- h -

• h1() : protocols::fldsgn::topology::HelixPairing
• h2() : protocols::fldsgn::topology::HelixPairing
• h2o_hbond_score_1way() : core::scoring::WaterAdductHBondPotential
• h3_base_type_enum_to_string() : protocols::antibody::AntibodyEnumManager
• h3_base_type_string_to_enum() : protocols::antibody::AntibodyEnumManager
• H3CterInsert() : protocols::antibody::H3CterInsert
• H3PerturbCCD() : protocols::antibody::H3PerturbCCD
• H3RefineCCD() : protocols::antibody::H3RefineCCD
• H_atom_id() : protocols::match::upstream::UpstreamResTypeGeometry
• H_pos() : protocols::match::upstream::ProteinBackboneBuildPoint
• HA_atom_id() : protocols::match::upstream::UpstreamResTypeGeometry
• 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
• Hairpin() : core::scoring::Hairpin
• hairpin_killing_score() : core::scoring::SecondaryStructurePotential
• Hairpins() : core::scoring::Hairpins
• hairpins() : core::scoring::SS_Killhairpins_Info
• HamiltonianExchange() : protocols::canonical_sampling::HamiltonianExchange
• 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() : 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::MSDJobDistributor , protocols::jd2::ShuffleFileSystemJobDistributor
• handle_variable_expression() : 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
• HarmonicFunc() : core::scoring::func::HarmonicFunc
• Haro_index() : core::chemical::ResidueType , core::conformation::Residue
• has() : core::chemical::ResidueType , 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 , protocols::abinitio::StructureStore , protocols::loops::Loops , protocols::noesy_assign::PeakAssignmentResidueMap
• has_algorithm() : protocols::match::upstream::BuildSet
• has_alias() : protocols::denovo_design::components::StructureData
• has_another_job() : protocols::stepwise::setup::StepWiseCSA_JobDistributor , protocols::stepwise::setup::StepWiseJobDistributor , protocols::stepwise::setup::StepWiseMonteCarloJobDistributor
• 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_atom() : core::chemical::AtomTypeSet , protocols::frag_picker::CSTalosIO , protocols::frag_picker::scores::AtomBasedConstraintsScore
• has_atom_id() : protocols::toolbox::AtomID_Mapper
• has_atom_info() : core::kinematics::Edge
• has_behavior() : core::pack::task::PackerTask , core::pack::task::PackerTask_ , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• 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_string() : protocols::denovo_design::components::StructureData
• 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_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
• has_conventional_residue() : core::pose::full_model_info::FullModelParameters
• has_coordinates() : core::fragment::BBTorsionSRFD
• 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_cut() : core::environment::FoldTreeSketch
• has_cycle() : core::environment::FoldTreeSketch::Node
• 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_dependencies() : protocols::forge::build::BuildInstruction
• has_disallowed_variant() : core::chemical::ResidueTypeFinder
• has_dof() : core::conformation::symmetry::SymDof , core::pose::Pose
• has_dof_constraints() : core::scoring::constraints::ConstraintSet
• has_domain() : protocols::toolbox::AtomLevelDomainMap
• 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_linkage_to_child_mainchain() : core::chemical::carbohydrates::CarbohydrateInfo
• has_extra_parameter() : core::chemical::AtomTypeSet
• 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_generated_residue_type() : core::chemical::ResidueTypeSetCache
• has_geometric_connection() : protocols::generalized_kinematic_closure::GeneralizedKIC
• has_H_atom() : protocols::match::upstream::UpstreamResTypeGeometry
• has_HA_atom() : protocols::match::upstream::UpstreamResTypeGeometry
• has_ideal_geometry() : protocols::simple_moves::MinimalRotamer
• has_incomplete_connection() : core::conformation::Residue
• has_interchangeability_group() : core::chemical::ResidueTypeSet
• has_intra_residue_constraints() : core::scoring::constraints::ConstraintSet
• has_job() : protocols::jd2::JobsContainer
• has_job_completed() : protocols::jd3::JobQueen
• 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_label() : protocols::noesy_assign::CrossPeak3D , protocols::noesy_assign::CrossPeak4D , protocols::noesy_assign::CrossPeak , protocols::noesy_assign::CrossPeakInfo , protocols::noesy_assign::PeakAssignment
• has_lower_connect() : core::conformation::Residue
• has_method_weights() : core::scoring::methods::EnergyMethodOptions
• has_methods() : core::pack::interaction_graph::ResidueArrayAnnealingEvaluator
• has_model() : protocols::abinitio::PairingStatEntry
• has_N_atom() : protocols::match::upstream::UpstreamResTypeGeometry
• has_name() : core::chemical::ResidueTypeSet
• has_name3() : core::chemical::ResidueTypeSet
• has_neighbor() : core::environment::FoldTreeSketch::Node
• has_next() : protocols::sewing::SegmentGraph
• has_next_level() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• 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_option() : protocols::jd2::JD2ResourceManager
• has_orbital() : core::chemical::ResidueType
• has_orbitals() : core::chemical::Atom
• has_orientation_and_pleating() : protocols::jumping::JumpSample
• 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_peptide_edge() : protocols::denovo_design::components::FoldGraph
• has_peptide_neighbor() : core::environment::FoldTreeSketch::Node
• has_precomputed_move() : protocols::stepwise::modeler::precomputed::PrecomputedLibraryMover
• has_previous() : protocols::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::ResidueType , 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_range1() : core::conformation::symmetry::SymDof
• has_range1_lower() : 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_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_residue() : protocols::noesy_assign::ResonanceList
• has_residue_pair_constraints() : core::scoring::constraints::ConstraintSet
• has_residue_type_set() : core::chemical::ChemicalManager
• has_resnum() : protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSamplerComb
• has_resource_with_description() : protocols::jd2::JD2ResourceManager
• has_restype() : protocols::match::upstream::BuildSet
• has_sc_orbitals() : core::chemical::ResidueType , core::conformation::Residue
• has_score() : protocols::mpi_refinement::MultiObjective
• has_segment() : protocols::backrub::BackrubMover , protocols::denovo_design::components::StructureData
• 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_struct_type() : core::io::silent::SilentStructFactory
• has_tag() : core::import_pose::atom_tree_diffs::AtomTreeDiff , core::io::silent::SilentFileData
• has_task() : protocols::toolbox::task_operations::STMStoredTask
• has_template() : protocols::abinitio::Templates , protocols::farna::libraries::RNA_JumpLibrary
• has_type() : core::chemical::rotamers::RotamerLibrarySpecificationFactory , core::pack::rotamers::SingleResidueRotamerLibraryFactory , core::pack::task::operation::ResFilterFactory , core::pack::task::operation::ResLvlTaskOperationFactory , core::pack::task::operation::TaskOperationFactory , core::select::residue_selector::ResidueSelectorFactory , protocols::loops::loops_definers::LoopsDefinerFactory
• has_upper_connect() : core::conformation::Residue
• has_upstream_only_geomcsts() : protocols::match::Matcher
• has_valid_moves() : protocols::hybridization::ChunkTrialMover
• has_value() : protocols::farna::libraries::BasePairStepLibrary
• has_variant_type() : core::chemical::ResidueType , core::conformation::Residue
• has_vec_inconsistency() : protocols::antibody::AntibodyDatabaseManager
• 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
• hash() : protocols::environment::AutoCutData , protocols::genetic_algorithm::EntityElement , protocols::multistate_design::PosType
• hash_hits() : protocols::match::HitNeighborFinder
• hash_index() : protocols::loophash::LoopHashMap
• hash_map() : protocols::sewing::Hasher
• hash_model() : protocols::sewing::Hasher
• hash_pdb_model() : protocols::sewing::AppendAssemblyMover
• hash_recent_history() : core::pack::annealer::FASTERAnnealer
• hash_sizes() : protocols::loophash::LoopHashLibrary
• hash_to_labal() : core::scoring::motif::ResPairMotifMetaBinner
• hash_value() : core::kinematics::FoldTree , core::scoring::dssp::StrandPairing
• HashEdge() : protocols::sewing::HashEdge
• hasher() : core::scoring::motif::MotifHash
• Hasher() : protocols::sewing::Hasher
• HashResult() : protocols::sewing::HashResult
• hasNext() : protocols::viewer::triangleIterator
• 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_params() : core::scoring::packing::HolesParams , core::scoring::packing::HolesParamsRes
• havesurf() : core::scoring::packing::PoseBalls
• hb_acc_chem_type() : core::scoring::hbonds::hbtrie::HBAtom
• hb_bb() : core::scoring::motif::ResPairMotif
• hb_bb_sc() : core::scoring::motif::ResPairMotif
• hb_chem_type() : core::scoring::hbonds::hbtrie::HBAtom
• hb_don_chem_type() : core::scoring::hbonds::hbtrie::HBAtom
• hb_env_dep_new_high_nneigh() : core::scoring::hbonds::HBondOptions
• hb_env_dep_new_low_nneigh() : core::scoring::hbonds::HBondOptions
• hb_env_dep_new_low_scale() : core::scoring::hbonds::HBondOptions
• hb_sc() : core::scoring::motif::ResPairMotif
• HbaGrid() : protocols::qsar::scoring_grid::HbaGrid
• HBAtom() : core::scoring::hbonds::hbtrie::HBAtom
• HBCPData() : core::scoring::hbonds::hbtrie::HBCPData
• HbdGrid() : protocols::qsar::scoring_grid::HbdGrid
• HBEvalTuple() : core::scoring::hbonds::HBEvalTuple
• HBFadeInterval_from_name() : core::scoring::hbonds::HBondDatabase
• HBond() : core::scoring::hbonds::HBond
• hbond() : core::scoring::hbonds::HBondSet
• hbond_cop() : core::scoring::hbonds::HBondSet
• hbond_derivs_1way() : core::scoring::hbonds::HBondEnergy
• hbond_energy() : protocols::toolbox::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator
• hbond_energy_comparer() : core::scoring::hbonds::HBond
• hbond_energy_shift() : core::scoring::hbonds::HBondOptions
• hbond_options() : core::scoring::hbonds::HBondSet , core::scoring::methods::EnergyMethodOptions
• HBondAcceptorFilter() : protocols::ligand_docking::HBondAcceptorFilter
• HBondDatabase() : core::scoring::hbonds::HBondDatabase
• HBondDonorFilter() : protocols::ligand_docking::HBondDonorFilter
• HBondEnergy() : core::scoring::hbonds::HBondEnergy
• HBondFeatures() : protocols::features::HBondFeatures
• HBondFeaturesCreator() : protocols::features::HBondFeaturesCreator
• HBondOptions() : core::scoring::hbonds::HBondOptions
• HBondParameterFeatures() : protocols::features::HBondParameterFeatures
• HBondParameterFeaturesCreator() : protocols::features::HBondParameterFeaturesCreator
• HBondResidueMinData() : core::scoring::hbonds::HBondResidueMinData
• HBondResPairMinData() : core::scoring::hbonds::HBondResPairMinData
• HBondSet() : core::scoring::hbonds::HBondSet
• HbondsToAtomFilter() : protocols::protein_interface_design::filters::HbondsToAtomFilter
• HbondsToResidueFilter() : protocols::protein_interface_design::filters::HbondsToResidueFilter
• HBPoly1D_from_name() : core::scoring::hbonds::HBondDatabase
• HbsPatcher() : protocols::simple_moves::hbs::HbsPatcher
• hConvergenceCheck() : protocols::abinitio::hConvergenceCheck , protocols::hybridization::hConvergenceCheck
• header() : core::io::StructFileRep
• header_information() : core::pose::PDBInfo
• HeaderInformation() : core::io::HeaderInformation
• heat_after_cycles() : protocols::moves::MonteCarlo
• heavy_atom_with_hydrogens() : core::chemical::ResidueType
• heavy_atom_with_polar_hydrogens() : core::chemical::ResidueType
• heavy_atoms() : core::chemical::ResidueType
• heavyatom_has_polar_hydrogens() : core::chemical::Atom , core::chemical::ResidueType , core::conformation::Residue
• heavyatom_heavyatom_energy() : core::scoring::elec::FA_ElecEnergy , 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::FA_ElecEnergy , 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_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
• HedgeArchive() : protocols::abinitio::HedgeArchive
• HelicalFragment() : protocols::features::helixAssembly::HelicalFragment
• HelicalGaussianMover() : protocols::rbsegment_relax::HelicalGaussianMover
• Helices() : core::scoring::Helices
• helices() : core::scoring::SS_Info , protocols::fldsgn::topology::SS_Info2
• helix() : protocols::fldsgn::topology::BetaAlphaBetaMotif
• Helix() : protocols::fldsgn::topology::Helix
• helix() : protocols::fldsgn::topology::HSSTriplet , protocols::fldsgn::topology::SS_Info2 , protocols::helical_bundle::MakeBundle
• helix_cop() : protocols::helical_bundle::MakeBundle
• 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_fraction() : core::fragment::SecondaryStructure
• helix_id() : core::scoring::MembraneTopology , protocols::fldsgn::topology::SS_Info2
• helix_index() : protocols::helical_bundle::PerturbBundleOptions
• helix_length() : protocols::helical_bundle::MakeBundleHelix
• helix_not_defined() : protocols::helical_bundle::PerturbBundle
• helix_pairing() : protocols::fldsgn::topology::HelixPairingSet
• helix_pairings() : protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::topology::HelixPairingSet , protocols::jd2::parser::BluePrint
• HelixBundleFeatures() : protocols::features::helixAssembly::HelixBundleFeatures
• HelixBundleFeaturesCreator() : protocols::features::helixAssembly::HelixBundleFeaturesCreator
• HelixCapFeatures() : protocols::features::HelixCapFeatures
• HelixCapFeaturesCreator() : protocols::features::HelixCapFeaturesCreator
• helixjump_picks() : protocols::abinitio::Templates
• HelixKinkFilter() : protocols::fldsgn::filters::HelixKinkFilter
• HelixNCapperMover() : protocols::helix_capper::HelixNCapperMover
• HelixPairing() : protocols::fldsgn::topology::HelixPairing
• HelixPairingFilter() : protocols::fldsgn::filters::HelixPairingFilter
• HelixPairingSet() : protocols::fldsgn::topology::HelixPairingSet
• HelixRotate() : protocols::nonlocal::HelixRotate
• HelixScore() : protocols::sic_dock::HelixScore
• helper() : core::scoring::constraints::AngleConstraint , core::scoring::constraints::DihedralConstraint
• hetero_atom_line() : core::scoring::packstat::CavityBall
• heterogen_formulae() : core::io::StructFileRep
• heterogen_names() : core::io::StructFileRep
• heterogen_synonyms() : core::io::StructFileRep
• HierarchicalLevel() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• high_res() : protocols::floppy_tail::FloppyTailMover
• high_temp() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• highest_job_index() : protocols::jd2::JobsContainer
• highest_probability() : protocols::frag_picker::quota::ABEGO_SS_Config
• highres_reference_energy() : protocols::docking::DockingEnsemble
• HighResDocker() : protocols::ligand_docking::HighResDocker
• highval() : protocols::match::downstream::AtomGeometrySecMatchRPE
• hijack_loop_reading_code_set_loop_line_begin_token() : protocols::loops::PoseNumberedLoopFileReader
• hires_fpdock_protocol() : protocols::flexpep_docking::FlexPepDockingProtocol
• Histogram() : protocols::canonical_sampling::BiasEnergy::Histogram< T >
• histograms() : protocols::simple_moves::DOFHistogramRecorder
• hit() : protocols::match::downstream::TargetRotamerCoords
• hit_hash_begin() : protocols::match::HitHasher
• hit_hash_end() : protocols::match::HitHasher
• hit_list_begin() : protocols::match::Matcher
• hit_list_end() : protocols::match::Matcher
• HitHasher() : protocols::match::HitHasher
• HitNeighborFinder() : protocols::match::HitNeighborFinder
• hits() : protocols::match::Matcher
• hits1() : core::scoring::motif::MotifHits
• hits2() : core::scoring::motif::MotifHits
• 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
• ho2prime_index() : core::chemical::rna::RNA_ResidueType
• hokey_template_workaround() : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::rotamers::SingleResiduePeptoidLibrary
• 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
• hoog_edge_paired() : core::scoring::rna::data::RNA_DMS_LowResolutionPotential
• host_chain() : protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::protein_interface_design::movers::PlacementMinimizationMover , protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• hotspot_length() : protocols::hotspot_hashing::HotspotStubSet
• HotspotDisjointedFoldTreeMover() : protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover
• HotspotHasherMover() : protocols::protein_interface_design::movers::HotspotHasherMover
• HotspotStub() : protocols::hotspot_hashing::HotspotStub
• HotspotStubSet() : protocols::hotspot_hashing::HotspotStubSet
• hpairset() : protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential
• hpatch_score() : core::pack::interaction_graph::SurfacePotential
• HPatchBackgroundEdge() : core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G >
• HPatchBackgroundNode() : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >
• HPatchCalculator() : protocols::toolbox::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 >
• Hpol_index() : core::chemical::ResidueType , core::conformation::Residue
• HPool_RMSD() : protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD
• Hpos_apolar() : core::chemical::ResidueType , core::conformation::Residue
• Hpos_polar() : core::chemical::ResidueType , core::conformation::Residue
• Hpos_polar_sc() : core::chemical::ResidueType , core::conformation::Residue
• hs1_dist() : protocols::fldsgn::topology::BetaAlphaBetaMotif , protocols::fldsgn::topology::HSSTriplet
• hs1_orient() : protocols::fldsgn::topology::HSSTriplet
• hs2_dist() : protocols::fldsgn::topology::BetaAlphaBetaMotif , protocols::fldsgn::topology::HSSTriplet
• hs2_orient() : protocols::fldsgn::topology::HSSTriplet
• hs_angle() : protocols::fldsgn::topology::BetaAlphaBetaMotif , protocols::fldsgn::topology::HSSTriplet
• hs_dp_initializer() : core::scoring::SecondaryStructurePotential
• hsheet_dist() : protocols::fldsgn::topology::BetaAlphaBetaMotif , protocols::fldsgn::topology::HSSTriplet
• hsheet_elev_angle() : protocols::fldsgn::topology::BetaAlphaBetaMotif
• hspair() : core::scoring::SecondaryStructurePotential
• HSPairPotential() : protocols::fldsgn::potentials::sspot::HSPairPotential
• hss_triplet() : protocols::fldsgn::topology::HSSTripletSet
• hss_triplet_set() : protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential
• hss_triplets() : protocols::fldsgn::topology::HSSTripletSet , protocols::jd2::parser::BluePrint
• HSSTriplet() : protocols::fldsgn::topology::HSSTriplet
• HSSTripletFilter() : protocols::fldsgn::filters::HSSTripletFilter
• HSSTripletSet() : protocols::fldsgn::topology::HSSTripletSet
• ht() : core::conformation::symmetry::SymmetryTransform
• ht_for_chitip_atom() : protocols::match::upstream::UpstreamResTypeGeometry
• ht_for_chitip_atoms() : protocols::match::upstream::UpstreamResTypeGeometry
• hurry() : protocols::protein_interface_design::movers::LoopRemodel , protocols::symmetric_docking::SymDockProtocol
• hybridization() : core::chemical::AtomType , core::chemical::orbitals::OrbitalType
• hybridization_rank() : core::chemical::gasteiger::PossibleAtomTypesForAtom
• hybridization_type_from_name() : core::scoring::hbonds::HBondTypeManager
• hybridize() : protocols::seeded_abinitio::SegmentHybridizer
• HybridizeFoldtreeDynamic() : protocols::hybridization::HybridizeFoldtreeDynamic
• HybridizeProtocol() : protocols::hybridization::HybridizeProtocol
• HybridVDW_Energy() : core::scoring::methods::HybridVDW_Energy
• hydrate() : protocols::magnesium::MgScanner
• hydrate_magnesium() : protocols::magnesium::MgHydrater
• hydrate_magnesium_in_pose() : protocols::magnesium::MgHydrater
• hydrate_magnesium_with_orbital_frame() : protocols::magnesium::MgHydrater
• hydrogen_interaction_cutoff() : core::scoring::elec::FA_ElecEnergy , core::scoring::methods::MMLJEnergyInter
• hydrogen_interaction_cutoff2() : core::scoring::elec::FA_ElecEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::etable::Etable , core::scoring::etable::EtableEvaluator , core::scoring::hbonds::HBondEnergy , core::scoring::lkball::lkbtrie::LKBTrieEvaluator , core::scoring::methods::MMLJEnergyInter , core::scoring::vdwaals::VDWTrieEvaluator
• hydrogenatom_heavyatom_energy() : core::scoring::elec::FA_ElecEnergy , 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::FA_ElecEnergy , 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
• hydrogens() : core::chemical::ResidueType
• HydrophobicityProfileSimilarity() : protocols::frag_picker::scores::HydrophobicityProfileSimilarity
• HydrophobicitySimilarity() : protocols::frag_picker::scores::HydrophobicitySimilarity