enzdes::EnzdesFlexibleRegion
• HackAroEnergy() : core::scoring::hackaro::HackAroEnergy
• hacky_parser_init_workaround() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser
• Hairpin() : core::scoring::Hairpin
• hairpin_killing_score() : core::scoring::SecondaryStructurePotential
• hairpin_list_ : core::scoring::Hairpins
• Hairpins() : core::scoring::Hairpins
• hairpins() : core::scoring::SS_Killhairpins_Info
• hairpins_ : core::scoring::SS_Killhairpins_Info
• half_bin_width_root_three_ : protocols::match::Bool3DGrid
• half_voxel_size_ : core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid
• half_width_ : core::scoring::func::LinearPenaltyFunction
• half_width_dom_ : core::pose::rna::RNA_SuiteName
• half_width_sat_ : core::pose::rna::RNA_SuiteName
• halfdimprods_ : protocols::match::Bool3DGrid
• halfdimsizes_ : protocols::match::Bool3DGrid
• halt_on_error_ : protocols::matdes::SchemePlaceMotifsMover
• HamiltonianExchange() : protocols::canonical_sampling::HamiltonianExchange
• hamiltonians_ : protocols::canonical_sampling::HamiltonianExchange
• handedness_score_ : protocols::simple_filters::SheetFilter
• handedness_score_flag_ : core::scoring::SecondaryStructureWeights
• handle_bumped_recent_history_state_for_node() : core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmMinimalistEdge
• handle_function_expression() : core::select::residue_selector::SelectorLogicParser , protocols::optimize_weights::WrappedOptEExpressionCreator , protocols::pack_daemon::EntityFuncExpressionCreator , protocols::pack_daemon::VectorExpressionCreator
• handle_interrupt() : protocols::jd2::archive::MPIArchiveJobDistributor , protocols::jd2::FileSystemJobDistributor , protocols::jd2::JobDistributor , protocols::jd2::MPIFileBufJobDistributor , protocols::jd2::MPIMultiCommJobDistributor , protocols::jd2::MPIWorkPartitionJobDistributor , protocols::jd2::MPIWorkPoolJobDistributor , protocols::jd2::ShuffleFileSystemJobDistributor , protocols::jd2::VectorPoseJobDistributor
• handle_lower_terminus() : protocols::cyclic_peptide::PeptideStubMover
• handle_mover_tag() : protocols::splice::SpliceOut
• handle_repeats_in_append_by_bond() : protocols::cyclic_peptide::PeptideStubMover
• handle_script_file_with_period() : protocols::relax::RelaxScriptManager
• handle_suites_ : protocols::rna::movers::RNAIdealizeMover
• handle_tail_mover_tag() : protocols::splice::SpliceOutAntibody
• handle_termini_and_store_terminal_dihedrals() : protocols::cyclic_peptide::PeptideStubMover
• handle_upper_terminus() : protocols::cyclic_peptide::PeptideStubMover
• handle_variable_expression() : core::select::residue_selector::SelectorLogicParser , protocols::optimize_weights::WrappedOptEExpressionCreator , protocols::pack_daemon::EntityFuncExpressionCreator , protocols::pack_daemon::VectorExpressionCreator
• handshake_stub_sets() : protocols::hotspot_hashing::HotspotStubSet
• hard_crossover() : core::scoring::etable::etrie::TrieCountPairGeneric
• hard_crossover_ : core::scoring::etable::etrie::TrieCountPairGeneric
• hard_scorefxn_ : protocols::ligand_docking::LigandBaseProtocol
• harmonic_ca_cst_std_dev : protocols::simple_moves::ShakeStructureMover
• HarmonicFunc() : core::scoring::func::HarmonicFunc
• Haro_index() : core::chemical::ResidueType , core::conformation::Residue
• Haro_index_ : core::chemical::ResidueType
• Haro_scOrbH : core::scoring::orbitals::OrbitalsLookup
• has() : core::chemical::MutableResidueType , core::chemical::ResidueType , core::chemical::ResidueTypeBase , core::conformation::Residue , core::id::AtomID_Map< T > , core::id::BondID , core::id::NamedAtomID_Map< T > , core::kinematics::AtomTree , core::pack::rotamer_set::RotamerLinks , core::scoring::constraints::ResidueConstraints , core::scoring::elec::CountPairRepMap , core::scoring::lkball::LKBallDatabase , protocols::abinitio::StructureStore , protocols::ligand_docking::ga_ligand_dock::Pharmacophore , protocols::loops::Loops , protocols::noesy_assign::PeakAssignmentResidueMap
• has_algorithm() : protocols::match::upstream::BuildSet
• has_alias() : protocols::denovo_design::components::StructureData
• has_alphas_ : protocols::fold_from_loops::NubInitioMover
• has_another_job() : protocols::rna::setup::RNA_CSA_JobDistributor , protocols::rna::setup::RNA_JobDistributor , protocols::rna::setup::RNA_MonteCarloJobDistributor
• has_another_matrix() : core::scoring::bin_transitions::BinTransitionCalculator
• has_another_pose() : core::import_pose::pose_stream::ExtendedPoseInputStream , core::import_pose::pose_stream::LazySilentFilePoseInputStream , core::import_pose::pose_stream::MetaPoseInputStream , core::import_pose::pose_stream::PDBPoseInputStream , core::import_pose::pose_stream::PoseInputStream , core::import_pose::pose_stream::SilentFilePoseInputStream , protocols::stepwise::modeler::protein::InputStreamWithResidueInfo
• has_antigen_ : protocols::antibody::AntibodyInfo
• has_atom() : core::chemical::AtomTypeSet , protocols::frag_picker::CSTalosIO , protocols::frag_picker::scores::AtomBasedConstraintsScore
• has_atom_id() : core::pose::toolbox::AtomID_Mapper
• has_atom_info() : core::kinematics::Edge
• has_atom_type() : protocols::ligand_docking::ga_ligand_dock::GridScorer
• has_bb_hbond() : core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy
• has_bb_hbond_connection() : core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy
• has_been_initialized_ : protocols::multistage_rosetta_scripts::MRSJobQueen
• has_been_initialized_from_task_ : core::pack::annealer::SmartFixbbSimAnnealer
• has_been_instantiated() : protocols::jd2::JobDistributor
• has_behavior() : core::pack::task::PackerTask , core::pack::task::PackerTask_ , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• has_betas_ : protocols::fold_from_loops::NubInitioMover
• has_bind : protocols::ligand_docking::ProtLigPair_info
• has_binder() : protocols::fold_from_loops::utils::Nub
• has_binder_ : protocols::fold_from_loops::utils::Nub
• has_bulge() : protocols::fldsgn::topology::StrandPairing
• has_C_atom() : protocols::match::upstream::UpstreamResTypeGeometry
• has_CA_atom() : protocols::match::upstream::UpstreamResTypeGeometry
• has_cache() : core::scoring::methods::PBLifetimeCache
• has_cached_data() : protocols::denovo_design::components::StructureDataFactory
• has_CB_atom() : protocols::match::upstream::UpstreamResTypeGeometry
• has_CDR() : protocols::antibody::AntibodyInfo
• has_chainbreak() : core::util::ChainbreakUtil
• has_chainbreaks_to_close() : protocols::topology_broker::TopologyBroker
• has_chemical_shifts() : protocols::frag_picker::VallResidue
• has_child_ : protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD
• has_clash() : core::scoring::nmr::NMRDummySpinlabelConformer
• has_cluster_for_cdr() : protocols::antibody::AntibodyInfo
• has_comment() : core::io::silent::SilentStruct
• has_common_pairing() : core::scoring::dssp::StrandPairing
• has_connected_resonances() : protocols::noesy_assign::Resonance
• has_constraints() : core::scoring::constraints::ConstraintSet , protocols::abinitio::Template , protocols::forge::remodel::LineObject
• has_conventional_residue() : core::pose::full_model_info::FullModelParameters
• has_converged() : protocols::mean_field::MeanField
• has_coordinates() : core::fragment::BBTorsionSRFD
• has_coords_ : core::fragment::BBTorsionSRFD
• has_cst_energies_ : protocols::ligand_docking::ga_ligand_dock::GridScorer
• has_custom_rama_cdf() : core::scoring::Ramachandran
• has_custom_rama_count_table() : core::scoring::Ramachandran
• has_custom_rama_energy_table() : core::scoring::Ramachandran
• has_custom_rama_probability_table() : core::scoring::Ramachandran
• has_custom_variant_types() : core::chemical::ResidueProperties
• has_custom_variant_types_ : core::chemical::ResidueProperties
• has_cut() : core::environment::FoldTreeSketch
• has_cutpoints() : protocols::fold_from_loops::movers::NubInitioLoopClosureMover
• has_cycle() : core::environment::FoldTreeSketch::Node
• has_data() : core::simple_metrics::SimpleMetricStruct , protocols::denovo_design::components::SheetDB , protocols::ligand_docking::ga_ligand_dock::OutputStructureStore
• has_data_int() : protocols::denovo_design::components::StructureData
• has_data_real() : protocols::denovo_design::components::StructureData
• has_data_str() : protocols::denovo_design::components::StructureData
• has_density() : protocols::loop_grower::DensSkeleton
• has_dependencies() : protocols::forge::build::BuildInstruction
• has_design_info_ : protocols::forge::remodel::RemodelData
• has_disallowed_variant() : core::chemical::ResidueTypeFinder
• has_dof() : core::conformation::symmetry::SymDof , core::pose::Pose
• has_dof_constraints() : core::scoring::constraints::ConstraintSet
• has_domain() : core::pose::toolbox::AtomLevelDomainMap
• has_double_percent_signs() : protocols::rosetta_scripts::RosettaScriptsParser
• has_edge() : protocols::denovo_design::components::FoldGraph
• has_energy() : core::io::silent::SilentStruct
• has_energy_method() : core::scoring::ScoringManager
• has_entry() : protocols::frag_picker::CSTalosIO , protocols::frag_picker::PhiPsiTalosIO
• has_evaluator() : protocols::jd2::archive::EvaluatedArchive
• has_exclude_residues_vector() : protocols::scoring::methods::pcs::PCS_Energy_parameters_manager , protocols::scoring::methods::pcsTs1::PCS_Energy_parameters_manager_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_parameters_manager_Ts4
• has_exclude_residues_vector_changed() : protocols::scoring::methods::pcs::PCS_Energy_parameters_manager , protocols::scoring::methods::pcsTs1::PCS_Energy_parameters_manager_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_parameters_manager_Ts4
• has_exocyclic_glycosidic_linkage() : core::conformation::carbohydrates::GlycanTreeSet
• has_exocyclic_linkage() : core::conformation::carbohydrates::GlycanNode
• has_exocyclic_linkage_ : core::conformation::carbohydrates::GlycanNode
• has_exocyclic_linkage_to_child_mainchain() : core::chemical::carbohydrates::CarbohydrateInfo
• has_exocyclic_linkage_to_child_mainchain_ : core::chemical::carbohydrates::CarbohydrateInfo
• has_extra_parameter() : core::chemical::AtomTypeSet
• has_f1_force() : core::scoring::epr_deer::DEERDataCache
• has_f2_force() : core::scoring::epr_deer::DEERDataCache
• has_finished() : protocols::jd2::archive::Batch
• has_finished_ : protocols::jd2::archive::Batch
• has_framework_dependant_cluster() : protocols::antibody::design::MutateFrameworkForCluster
• has_framework_dependant_clusters() : protocols::antibody::design::MutateFrameworkForCluster
• has_free_lower_terminus() : protocols::denovo_design::components::Segment , protocols::denovo_design::components::StructureData
• has_free_upper_terminus() : protocols::denovo_design::components::Segment , protocols::denovo_design::components::StructureData
• has_frequencies() : protocols::denovo_design::task_operations::ConsensusLoopDatabase
• has_frequency() : protocols::denovo_design::task_operations::AAFrequencies , protocols::denovo_design::task_operations::ConsensusLoopDatabase
• has_generated_residue_type() : core::chemical::ResidueTypeSetCache
• has_geometric_connection() : protocols::generalized_kinematic_closure::GeneralizedKIC
• has_glycan_residue() : core::conformation::carbohydrates::GlycanTree
• has_grid() : protocols::qsar::scoring_grid::GridSet
• has_H_atom() : protocols::match::upstream::UpstreamResTypeGeometry
• has_HA_atom() : protocols::match::upstream::UpstreamResTypeGeometry
• has_hbond() : core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy
• has_ideal_geometry() : protocols::minimization_packing::MinimalRotamer
• has_incomplete_connection() : core::conformation::Residue
• has_inherent_position : core::chemical::carbohydrates::SugarModificationsNomenclatureTableRow
• has_interchangeability_group() : core::chemical::ResidueTypeSet
• has_intra_residue_constraints() : core::scoring::constraints::ConstraintSet
• has_job() : protocols::jd2::JobsContainer
• has_job_previously_been_output() : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::JobQueen , protocols::jd3::standard::StandardJobQueen
• has_jump() : core::environment::FoldTreeSketch
• has_jump_access() : core::environment::DofPassport
• has_jump_neighbor() : core::environment::FoldTreeSketch::Node
• has_just_simple_cycles() : core::scoring::loop_graph::LoopGraph
• has_just_simple_cycles_ : core::scoring::loop_graph::LoopGraph
• has_key_ : protocols::frag_picker::VallChunk
• has_label() : protocols::noesy_assign::CrossPeak3D , protocols::noesy_assign::CrossPeak4D , protocols::noesy_assign::CrossPeak , protocols::noesy_assign::CrossPeakInfo , protocols::noesy_assign::PeakAssignment
• has_ligand_ : protocols::forge::remodel::RemodelMover::instruction_flags
• has_low_per_atom_sasa() : protocols::constel::FilterBySASA
• has_lower_connect() : core::conformation::Residue
• has_lower_residue() : protocols::denovo_design::components::Segment
• has_metapatch() : core::chemical::PoseResidueTypeSet , core::chemical::ResidueTypeSet
• has_method_weights() : core::scoring::methods::EnergyMethodOptions
• has_methods() : core::pack::interaction_graph::ResidueArrayAnnealingEvaluator
• has_mirror_symm_ : core::pack::interaction_graph::ResidueArrayAnnealingEvaluator
• has_model() : protocols::abinitio::PairingStatEntry
• has_movable_residues() : protocols::fold_from_loops::movers::NubInitioLoopClosureMover
• has_N_atom() : protocols::match::upstream::UpstreamResTypeGeometry
• has_name() : core::chemical::ResidueTypeSet
• has_name3() : core::chemical::ResidueTypeSet
• has_name_write_locked() : core::chemical::ResidueTypeSet
• has_ncaa : protocols::forge::remodel::LineObject
• has_neighbor() : core::environment::FoldTreeSketch::Node
• has_next() : protocols::legacy_sewing::SegmentGraph
• has_next_level() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• has_node() : core::conformation::carbohydrates::GlycanTree , core::conformation::carbohydrates::GlycanTreeSet
• has_node_corresponding_to_residue() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph
• has_non_residue_pair_constraints() : core::scoring::constraints::ConstraintSet
• has_nonzero_weight() : core::scoring::ScoreFunction
• has_O_atom() : protocols::match::upstream::UpstreamResTypeGeometry
• has_omega() : core::chemical::carbohydrates::LinkageConformerData
• has_open_slaves() : protocols::jd2::SingleFileBuffer
• has_orbital() : core::chemical::ResidueTypeBase
• has_orbital_types() : core::chemical::ResidueTypeBase
• has_orientation_and_pleating() : protocols::jumping::JumpSample
• has_packer_palette() : core::pack::task::TaskFactory
• has_paired_residue() : protocols::fldsgn::topology::StrandPairing
• has_pairing() : core::scoring::dssp::StrandPairing , core::scoring::dssp::StrandPairingSet
• has_pairings() : protocols::abinitio::Templates
• has_parent_remark() : core::io::silent::SilentStruct
• has_passport() : core::conformation::Conformation , protocols::environment::ClientMover , protocols::environment::ProtectedConformation
• has_path() : protocols::motifs::Motif
• has_path_ : protocols::motifs::Motif
• has_peptide_edge() : protocols::denovo_design::components::FoldGraph
• has_peptide_neighbor() : core::environment::FoldTreeSketch::Node
• has_pH_His() : protocols::hbnet::HBNetStapleInterface
• has_physical_cut : protocols::environment::claims::JumpElement
• has_polymer_dependent_groups() : core::chemical::ResidueType
• has_polymer_dependent_groups_ : core::chemical::ResidueType
• has_pore() : core::conformation::membrane::ImplicitLipidInfo
• has_pore_ : core::conformation::membrane::ImplicitLipidInfo
• has_precomputed_move() : protocols::stepwise::modeler::precomputed::PrecomputedLibraryMover
• has_previous() : protocols::legacy_sewing::SegmentGraph
• has_profile() : core::fragment::picking_old::vall::VallResidue , protocols::frag_picker::VallResidue
• has_profile_struct() : protocols::frag_picker::VallResidue
• has_property() : core::chemical::Atom , core::chemical::AtomProperties , core::chemical::ResidueProperties , core::chemical::ResidueTypeBase , core::conformation::Residue , core::scoring::bin_transitions::BinTransitionData
• has_proton() : protocols::noesy_assign::CrossPeak , protocols::noesy_assign::PeakAssignment
• has_pseudobonds() : core::scoring::trie::CPDataCorrespondence
• has_pseudobonds_ : core::scoring::trie::CPDataCorrespondence
• has_range1() : core::conformation::symmetry::SymDof
• has_range1_lower() : core::conformation::symmetry::SymDof
• has_range1_lower_ : core::conformation::symmetry::SymDof
• has_range1_upper() : core::conformation::symmetry::SymDof
• has_range1_upper_ : core::conformation::symmetry::SymDof
• has_range2() : core::conformation::symmetry::SymDof
• has_range2_lower() : core::conformation::symmetry::SymDof
• has_range2_lower_ : core::conformation::symmetry::SymDof
• has_range2_upper() : core::conformation::symmetry::SymDof
• has_range2_upper_ : core::conformation::symmetry::SymDof
• has_reactivities() : core::io::rna::RNA_DataReader
• has_ref_pose() : core::import_pose::atom_tree_diffs::AtomTreeDiff
• has_ref_tag() : core::import_pose::atom_tree_diffs::AtomTreeDiff
• has_reference_pose() : core::pose::Pose
• has_remark() : protocols::motifs::Motif
• has_remark_ : protocols::motifs::Motif
• has_res_type_set() : core::chemical::CacheableResidueTypeSets
• has_residue() : protocols::noesy_assign::ResonanceList
• has_residue_pair_constraints() : core::scoring::constraints::ConstraintSet
• has_residue_selector() : protocols::aa_composition::AddHelixSequenceConstraintsMover
• has_residue_type_set() : core::chemical::ChemicalManager
• has_resnum() : protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSamplerComb
• has_restype() : protocols::match::upstream::BuildSet
• has_restype_with_name3() : core::chemical::ResidueTypeSetCache
• has_rotamer_set_for_residue() : core::pack::rotamer_set::RotamerSets
• has_sc_orbitals() : core::chemical::ResidueType , core::conformation::Residue
• has_score() : protocols::mpi_refinement::MultiObjective
• has_segment() : protocols::backrub::BackrubMover , protocols::denovo_design::components::SegmentPairing , protocols::denovo_design::components::StructureData , protocols::sewing::data_storage::SmartAssembly
• has_segment_group() : protocols::denovo_design::components::StructureData
• has_seq_label() : core::environment::SequenceAnnotation
• has_sequence_claimer() : protocols::topology_broker::TopologyBroker
• has_shadow_atoms() : core::chemical::ResidueType , core::conformation::Residue
• has_shared_silent_data() : core::io::silent::SilentFileData
• has_sibling() : core::scoring::trie::TrieNode< AT, CPDATA >
• has_silent_in() : protocols::jd2::archive::Batch
• has_silent_in_ : protocols::jd2::archive::Batch
• has_silent_struct_type() : core::io::silent::SilentStructFactory
• has_slash_at_end() : protocols::rosetta_scripts::RosettaScriptsParser
• has_stored_constraints() : protocols::constraint_generator::ConstraintsManager
• has_subset() : core::select::residue_selector::CachedResidueSubset
• has_tag() : core::import_pose::atom_tree_diffs::AtomTreeDiff , core::io::silent::SilentFileData
• has_task() : protocols::task_operations::STMStoredTask
• has_template() : core::import_pose::libraries::RNA_JumpLibrary , protocols::abinitio::Templates
• has_template_pose() : protocols::denovo_design::components::Segment
• has_tree() : core::conformation::carbohydrates::GlycanTreeSet
• has_type() : core::chemical::rotamers::RotamerLibrarySpecificationFactory , core::pack::palette::CustomBaseTypePackerPalette , core::pack::palette::PackerPaletteFactory , core::pack::rotamers::SingleResidueRotamerLibraryFactory , core::pack::task::operation::ResFilterFactory , core::pack::task::operation::ResLvlTaskOperationFactory , core::pack::task::operation::TaskOperationFactory , core::select::jump_selector::JumpSelectorFactory , core::select::residue_selector::ResidueSelectorFactory , core::simple_metrics::SimpleMetricFactory , protocols::constraint_generator::ConstraintGeneratorFactory , protocols::loops::loops_definers::LoopsDefinerFactory , protocols::multistage_rosetta_scripts::cluster::ClusterMetricFactory
• has_upper_connect() : core::conformation::Residue
• has_upper_residue() : protocols::denovo_design::components::Segment
• has_upstream_only_geomcsts() : protocols::match::Matcher
• has_valid_moves() : protocols::hybridization::ChunkTrialMover
• has_valid_moves_ : protocols::hybridization::ChunkTrialMover
• has_value() : core::import_pose::libraries::BasePairStepLibrary , protocols::mean_field::jagged_array< T, A >
• has_variant_type() : core::chemical::ResidueTypeBase , core::conformation::Residue
• has_vec_inconsistency() : protocols::antibody::AntibodyDatabaseManager
• has_waters() : core::scoring::lkball::LKB_ResidueInfo
• has_waters_ : core::scoring::lkball::LKB_ResidueInfo
• has_zero_weight() : core::scoring::ScoreFunction
• hASA_energy() : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G >
• hASA_patch_energy() : core::pack::interaction_graph::SurfacePotential
• hASA_to_score_ : core::pack::interaction_graph::SurfacePotential
• hash() : protocols::environment::AutoCutData , protocols::genetic_algorithm::EntityElement , protocols::multistate_design::PosType
• Hash : protocols::sic_dock::Rose
• hash_ : protocols::environment::AutoCutData , protocols::legacy_sewing::SewSegment , protocols::loophash::LoopHashLibrary , protocols::loophash::LoopHashMap , protocols::match::HitNeighborFinder , protocols::match::MatchCounter , protocols::match::MatchOutputTracker , protocols::match::OccupiedSpaceHash , protocols::mean_field::ResHashMap
• hash_between_termini : protocols::sewing::hashing::HasherSettings
• hash_edge_pool_ : protocols::legacy_sewing::SewGraph
• hash_file_names_ : protocols::ligand_docking::WriteLigandMolFile
• hash_fingerprint() : protocols::qsar::scoring_grid::AtrGrid , protocols::qsar::scoring_grid::ChargeGrid , protocols::qsar::scoring_grid::ClassicGrid , 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
• hash_grid_ : protocols::ligand_docking::ga_ligand_dock::GridScorer
• hash_hits() : protocols::match::HitNeighborFinder
• hash_id : protocols::indexed_structure_store::FragmentStore
• hash_index() : protocols::loophash::LoopHashMap
• hash_map() : protocols::legacy_sewing::Hasher
• hash_map_ : protocols::legacy_sewing::Hasher , protocols::sewing::hashing::Hasher
• hash_model() : protocols::legacy_sewing::Hasher
• hash_pdb_model() : protocols::legacy_sewing::LegacyAppendAssemblyMover
• hash_pose1_ : protocols::sic_dock::CBScore , protocols::sic_dock::scores::MotifHashRigidScore
• hash_recent_history() : core::pack::annealer::FASTERAnnealer
• hash_segments() : protocols::sewing::hashing::Hasher
• hash_size_ : core::pack::annealer::FASTERAnnealer
• hash_sizes() : protocols::loophash::LoopHashLibrary
• hash_sizes_ : protocols::loophash::LoopHashLibrary
• hash_starting_positions_ : protocols::ligand_docking::StartFrom
• hash_subgrid_ : protocols::ligand_docking::ga_ligand_dock::GridScorer
• hash_to_labal() : core::scoring::motif::ResPairMotifMetaBinner
• hash_value() : core::kinematics::FoldTree , core::scoring::dssp::StrandPairing
• HashCOP : protocols::sic_dock::Rose
• hashed_ : protocols::sewing::movers::AssemblyMover
• HashEdge() : protocols::legacy_sewing::HashEdge
• HashedSmartAssembly() : protocols::sewing::data_storage::HashedSmartAssembly
• hasher : core::kinematics::FoldTree , core::scoring::motif::MotifHash , protocols::abinitio::IterativeBase
• Hasher() : protocols::legacy_sewing::Hasher , protocols::sewing::hashing::Hasher
• hasher_ : core::scoring::motif::MotifHash , core::scoring::motif::XformScore , core::scoring::motif::XfragSet
• hasher_settings() : protocols::sewing::hashing::AlignmentGenerator , protocols::sewing::hashing::BasisMapGenerator , protocols::sewing::hashing::EdgeMapGenerator , protocols::sewing::hashing::Hasher
• hasher_settings_ : protocols::sewing::hashing::AlignmentGenerator , protocols::sewing::hashing::BasisMapGenerator , protocols::sewing::hashing::EdgeMapGenerator , protocols::sewing::hashing::Hasher
• HasherSettings() : protocols::sewing::hashing::HasherSettings
• hashin_fname_ : protocols::protein_interface_design::movers::HotspotHasherMover
• HashOP : protocols::sic_dock::Rose
• hashout_fname_ : protocols::protein_interface_design::movers::HotspotHasherMover
• HashResult() : protocols::legacy_sewing::HashResult
• hashsize_ : protocols::ligand_docking::ga_ligand_dock::GALigandDock
• hasInsertion : protocols::forge::remodel::RemodelWorkingSet
• hasNext() : protocols::viewer::triangleIterator
• hasnt_excluded() : protocols::constel::ExcludedFilter
• have_contributed_deltaE_following_perturbation_ : core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::FASTERNode
• have_cst_ : core::scoring::methods::CustomAtomPairEnergy
• have_edges_copy_alternate_to_current() : protocols::flexpack::interaction_graph::FlexbbNode
• have_edges_copy_alternate_to_current_following_flexbb_accept() : protocols::flexpack::interaction_graph::FlexbbNode
• have_motif_set_named() : core::scoring::motif::MotifHashManager
• have_motifs() : core::scoring::motif::MotifHashManager
• have_mutated_residue() : protocols::simple_moves::sidechain_moves::SidechainMoverBase
• have_native_pose_ : protocols::loop_modeling::utilities::TrajectoryLogger
• have_not_committed_last_substitution_ : core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistInteractionGraph
• have_params() : core::scoring::packing::HolesParams , core::scoring::packing::HolesParamsRes
• have_prepared_for_simA_ : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G >
• have_prepared_once_for_FASTER_ : core::pack::interaction_graph::FASTERNode
• have_relaxed_since_neighbors_perturbation_ : core::pack::interaction_graph::FASTERNode
• havesurf() : core::scoring::packing::PoseBalls
• hb_acc_chem_type() : core::scoring::hbonds::hbtrie::HBAtom
• hb_atom() : protocols::constraint_generator::HydrogenBondingAtom
• hb_bb() : core::scoring::motif::ResPairMotif
• hb_bb_ : core::scoring::motif::ResPairMotif
• hb_bb_sc() : core::scoring::motif::ResPairMotif
• hb_bb_sc_ : core::scoring::motif::ResPairMotif
• hb_chem_type() : core::scoring::hbonds::hbtrie::HBAtom
• hb_chem_type_ : core::scoring::hbonds::hbtrie::HBAtom
• hb_database : protocols::constel::HBondCommon
• hb_database_ : core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy , core::scoring::geometric_solvation::GeometricSolEnergyEvaluator , core::scoring::geometric_solvation::WaterWeightGridSet , core::scoring::WaterAdductHBondPotential , protocols::dna::RotamerDNAHBondFilter , protocols::hbnet::HBNet , protocols::ligand_docking::ga_ligand_dock::GridScorer , protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator
• HB_DHO_AngleList : protocols::sparta::PDB
• hb_don_chem_type() : core::scoring::hbonds::hbtrie::HBAtom
• hb_e_cutoff_ : protocols::simple_filters::SimpleHbondsToAtomFilter
• hb_eval_tuples_ : protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker
• hb_fade_energy : core::init::pre_talaris_2013_behavior_settings
• hb_filter : protocols::flexpep_docking::FlexPepDockingFlags
• HB_HOA_AngleList : protocols::sparta::PDB
• hb_sc() : core::scoring::motif::ResPairMotif
• hb_sc_ : core::scoring::motif::ResPairMotif
• hb_sp2_chipen : core::init::pre_talaris_2013_behavior_settings
• hb_sp2_outer_width : core::init::pre_talaris_2013_behavior_settings
• hbacceptors_ : protocols::ligand_docking::ga_ligand_dock::GridScorer
• HbaGrid() : protocols::qsar::scoring_grid::HbaGrid
• HBAtom() : core::scoring::hbonds::hbtrie::HBAtom
• HBCPData() : core::scoring::hbonds::hbtrie::HBCPData
• HBDerivAssigner() : core::scoring::hbonds::HBDerivAssigner
• HbdGrid() : protocols::qsar::scoring_grid::HbdGrid
• HBDistList : protocols::sparta::PDB
• hbdonors_ : protocols::ligand_docking::ga_ligand_dock::GridScorer
• HBEnergyList : protocols::sparta::PDB
• HBEvalTuple() : core::scoring::hbonds::HBEvalTuple
• HBFadeInterval_from_name() : core::scoring::hbonds::HBondDatabase
• HBFadeInterval_lookup_ : core::scoring::hbonds::HBondDatabase
• HBFadeInterval_lookup_by_name_ : core::scoring::hbonds::HBondDatabase
• HBNet() : protocols::hbnet::HBNet
• hbnet_bonus_function_ramping() : core::scoring::methods::EnergyMethodOptions
• hbnet_bonus_ramping_function_ : core::scoring::methods::EnergyMethodOptions
• hbnet_energy_ramping_enum_from_string() : core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy
• hbnet_energy_ramping_string_from_enum() : core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy
• hbnet_max_network_size() : core::scoring::methods::EnergyMethodOptions
• hbnet_max_network_size_ : core::scoring::methods::EnergyMethodOptions
• HBNetEnergy() : core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy
• HBNetScore() : protocols::hbnet::HBNetScore
• HBNetStapleInterface() : protocols::hbnet::HBNetStapleInterface
• hbond() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyEdge
• HBond() : core::scoring::hbonds::HBond
• hbond() : core::scoring::hbonds::HBondSet
• hbond_acc_npd_weight() : core::scoring::hbonds::HBondSet
• hbond_acceptor_limit_ : protocols::ligand_docking::HBondAcceptorFilter
• hbond_bb_pair_score_ : core::scoring::dssp::Dssp
• hbond_bonus_opt_ : core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty
• hbond_cop() : core::scoring::hbonds::HBondSet
• hbond_cutoff() : protocols::cyclic_peptide::PeptideInternalHbondsFilter
• hbond_cutoff_ : protocols::cyclic_peptide::PeptideInternalHbondsFilter
• hbond_database() : core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > , core::pack::interaction_graph::NPDHBSimpleInteractionGraph
• hbond_database_ : core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > , core::pack::interaction_graph::NPDHBSimpleInteractionGraph , protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker
• hbond_default_ : protocols::hbnet::HBNet
• hbond_derivs_1way() : core::scoring::hbonds::HBondEnergy
• hbond_disallow_ : protocols::hbnet::HBNet
• hbond_disallow_default_ : protocols::hbnet::HBNet
• hbond_don_npd_weight() : core::scoring::hbonds::HBondSet
• hbond_donor_limit_ : protocols::ligand_docking::HBondDonorFilter
• hbond_E_fraction : protocols::analysis::InterfaceData
• hbond_energy() : protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator
• hbond_energy_comparer() : core::scoring::hbonds::HBond
• hbond_energy_cutoff() : protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter , protocols::cyclic_peptide::PeptideInternalHbondsFilter , protocols::cyclic_peptide::PeptideInternalHbondsMetric , protocols::hbnet::UnsatSelector
• hbond_energy_cutoff_ : protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter , protocols::cyclic_peptide::PeptideInternalHbondsMetric , protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication , protocols::hbnet::UnsatSelector , protocols::residue_selectors::HBondSelector
• hbond_energy_shift() : core::scoring::hbonds::HBondOptions
• hbond_energy_shift_ : core::scoring::hbonds::HBondOptions
• hbond_energy_threshold() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphOptions
• hbond_energy_threshold_ : core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty , core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphOptions , protocols::protein_interface_design::movers::DesignMinimizeHbonds
• hbond_graph_ : core::pack::hbonds::HBondGraphInitializerIG , protocols::hbnet::HBNet
• hbond_measure_sp3acc_BAH_from_hvy : core::init::pre_talaris_2013_behavior_settings
• hbond_metric() : protocols::cyclic_peptide::PeptideInternalHbondsFilter
• hbond_metric_ : protocols::cyclic_peptide::PeptideInternalHbondsFilter
• hbond_options() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNodeData , core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > , core::pack::interaction_graph::NPDHBSimpleInteractionGraph , core::scoring::hbonds::HBondSet , core::scoring::methods::EnergyMethodOptions
• hbond_options_ : core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty , core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph , core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNodeData , core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > , core::pack::interaction_graph::NPDHBSimpleInteractionGraph , core::scoring::methods::EnergyMethodOptions , protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker
• hbond_params : core::init::pre_talaris_2013_behavior_settings
• hbond_set() : core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy , protocols::hbnet::HBondNetStruct
• hbond_set_ : core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy , core::scoring::rna::data::RNA_DMS_Potential , protocols::ligand_docking::rdf::RDFHbondFunction , protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator
• hbond_threshold_ : core::pack::hbonds::HBondGraphInitializerIG , protocols::hbnet::HBNetScore
• hbond_vec : protocols::hbnet::HBondNetStruct
• hbond_weight() : core::scoring::hbonds::NPDHBondSet
• hbond_wtd_ : protocols::ligand_docking::ga_ligand_dock::ReweightableRepEnergy
• HBondAcceptorFilter() : protocols::ligand_docking::HBondAcceptorFilter
• HBondAtomMap : core::scoring::hbonds::HBondSet
• HBondBonusOptions() : core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::HBondBonusOptions
• HBondDatabase() : core::scoring::hbonds::HBondDatabase
• HBondDonorFilter() : protocols::ligand_docking::HBondDonorFilter
• HBondEdge() : core::scoring::hbonds::graph::HBondEdge
• HBondEnergy() : core::scoring::hbonds::HBondEnergy
• HBondFeatures() : protocols::features::HBondFeatures
• HBondGraph() : core::scoring::hbonds::graph::HBondGraph
• HBondGraphInitializerIG() : core::pack::hbonds::HBondGraphInitializerIG
• HBondInfo() : core::scoring::hbonds::graph::HBondInfo
• hbonding_to_res() : core::pack::interaction_graph::NPDHBSimpleInteractionGraph
• hbonding_to_res_ : core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > , core::pack::interaction_graph::NPDHBSimpleInteractionGraph
• hbonding_to_res_vector() : core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >
• HBondMap : protocols::sparta::PDB
• HbondMetric() : core::simple_metrics::per_residue_metrics::HbondMetric
• HBondNetStruct() : protocols::hbnet::HBondNetStruct
• HBondNode() : core::scoring::hbonds::graph::HBondNode
• HBondOptions() : core::scoring::hbonds::HBondOptions
• hbondoptions_ : core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy , core::scoring::geometric_solvation::WaterWeightGridSet , core::scoring::WaterAdductHBondPotential , protocols::dna::RotamerDNAHBondFilter
• HBondParameterFeatures() : protocols::features::HBondParameterFeatures
• HBondResidueMinData() : core::scoring::hbonds::HBondResidueMinData
• HBondResPairMinData() : core::scoring::hbonds::HBondResPairMinData
• HBondResStruct() : protocols::hbnet::HBondResStruct
• hbonds() : core::scoring::hbonds::graph::HBondEdge , core::scoring::hbonds::HBondSet , protocols::cyclic_peptide_predict::HierarchicalHybridJD_JobResultsSummary
• hbonds_ : core::scoring::hbonds::graph::HBondEdge , core::scoring::hbonds::HBondSet , protocols::cyclic_peptide_predict::HierarchicalHybridJD_JobResultsSummary
• hbonds_energy_cutoff_ : protocols::simple_filters::InterfaceHbondsFilter
• hbonds_graph_ : core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy
• hbonds_graph_last_accepted_ : core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy
• hbonds_list() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyEdgeData
• hbonds_list_ : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyEdgeData
• hbonds_num_threshold_ : protocols::simple_filters::InterfaceHbondsFilter
• hbonds_queue_ : core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > , core::pack::interaction_graph::NPDHBSimpleInteractionGraph
• HBondSelector() : protocols::residue_selectors::HBondSelector
• HBondSet() : core::scoring::hbonds::HBondSet
• HbondsToAtomFilter() : protocols::protein_interface_design::filters::HbondsToAtomFilter
• HbondsToResidueFilter() : protocols::protein_interface_design::filters::HbondsToResidueFilter
• HBondsTrieVsTrieCachedDataContainer() : core::scoring::hbonds::hbtrie::HBondsTrieVsTrieCachedDataContainer
• HBP_FinalFullatomRefinementMoveGenerator() : protocols::helical_bundle_predict::HBP_FinalFullatomRefinementMoveGenerator
• HBP_HelixCoilMoveGenerator() : protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator
• HBP_MoveGenerator() : protocols::helical_bundle_predict::HBP_MoveGenerator
• HBP_SigmoidalTemperatureScheduleGenerator() : protocols::helical_bundle_predict::HBP_SigmoidalTemperatureScheduleGenerator
• HBP_TemperatureScheduleGenerator() : protocols::helical_bundle_predict::HBP_TemperatureScheduleGenerator
• HBPHelix() : protocols::helical_bundle_predict::HBPHelix
• HBPHelixAssignments() : protocols::helical_bundle_predict::HBPHelixAssignments
• HBPHelixParameters() : protocols::helical_bundle_predict::HBPHelixParameters
• HBPoly1D_from_name() : core::scoring::hbonds::HBondDatabase
• HBPoly1D_lookup_ : core::scoring::hbonds::HBondDatabase
• HBPoly1D_lookup_by_name_ : core::scoring::hbonds::HBondDatabase
• hbs_post_pos_ : protocols::simple_moves::a3b_hbs::A3BHbsPatcher , protocols::simple_moves::hbs::HbsPatcher
• hbs_pre_pos_ : protocols::simple_moves::a3b_hbs::A3BHbsPatcher , protocols::simple_moves::hbs::HbsPatcher
• HbsPatcher() : protocols::simple_moves::hbs::HbsPatcher
• hConvergenceCheck() : protocols::abinitio::hConvergenceCheck , protocols::hybridization::hConvergenceCheck
• hcut_ : protocols::hybridization::DDomainParse , protocols::hybridization::HybridizeProtocol
• HDX_data_defined_ : core::scoring::methods::D2H_SA_Energy
• he : protocols::sic_dock::XfoxmScore
• header() : core::io::StructFileRep , protocols::wum::WorkUnitBase
• header_ : core::io::StructFileRep , protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter
• header_file : update_ResidueType_enum_files.EnumInfo
• header_information() : core::pose::PDBInfo
• header_information_ : core::pose::PDBInfo
• HeaderInformation() : core::io::HeaderInformation
• headgroup_type() : core::conformation::membrane::ImplicitLipidInfo
• headgroup_type_ : core::conformation::membrane::ImplicitLipidInfo
• heat_after_cycles() : protocols::moves::MonteCarlo
• heat_after_cycles_ : protocols::moves::MonteCarlo
• heavy_atom_limit_ : protocols::ligand_docking::HeavyAtomFilter
• heavy_chain : protocols::task_operations::RestrictToCDRH3Loop
• heavy_coords_ : core::conformation::UltraLightResidue
• heavy_coords_vector() : core::conformation::UltraLightResidue
• heavyatom_has_polar_hydrogens() : core::chemical::ResidueType , core::conformation::Residue
• heavyatom_has_polar_hydrogens_ : core::chemical::ResidueType
• heavyatom_heavyatom_energy() : core::scoring::elec::electrie::ElecTrieEvaluator , core::scoring::etable::AnalyticEtableEvaluator , core::scoring::etable::TableLookupEvaluator , core::scoring::hbonds::HBondEnergy , core::scoring::lkball::lkbtrie::LKBTrieEvaluator , core::scoring::methods::MMLJEnergyInter , core::scoring::vdwaals::VDWTrieEvaluator
• heavyatom_hydrogenatom_energy() : core::scoring::elec::electrie::ElecTrieEvaluator , core::scoring::etable::AnalyticEtableEvaluator , core::scoring::etable::TableLookupEvaluator , core::scoring::hbonds::HBondEnergy , core::scoring::lkball::lkbtrie::LKBTrieEvaluator , core::scoring::methods::MMLJEnergyInter , core::scoring::vdwaals::VDWTrieEvaluator
• heavyatom_index() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup
• heavyatom_index_ : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup
• heavyatom_is_an_acceptor() : core::chemical::ResidueType , core::conformation::Residue
• HeavyAtomFilter() : core::chemical::HeavyAtomFilter , protocols::ligand_docking::HeavyAtomFilter
• HeavyAtomNormalization() : protocols::qsar::scoring_grid::HeavyAtomNormalization
• heavyAtoms_end() : core::conformation::Residue
• HeavyAtomWithHydrogensFilter() : core::chemical::HeavyAtomWithHydrogensFilter
• HeavyAtomWithPolarHydrogensFilter() : core::chemical::HeavyAtomWithPolarHydrogensFilter
• hedge_archive_ : protocols::abinitio::IterativeBase
• HedgeArchive() : protocols::abinitio::HedgeArchive
• height : core::scoring::sc::_PROBE
• helical_sigOffAxisR : protocols::rbsegment_relax::RBSegmentRelax
• helical_sigOffAxisT : protocols::rbsegment_relax::RBSegmentRelax
• helical_sigR : protocols::rbsegment_relax::RBSegmentRelax
• helical_sigT : protocols::rbsegment_relax::RBSegmentRelax
• helical_substruct_res() : core::import_pose::options::RNA_FragmentMonteCarloOptions
• helical_substruct_res_ : core::import_pose::options::RNA_FragmentMonteCarloOptions
• helical_substructs() : core::import_pose::options::RNA_FragmentMonteCarloOptions
• helical_substructs_ : core::import_pose::options::RNA_FragmentMonteCarloOptions , core::import_pose::RNA_DeNovoSetup , protocols::rna::denovo::movers::RNA_DeNovoProtocolMover
• HelicalBundlePredictApplication() : protocols::helical_bundle_predict::HelicalBundlePredictApplication
• HelicalBundlePredictApplicationOptions() : protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions
• HelicalFragment() : protocols::features::helixAssembly::HelicalFragment
• HelicalGaussianMover() : protocols::rbsegment_relax::HelicalGaussianMover
• Helices() : core::scoring::Helices
• helices() : core::scoring::SS_Info , protocols::fldsgn::topology::SS_Info2
• helices_ : core::scoring::SS_Info , protocols::fldsgn::topology::SS_Info2 , protocols::helical_bundle_predict::HBPHelixAssignments , protocols::rbsegment_relax::IdealizeHelicesMover
• HELIX : protocols::denovo_design::components::SegmentCounts , protocols::denovo_design::components::SegmentPairing
• helix() : protocols::fldsgn::topology::BetaAlphaBetaMotif
• Helix() : protocols::fldsgn::topology::Helix
• helix() : protocols::fldsgn::topology::HSSTriplet , protocols::fldsgn::topology::SS_Info2 , protocols::fldsgn::topology::TripletID , protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle
• helix2hss_ : protocols::fldsgn::topology::HSSTripletSet
• helix_ : protocols::fldsgn::topology::BetaAlphaBetaMotif , protocols::fldsgn::topology::HSSTriplet , protocols::nonlocal::HelixRotate
• helix_assignment_file() : protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions
• helix_assignment_file_ : protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions
• helix_assignment_file_contents() : protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions
• helix_assignment_file_contents_ : protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions
• helix_boundaries_ : protocols::hbnet::HBNetStapleInterface
• helix_cap_dist_cutoff_ : protocols::features::helixAssembly::HelixBundleFeatures
• helix_cop() : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle
• helix_cycle() : protocols::fldsgn::topology::BetaAlphaBetaMotif
• helix_cycle_ : protocols::fldsgn::topology::BetaAlphaBetaMotif
• helix_cycle_as_string() : protocols::fldsgn::topology::BetaAlphaBetaMotif
• helix_end() : core::scoring::SecondaryStructurePotential , protocols::fldsgn::potentials::sspot::HSPairPotential
• helix_end_ : protocols::fldsgn::filters::HelixKinkFilter , protocols::membrane::benchmark::MakeCanonicalHelix
• helix_ends_ : protocols::rna::denovo::movers::RNA_HelixMover
• helix_ends_final_ : protocols::rna::denovo::movers::RNA_HelixMover
• helix_fraction() : core::fragment::SecondaryStructure
• helix_from_seqpos() : protocols::helical_bundle_predict::HBPHelixAssignments
• helix_id() : core::scoring::MembraneTopology , protocols::fldsgn::filters::HelixBendFilter , protocols::fldsgn::filters::StrandHelixGeometryFilter , protocols::fldsgn::topology::SS_Info2
• helix_id_ : core::scoring::MembraneTopology , protocols::fldsgn::filters::HelixBendFilter , protocols::fldsgn::filters::StrandHelixGeometryFilter , protocols::fldsgn::topology::SS_Info2
• helix_length() : protocols::helical_bundle::MakeBundleHelix
• helix_length_ : protocols::helical_bundle::MakeBundleHelix
• helix_name : core::io::HELIXInformation
• helix_not_defined() : protocols::helical_bundle::PerturbBundle
• helix_num_1_ : protocols::simple_filters::HelixHelixAngleFilter
• helix_num_2_ : protocols::simple_filters::HelixHelixAngleFilter
• helix_pairing() : protocols::fldsgn::topology::HelixPairingSet
• helix_pairings() : protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::topology::HelixPairingSet , protocols::parser::BluePrint
• helix_pairings_ : protocols::abinitio::TemplateJumpSetup , protocols::fldsgn::topology::HelixPairingSet , protocols::parser::BluePrint
• helix_regions_ : protocols::rna::denovo::movers::RNA_HelixMover
• helix_regions_jumps_ : protocols::rna::denovo::movers::RNA_HelixMover
• helix_regions_jumps_final_ : protocols::rna::denovo::movers::RNA_HelixMover
• helix_regions_with_jumps_and_ends_ : protocols::rna::denovo::movers::RNA_HelixMover
• HELIX_SHEET : protocols::denovo_design::components::SegmentPairing
• helix_start_ : protocols::fldsgn::filters::HelixKinkFilter , protocols::membrane::benchmark::MakeCanonicalHelix
• helix_start_positions_ : protocols::helix_capper::HelixNCapperMover
• helix_types_match() : protocols::helical_bundle_predict::HBPHelixAssignments
• HelixArchitect() : protocols::denovo_design::architects::HelixArchitect , protocols::denovo_design::components::HelixPerturber
• HelixArchitectCOP : protocols::denovo_design::components::HelixPerturber
• HelixBendFilter() : protocols::fldsgn::filters::HelixBendFilter
• HelixBundleFeatures() : protocols::features::helixAssembly::HelixBundleFeatures
• HelixCapFeatures() : protocols::features::HelixCapFeatures
• helixClass : core::io::HELIXInformation
• HelixFromSequence() : protocols::membrane::HelixFromSequence
• HelixHelixAngleFilter() : protocols::simple_filters::HelixHelixAngleFilter
• helixID : core::io::HELIXInformation
• HELIXInformations() : core::io::StructFileRep
• HELIXInformations_ : core::io::StructFileRep
• helixjump_pick_list_ : protocols::abinitio::Templates
• helixjump_picks() : protocols::abinitio::Templates
• HelixKinkFilter() : protocols::fldsgn::filters::HelixKinkFilter
• HelixMoveSet_ : protocols::rbsegment_relax::RBSegmentRelax
• HelixNCapperMover() : protocols::helix_capper::HelixNCapperMover
• HelixPairing() : protocols::denovo_design::components::HelixPairing , protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential , protocols::fldsgn::topology::HelixPairing
• HelixPairingFilter() : protocols::fldsgn::filters::HelixPairingFilter
• HelixPairings : protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential
• HelixPairingSet : protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential , protocols::fldsgn::topology::HelixPairingSet
• HelixPairingSetOP : protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential , protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy
• HelixPerturber() : protocols::denovo_design::components::HelixPerturber
• HelixRotate() : protocols::nonlocal::HelixRotate
• HelixSheetPairing() : protocols::denovo_design::components::HelixSheetPairing
• help_ : protocols::forge::remodel::RemodelMover::instruction_flags
• helper() : core::scoring::constraints::AngleConstraint , core::scoring::constraints::DihedralConstraint
• helper_adds_linker_residue() : protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper , protocols::cyclic_peptide::crosslinker::Metal_HelperBase , protocols::cyclic_peptide::crosslinker::TBMB_Helper , protocols::cyclic_peptide::crosslinker::TMA_Helper
• hetatm_prot_cst_weight_ : protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol
• hetatm_self_cst_weight_ : protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol
• hetero_atom_line() : core::scoring::packstat::CavityBall
• heterogen_formulae() : core::io::StructFileRep
• heterogen_formulae_ : core::io::StructFileRep
• heterogen_names() : core::io::StructFileRep
• heterogen_names_ : core::io::StructFileRep
• heterogen_synonyms() : core::io::StructFileRep
• heterogen_synonyms_ : core::io::StructFileRep
• hfr_ : protocols::antibody_legacy::Antibody
• Hfr_t_name_ : protocols::antibody::Ab_TemplateInfo
• hh : protocols::sic_dock::XfoxmScore
• hh_align_angle_ : protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential
• hh_align_angle_sigma2_ : protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential
• hh_align_angle_wts_ : protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential
• HH_cutoff_ : core::scoring::NeighborList
• HH_cutoff_wide_ : core::scoring::NeighborList
• HH_helix_end : core::scoring::Helices
• hh_pair_ : protocols::fldsgn::potentials::SetSecStructEnergies
• HH_resnum : core::scoring::Helices
• hh_scores_ : protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential , protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential
• hh_weight_ : protocols::fldsgn::potentials::SetSecStructEnergies
• hhpot_ : protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy
• HI_AMBIG : protocols::noesy_assign::CrossPeak
• HI_NEAR_UNAMBIG : protocols::noesy_assign::CrossPeak
• hi_poly_ : core::scoring::etable::coulomb::Coulomb
• hi_poly_end2_ : core::scoring::etable::coulomb::Coulomb
• hi_poly_end_ : core::scoring::etable::coulomb::Coulomb
• hi_poly_start2_ : core::scoring::etable::coulomb::Coulomb
• hi_poly_start_ : core::scoring::etable::coulomb::Coulomb
• HI_UNAMBIG : protocols::noesy_assign::CrossPeak
• HierarchicalHybridJD_JobResultsSummary() : protocols::cyclic_peptide_predict::HierarchicalHybridJD_JobResultsSummary
• HierarchicalHybridJD_PNearToArbitraryStateSummary() : protocols::cyclic_peptide_predict::HierarchicalHybridJD_PNearToArbitraryStateSummary
• HierarchicalHybridJD_ResultsSummaryBase() : protocols::cyclic_peptide_predict::HierarchicalHybridJD_ResultsSummaryBase
• HierarchicalHybridJD_RMSDToBestSummary() : protocols::cyclic_peptide_predict::HierarchicalHybridJD_RMSDToBestSummary
• HierarchicalHybridJD_SASASummary() : protocols::cyclic_peptide_predict::HierarchicalHybridJD_SASASummary
• HierarchicalLevel() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• high : protocols::cryst::CheshireCell , protocols::make_rot_lib::TorsionRange
• high_ : core::scoring::func::SmoothStepFunc
• high_color_ : protocols::qsar::RenderGridsToKinemage
• high_cst_ : protocols::antibody::AntibodyModelerProtocol , protocols::antibody::H3RefineCCD , protocols::antibody_legacy::CDRH3Modeler
• high_entropy_rms_cutoff_ : protocols::optimize_weights::PNatStructureOptEData
• high_hbond_weight_multiplier_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• high_mem_mode_ : protocols::antibody::AntibodyDatabaseManager
• high_move_temp_ : protocols::antibody::H3RefineCCD
• high_res() : protocols::floppy_tail::FloppyTailMover
• high_res_angstroms_ : protocols::ligand_docking::LigandArea
• high_res_degrees_ : protocols::ligand_docking::LigandArea
• high_res_kink_constraint() : protocols::antibody::snugdock::SnugDock , protocols::antibody::snugdock::SnugDockProtocol
• high_res_kink_constraint_ : protocols::antibody::snugdock::SnugDock , protocols::antibody::snugdock::SnugDockProtocol
• high_resolution_step_ : protocols::antibody::snugdock::SnugDock
• high_temp() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• high_temp_ : core::pack::task::PackerTask_ , protocols::task_operations::ModifyAnnealer
• highAddRes_ : protocols::pose_length_moves::InsertResMover
• higher_d77_pert_mode_ : protocols::ub_e2c::ubi_e2c_modeler
• higher_numbered_node_symmetry_copy_index() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbond
• higher_numbered_node_symmetry_copy_index_ : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbond
• highest_job_index() : protocols::jd2::JobsContainer
• highest_job_index_ : protocols::jd2::JobsContainer
• highest_probability() : protocols::frag_picker::quota::ABEGO_SS_Config
• highest_tmpl_resnum_ : protocols::hybridization::ChunkTrialMover
• highres_ : protocols::docking::membrane::MPDockingMover
• highres_conformer_filter_type_ : core::scoring::nmr::NMRSpinlabel
• highres_filter_ : protocols::docking::DockingProtocol
• highres_reference_energies_ : protocols::docking::DockingEnsemble
• highres_reference_energy() : protocols::docking::DockingEnsemble
• highres_scorefxn_ : protocols::antibody::H3RefineCCD , protocols::antibody_legacy::CDRH3Modeler , protocols::antibody_legacy::LoopRlxMover , protocols::docking::membrane::MPDockingMover , protocols::seeded_abinitio::SegmentHybridizer
• HighResDocker() : protocols::ligand_docking::HighResDocker
• HighResEnsemble() : protocols::ligand_docking::HighResEnsemble
• hightemp : core::pack::annealer::SimAnnealerBase
• hightemp_ : core::pack::annealer::SimAnnealerBase
• highval() : protocols::match::downstream::AtomGeometrySecMatchRPE
• highval_ : protocols::match::downstream::AtomGeometrySecMatchRPE
• hijack_loop_reading_code_set_loop_line_begin_token() : protocols::loops::PoseNumberedLoopFileReader
• hires_fpdock_protocol() : protocols::flexpep_docking::FlexPepDockingProtocol
• hires_score_ : protocols::protein_interface_design::movers::LoopMoverFromCommandLine , protocols::protein_interface_design::movers::LoopRemodel
• hires_scorefxn_ : protocols::protein_interface_design::movers::PlaceOnLoop , protocols::rna::denovo::movers::RNA_DeNovoProtocolMover , protocols::rna::denovo::RNA_DeNovoProtocol , protocols::rna::denovo::RNA_FragmentMonteCarlo
• his_can_be_pi_ : core::scoring::methods::ArgCationPiEnergy
• his_tyr_ : protocols::hbnet::HBNetStapleInterface
• hist_ : protocols::recces::Histogram
• hist_list_ : protocols::recces::RECCES_Mover
• histogram() : core::scoring::epr_deer::EPRSpinLabel
• Histogram() : protocols::canonical_sampling::BiasEnergy::Histogram< T > , protocols::recces::Histogram
• histogram_files_ : protocols::nmr::pre::PREMover
• histogram_max() : protocols::recces::options::RECCES_Options
• histogram_max_ : protocols::recces::options::RECCES_Options
• histogram_min() : protocols::recces::options::RECCES_Options
• histogram_min_ : protocols::recces::options::RECCES_Options
• histogram_spacing() : protocols::recces::options::RECCES_Options
• histogram_spacing_ : protocols::recces::options::RECCES_Options
• histogram_vector_ : core::scoring::orbitals::OrbitalsStatistics
• HistogramFloatOP : protocols::canonical_sampling::BiasEnergy
• HistogramIntOP : protocols::canonical_sampling::BiasEnergy
• histograms() : protocols::simple_moves::DOFHistogramRecorder
• histograms_ : protocols::simple_moves::DOFHistogramRecorder
• history_ : protocols::hybridization::TemplateHistory , protocols::monte_carlo::GenericSimulatedAnnealer
• history_size_ : core::pack::task::operation::EnableMultiCoolAnnealer
• hit() : protocols::match::downstream::TargetRotamerCoords
• Hit() : protocols::simple_moves::Hit
• hit_cacher_ : protocols::match::output::SameChiBinComboGrouper , protocols::match::output::SameSequenceGrouper
• hit_data_ : protocols::match::downstream::TargetRotamerCoords
• hit_hash_begin() : protocols::match::HitHasher
• hit_hash_end() : protocols::match::HitHasher
• hit_hashes_ : protocols::match::HitHasher
• hit_list_begin() : protocols::match::Matcher
• hit_list_end() : protocols::match::Matcher
• hit_score_cutoff_ : protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• HitCounts : protocols::match::MatchCounter
• HitHash : protocols::match::HitHasher , protocols::match::HitNeighborFinder , protocols::match::MatchCounter
• HitHasher() : protocols::match::HitHasher
• HitIndexList : protocols::match::HitNeighborFinder
• HitList : protocols::match::Matcher
• HitListConstIterator : protocols::match::Matcher
• HitListIterator : protocols::match::Matcher
• HitNeighborFinder() : protocols::match::HitNeighborFinder
• HitPtrList : protocols::match::HitNeighborFinder
• hits() : protocols::match::Matcher
• hits1() : core::scoring::motif::MotifHits
• hits2() : core::scoring::motif::MotifHits
• hits_ : protocols::match::Matcher
• hits_for_focused_geomcst_and_build_point_begin_ : protocols::match::downstream::SecondaryMatcherToDownstreamResidue
• hits_for_focused_geomcst_and_build_point_end_ : protocols::match::downstream::SecondaryMatcherToDownstreamResidue
• hits_for_focused_geomcst_end_ : protocols::match::downstream::SecondaryMatcherToDownstreamResidue
• hits_potentially_incompatible() : protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder
• hits_to_include_with_partial_match() : protocols::match::downstream::ClassicMatchAlgorithm , protocols::match::downstream::DownstreamAlgorithm , protocols::match::downstream::SecondaryMatcherToDownstreamResidue , protocols::match::downstream::SecondaryMatcherToUpstreamResidue , protocols::match::output::WriteUpstreamCoordinateKinemage
• hl : protocols::sic_dock::XfoxmScore
• Hmatrices : core::kinematics::jacobian::ModuleType1::screw_construct_struct
• HN_S2 : protocols::sparta::PDB
• ho2prime_index() : core::chemical::rna::RNA_Info
• ho2prime_index_ : core::chemical::rna::RNA_Info
• hoh_ref_score_ : core::scoring::magnesium::MgEnergy
• hoist_angle_degrees_ : protocols::legacy_sewing::Model
• hokey_template_workaround() : core::pack::dunbrack::SingleResidueDunbrackLibrary
• holes2atype_ : core::scoring::packing::HolesParams
• HOLES_POSE_INFO : core::pose::datacache::CacheableDataType
• HolesEnergy() : core::scoring::packing::HolesEnergy
• HolesEnergyRes() : core::scoring::packing::HolesEnergyRes
• HolesFilter() : protocols::simple_filters::HolesFilter
• HolesParams() : core::scoring::packing::HolesParams
• HolesParamsRes() : core::scoring::packing::HolesParamsRes
• HolesResult() : core::scoring::packing::HolesResult
• HOMO_Tab : protocols::sparta::Sparta::SpartaLib
• homoFileName : protocols::sparta::Sparta::SpartaLib
• homologs_ : protocols::loophash::BackboneDB
• homology_exclusion_ : protocols::rna::denovo::movers::RNA_FragmentMover
• homooligomer_swap_ : protocols::energy_based_clustering::EnergyBasedClusteringOptions
• hoog_edge_paired() : core::scoring::rna::data::RNA_DMS_LowResolutionPotential
• hoog_edge_paired_ : core::scoring::rna::data::RNA_DMS_LowResolutionPotential
• host : protocols::network::NetworkQueue::ServerAddress
• host_chain() : protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::protein_interface_design::movers::PlacementMinimizationMover , protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• host_chain_ : protocols::protein_interface_design::filters::StubScoreFilter , protocols::protein_interface_design::movers::BestHotspotCstMover , 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::SetAtomTree
• hotspot_distcb_weight_ : protocols::protein_interface_design::movers::DockWithHotspotMover
• hotspot_filenames_ : protocols::protein_interface_design::movers::DockWithHotspotMover
• hotspot_filter : protocols::flexpep_docking::FlexPepDockingFlags
• hotspot_filter_ : protocols::protein_interface_design::movers::HotspotHasherMover
• hotspot_label() : protocols::fold_from_loops::utils::Nub
• hotspot_length() : protocols::hotspot_hashing::HotspotStubSet
• hotspot_length_ : protocols::hotspot_hashing::HotspotStubSet
• hotspot_score_weight_ : protocols::protein_interface_design::movers::DockWithHotspotMover
• hotspot_stub_set_ : protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover , protocols::protein_interface_design::movers::SetupHotspotConstraintsMover
• hotspotcst_filter_ : protocols::protein_interface_design::movers::DockWithHotspotMover
• HotspotDisjointedFoldTreeMover() : protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover
• HotspotHasherMover() : protocols::protein_interface_design::movers::HotspotHasherMover
• Hotspots : protocols::hotspot_hashing::HotspotStubSet
• HotspotStub() : protocols::hotspot_hashing::HotspotStub , protocols::hotspot_hashing::HotspotStubSet
• HotspotStubSet : protocols::hotspot_hashing::HotspotStub , protocols::hotspot_hashing::HotspotStubSet
• hpairpot_ : protocols::fldsgn::potentials::SetSecStructEnergies
• hpairset() : protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential
• hpairset_ : protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential , protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential
• hpairset_name_ : protocols::fldsgn::topology::HelixPairingSet
• hpatch_energy_alternate_state_assignment_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• hpatch_energy_current_state_assignment_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• hpatch_score() : core::pack::interaction_graph::SurfacePotential
• HPATCH_SCORE_BIN_SIZE : core::pack::interaction_graph::SurfacePotential
• hpatch_score_min_last_100_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• hpatch_score_min_recent_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• hpatch_score_weight_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• HPatchBackgroundEdge() : core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G >
• HPatchBackgroundNode() : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >
• HPatchCalculator() : protocols::pose_metric_calculators::HPatchCalculator
• HPatchEdge() : core::pack::interaction_graph::HPatchEdge< V, E, G >
• HPatchEnergy() : core::pack::interaction_graph::HPatchEnergy
• HPatchInteractionGraph() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• HPatchNode() : core::pack::interaction_graph::HPatchNode< V, E, G >
• hphobe_ats_ : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >
• hphobe_ats_for_restype_group_ : core::pack::interaction_graph::HPatchNode< V, E, G >
• Hpol_bbOrbH : core::scoring::orbitals::OrbitalsLookup
• Hpol_index() : core::chemical::ResidueType , core::conformation::Residue
• Hpol_index_ : core::chemical::ResidueType
• Hpol_scOrbH : core::scoring::orbitals::OrbitalsLookup
• HPool_RMSD() : protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD
• Hpos_apolar() : core::chemical::ResidueType , core::conformation::Residue
• Hpos_apolar_ : core::chemical::ResidueType
• Hpos_polar() : core::chemical::ResidueType , core::conformation::Residue
• Hpos_polar_ : core::chemical::ResidueType
• Hpos_polar_sc() : core::chemical::ResidueType , core::conformation::Residue
• Hpos_polar_sc_ : core::chemical::ResidueType
• hrf_dynamics_input() : core::scoring::methods::EnergyMethodOptions
• hrf_dynamics_input_ : core::scoring::methods::EnergyMethodOptions
• hrf_dynamics_input_file_ : core::scoring::methods::HRFDynamicsEnergy
• HRF_MSLabelingEnergy() : core::scoring::methods::HRF_MSLabelingEnergy
• HRFDynamicsEnergy() : core::scoring::methods::HRFDynamicsEnergy
• hs1_dist() : protocols::fldsgn::topology::BetaAlphaBetaMotif , protocols::fldsgn::topology::HSSTriplet
• hs1_dist_ : protocols::fldsgn::topology::BetaAlphaBetaMotif , protocols::fldsgn::topology::HSSTriplet
• hs1_orient() : protocols::fldsgn::topology::HSSTriplet
• hs1_orient_ : protocols::fldsgn::topology::HSSTriplet
• hs2_dist() : protocols::fldsgn::topology::BetaAlphaBetaMotif , protocols::fldsgn::topology::HSSTriplet
• hs2_dist_ : protocols::fldsgn::topology::BetaAlphaBetaMotif , protocols::fldsgn::topology::HSSTriplet
• hs2_orient() : protocols::fldsgn::topology::HSSTriplet
• hs2_orient_ : protocols::fldsgn::topology::HSSTriplet
• hs_angle() : protocols::fldsgn::topology::BetaAlphaBetaMotif , protocols::fldsgn::topology::HSSTriplet
• hs_angle_ : protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential , protocols::fldsgn::topology::BetaAlphaBetaMotif , protocols::fldsgn::topology::HSSTriplet
• hs_angle_sigma2_ : protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential
• hs_angle_wts_ : protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential
• Hs_data : protocols::hotspot_hashing::HotspotStubSet
• hs_dist_ : protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential , protocols::fldsgn::topology::BetaAlphaBetaMotif
• hs_dist_sigma2_ : protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential
• hs_dist_wts_ : protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential
• hs_dp_ : core::scoring::SecondaryStructurePotential
• hs_dp_initializer() : core::scoring::SecondaryStructurePotential
• Hs_map : protocols::hotspot_hashing::HotspotStubSet
• hs_pair_weight_ : protocols::fldsgn::potentials::SetSecStructEnergies
• hs_scores_ : protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential
• Hs_vec : protocols::hotspot_hashing::HotspotStubSet
• hs_weight_ : protocols::fldsgn::potentials::SetSecStructEnergies
• hsheet_dist() : protocols::fldsgn::topology::BetaAlphaBetaMotif , protocols::fldsgn::topology::HSSTriplet
• hsheet_dist_ : protocols::fldsgn::topology::HSSTriplet
• hsheet_dist_repulsive_ : protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential
• hsheet_elev_angle() : protocols::fldsgn::topology::BetaAlphaBetaMotif
• hsheet_elev_angle_ : protocols::fldsgn::topology::BetaAlphaBetaMotif
• hspair() : core::scoring::SecondaryStructurePotential
• HSPairPotential() : protocols::fldsgn::potentials::sspot::HSPairPotential
• hspot_ : protocols::fldsgn::potentials::SetSecStructEnergies , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy
• hss3set_ : protocols::fldsgn::filters::HSSTripletFilter , protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential
• hss_triplet() : protocols::fldsgn::topology::HSSTripletSet
• hss_triplet_ : protocols::fldsgn::potentials::SetSecStructEnergies
• hss_triplet_set() : protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential
• hss_triplets() : protocols::fldsgn::topology::HSSTripletSet , protocols::parser::BluePrint
• hss_triplets_ : protocols::fldsgn::topology::HSSTripletSet , protocols::parser::BluePrint
• HSSConstIterator : protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential
• HSSTriplet : protocols::fldsgn::filters::HSSTripletFilter , protocols::fldsgn::topology::HSSTriplet
• HSSTripletFilter() : protocols::fldsgn::filters::HSSTripletFilter
• HSSTripletOP : protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential
• HSSTriplets : protocols::fldsgn::filters::HSSTripletFilter
• HSSTripletSet : protocols::fldsgn::filters::HSSTripletFilter , protocols::fldsgn::topology::HSSTripletSet
• HSSTripletSetOP : protocols::fldsgn::filters::HSSTripletFilter , protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy
• HSURFACE : protocols::pockets::ComparisonGrid , protocols::pockets::PocketGrid
• ht() : core::conformation::symmetry::SymmetryTransform
• ht_for_chitip_atom() : protocols::match::upstream::UpstreamResTypeGeometry
• ht_for_chitip_atoms() : protocols::match::upstream::UpstreamResTypeGeometry
• ht_for_chitip_atoms_ : protocols::match::upstream::UpstreamResTypeGeometry
• htransform_ : core::conformation::symmetry::SymmetryTransform
• HTReal : core::pack::interaction_graph::SymmOnTheFlyInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyNode , protocols::match::downstream::ClassicMatchAlgorithm , protocols::match::downstream::DownstreamBuilder , protocols::match::upstream::FullChiSampleSet , protocols::match::upstream::ProteinUpstreamBuilder , protocols::match::upstream::UpstreamResTypeGeometry , protocols::toolbox::match_enzdes_util::ExternalGeomSampler , protocols::toolbox::match_enzdes_util::LigandConformer , protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• hurry() : protocols::protein_interface_design::movers::LoopRemodel , protocols::symmetric_docking::SymDockProtocol
• hurry_ : protocols::protein_interface_design::movers::LoopRemodel , protocols::protein_interface_design::movers::PlaceStubMover , protocols::symmetric_docking::SymDockProtocol
• hxl_tors_potential_ : core::scoring::ScoringManager
• hybrid_protocol_ : protocols::carbohydrates::GlycanTreeModeler
• hybridization() : core::chemical::AtomType , core::chemical::orbitals::OrbitalType
• hybridization_ : core::chemical::AtomType , core::chemical::gasteiger::GasteigerAtomTypeData , core::chemical::orbitals::OrbitalType
• hybridization_rank() : core::chemical::gasteiger::PossibleAtomTypesForAtom
• hybridization_type2name_ : core::scoring::hbonds::HBondTypeManager
• hybridization_type_from_name() : core::scoring::hbonds::HBondTypeManager
• hybridize() : protocols::seeded_abinitio::SegmentHybridizer
• HybridizeFoldtreeDynamic() : protocols::hybridization::HybridizeFoldtreeDynamic
• HybridizeProtocol() : protocols::hybridization::HybridizeProtocol
• HybridOrbitalType : core::chemical::gasteiger::GasteigerAtomTypeData
• HybridVDW_Energy() : core::scoring::methods::HybridVDW_Energy
• hyd_ : protocols::membrane::scoring::MEnvAtomParams
• hyd_deriv_ : protocols::membrane::scoring::MEnvAtomParams
• Hydrate() : protocols::hydrate::Hydrate
• hydrate() : protocols::magnesium::MgScanner
• hydrate_ : protocols::magnesium::MgScanner
• hydrate_all_ : protocols::hydrate::Hydrate
• hydrate_magnesium() : protocols::magnesium::MgHydrater
• hydrate_magnesium_in_pose() : protocols::magnesium::MgHydrater
• hydrate_magnesium_with_orbital_frame() : protocols::magnesium::MgHydrater
• hydrate_magnesiums() : protocols::stepwise::options::StepWiseBasicOptions
• hydrate_magnesiums_ : protocols::stepwise::options::StepWiseBasicOptions
• hydration() : protocols::membrane::scoring::MEnvAtomParams
• hydration_deriv() : protocols::membrane::scoring::MEnvAtomParams
• hydrogen_bond_threshold_ : protocols::hbnet::HBNet
• hydrogen_interaction : core::scoring::etable::EtableParamsOnePair
• hydrogen_interaction_cutoff() : core::scoring::elec::FA_ElecEnergy , core::scoring::methods::MMLJEnergyInter
• hydrogen_interaction_cutoff2() : core::scoring::elec::electrie::ElecTrieEvaluator , core::scoring::elec::FA_ElecEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::etable::Etable , core::scoring::etable::EtableEvaluator , core::scoring::hbonds::HBondEnergy , core::scoring::hbonds::NPDHBondEnergy , core::scoring::lkball::lkbtrie::LKBTrieEvaluator , core::scoring::methods::MMLJEnergyInter , core::scoring::vdwaals::VDWTrieEvaluator
• hydrogen_interaction_cutoff2_ : core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::etable::Etable , core::scoring::etable::EtableEvaluator , core::scoring::vdwaals::VDW_Energy , core::scoring::vdwaals::VDWTrieEvaluator
• hydrogenatom_heavyatom_energy() : core::scoring::elec::electrie::ElecTrieEvaluator , core::scoring::etable::AnalyticEtableEvaluator , core::scoring::etable::TableLookupEvaluator , core::scoring::hbonds::HBondEnergy , core::scoring::lkball::lkbtrie::LKBTrieEvaluator , core::scoring::methods::MMLJEnergyInter , core::scoring::vdwaals::VDWTrieEvaluator
• hydrogenatom_hydrogenatom_energy() : core::scoring::elec::electrie::ElecTrieEvaluator , core::scoring::etable::AnalyticEtableEvaluator , core::scoring::etable::TableLookupEvaluator , core::scoring::hbonds::HBondEnergy , core::scoring::lkball::lkbtrie::LKBTrieEvaluator , core::scoring::methods::MMLJEnergyInter , core::scoring::vdwaals::VDWTrieEvaluator
• HydrogenAtomFilter() : core::chemical::HydrogenAtomFilter
• HydrogenBondConstraintGenerator() : protocols::constraint_generator::HydrogenBondConstraintGenerator
• HydrogenBondInfo() : protocols::constraint_generator::HydrogenBondInfo
• HydrogenBondingAtom() : protocols::constraint_generator::HydrogenBondingAtom
• hydrophobic_ : protocols::simple_filters::InterfaceSasaFilter , protocols::simple_filters::TotalSasaFilter
• hydrophobic_constraint_strength() : protocols::aa_composition::AddHelixSequenceConstraintsMover
• hydrophobic_constraint_strength_ : protocols::aa_composition::AddHelixSequenceConstraintsMover
• hydrophobic_residue_contacts_threshold_ : protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter
• hydrophobic_residues_ : protocols::denovo_design::filters::ExposedHydrophobicsFilter
• hydrophobic_sasa() : protocols::cyclic_peptide_predict::HierarchicalHybridJD_SASASummary
• hydrophobic_sasa_ : protocols::cyclic_peptide_predict::HierarchicalHybridJD_SASASummary
• HydrophobicityProfileSimilarity() : protocols::frag_picker::scores::HydrophobicityProfileSimilarity
• HydrophobicitySimilarity() : protocols::frag_picker::scores::HydrophobicitySimilarity
• hydroxyl_wants_h : core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::UnsatCorrectionOptions
• hydroxyls_must_donate_ : protocols::hbnet::HBNet
• HydroxylTorsionEnergy() : core::scoring::methods::HydroxylTorsionEnergy
• HydroxylTorsionPotential() : core::scoring::HydroxylTorsionPotential