Index – H

H1_pattern() (pyrosetta.rosetta.protocols.antibody.grafting.RegExManager method) h1_sequence() (pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence method) h2_sequence() (pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence method) h2o_hbond_score_1way() (pyrosetta.rosetta.core.scoring.WaterAdductHBondPotential method) h3_base_type_enum_to_string() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) h3_base_type_string_to_enum() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) H3_pattern() (pyrosetta.rosetta.protocols.antibody.grafting.RegExManager method) h3_sequence() (pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence method) H3CterInsert (class in pyrosetta.rosetta.protocols.antibody) H_atom_id() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) HA_atom_id() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) HACK_dump_helices() (in module pyrosetta.rosetta.core.scoring.motif) HACK_dump_helix() (in module pyrosetta.rosetta.core.scoring.motif) Hairpin (class in pyrosetta.rosetta.core.scoring) hairpins() (pyrosetta.rosetta.core.scoring.SS_Killhairpins_Info method) halfbin6() (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) halfbin_widths() (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) HamiltonianExchangeCreator (class in pyrosetta.rosetta.protocols.canonical_sampling) handle_function_expression() (pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator method) handle_structured_xml_error() (in module pyrosetta.rosetta.utility.tag) handle_variable_expression() (pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator method) handle_xml_error() (in module pyrosetta.rosetta.utility.tag) handle_xml_warning() (in module pyrosetta.rosetta.utility.tag) handles_metric_value() (in module pyrosetta.rosetta.basic) hankel_free() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) hankel_get_p0() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) hankel_get_rc() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) hankel_in_machine() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) hankel_make_j() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) hankel_make_rp() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) hankel_make_snn() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) hankel_r_div() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) hankel_r_mult() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) hankel_set_alpha() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) hankel_trans_no_lec() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) Haro_index() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) has() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) (pyrosetta.rosetta.basic.datacache.BasicDataCache method) (pyrosetta.rosetta.basic.datacache.ConstDataMap method) (pyrosetta.rosetta.basic.datacache.DataMap method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableMap method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.id.BondID method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.pose.datacache.ObserverCache method) (pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints method) (pyrosetta.rosetta.core.scoring.elec.CountPairRepMap method) (pyrosetta.rosetta.core.scoring.lkball.LKBallDatabase method) (pyrosetta.rosetta.protocols.loops.Loops method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap method) (pyrosetta.rosetta.utility.options.OptionCollection method) has_algorithm() (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) has_another_pose() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) has_any_false_selection() (in module pyrosetta.rosetta.core.select.residue_selector) has_any_of() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) has_any_of_characters() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) has_any_true_selection() (in module pyrosetta.rosetta.core.select.residue_selector) has_atom() (pyrosetta.rosetta.core.chemical.AtomTypeSet method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomBasedConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.AtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.DihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.InterbondAngleScore method) has_atom_info() (pyrosetta.rosetta.core.kinematics.Edge method) has_behavior() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) has_C_atom() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) has_CA_atom() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) has_cached_data() (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory method) has_CB_atom() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) has_CDR() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) has_chain() (in module pyrosetta.rosetta.core.pose) has_chemical_shifts() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) has_cluster_for_cdr() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) has_comment() (pyrosetta.rosetta.core.io.silent.SilentStruct method) has_common_pairing() (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) has_connected_resonances() (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) has_constraints() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) has_coordinates() (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) has_custom_variant_types() (pyrosetta.rosetta.core.chemical.ResidueProperties method) has_default() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) has_dependencies() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) has_dof() (pyrosetta.rosetta.core.pose.Pose method) has_dof_constraints() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) has_domain() (pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap method) has_energy() (pyrosetta.rosetta.core.io.silent.SilentStruct method) has_evaluator() (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) has_exocyclic_glycosidic_linkage() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) has_exocyclic_linkage() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanNode method) has_extra_parameter() (pyrosetta.rosetta.core.chemical.AtomTypeSet method) has_fallback_for_resource() (pyrosetta.rosetta.basic.resource_manager.FallbackConfigurationFactory method) has_file_contents() (pyrosetta.rosetta.utility.io.FileContentsMap method) has_finished() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) has_framework_dependant_cluster() (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) has_framework_dependant_clusters() (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) has_free_lower_terminus() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) has_free_upper_terminus() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) has_glycan_residue() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree method) has_grid() (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) has_H_atom() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) has_HA_atom() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) has_incomplete_connection() (pyrosetta.rosetta.core.conformation.Residue method) has_incomplete_connections() (in module pyrosetta.rosetta.protocols.ligand_docking) has_insertion_operator() (in module pyrosetta.rosetta.utility) has_interchangeability_group() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) has_intra_residue_constraints() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) has_job() (pyrosetta.rosetta.protocols.jd2.JobsContainer method) has_job_options() (pyrosetta.rosetta.basic.resource_manager.LazyResourceManager method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManager method) has_label() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) has_lower_connect() (pyrosetta.rosetta.core.conformation.Residue method) has_lower_residue() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) has_metapatch() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) has_method_weights() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) has_N_atom() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) has_name() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) has_name3() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) has_native_sequence() (in module pyrosetta.rosetta.protocols.antibody.design) has_next() (pyrosetta.rosetta.protocols.sewing.SegmentGraph method) has_non_residue_pair_constraints() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) has_nonzero_weight() (pyrosetta.rosetta.core.scoring.ScoreFunction method) has_O_atom() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) has_observer() (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.Observer method) (pyrosetta.rosetta.ObjexxFCL.ObserverMulti method) (pyrosetta.rosetta.ObjexxFCL.ObserverSingle method) has_omega() (pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData method) has_open_slaves() (pyrosetta.rosetta.protocols.jd2.SingleFileBuffer method) has_option() (pyrosetta.rosetta.basic.resource_manager.JobOptions method) (pyrosetta.rosetta.basic.resource_manager.LazyResourceManager method) (pyrosetta.rosetta.basic.resource_manager.ResourceManager method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManager method) has_orbital() (pyrosetta.rosetta.core.chemical.ResidueType method) has_orbitals() (pyrosetta.rosetta.core.chemical.Atom method) has_orientation_and_pleating() (in module pyrosetta.rosetta.core.scoring.dssp) has_pairing() (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet method) has_parent_remark() (pyrosetta.rosetta.core.io.silent.SilentStruct method) has_passport() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) has_polymer_dependent_groups() (pyrosetta.rosetta.core.chemical.ResidueType method) has_prefix() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) has_previous() (pyrosetta.rosetta.protocols.sewing.SegmentGraph method) has_profile() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) has_profile_struct() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) has_property() (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.AtomProperties method) (pyrosetta.rosetta.core.chemical.ResidueProperties method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) has_proton() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) has_reactivities() (pyrosetta.rosetta.core.io.rna.RNA_DataReader method) has_read_limit_for_file() (pyrosetta.rosetta.utility.io.FileContentsMap method) has_ref_pose() (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff method) has_ref_tag() (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff method) has_reference_pose() (pyrosetta.rosetta.core.pose.Pose method) has_res_type_set() (pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets method) has_residue() (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList method) has_residue_pair_constraints() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) has_residue_selector() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) has_residue_type_set() (pyrosetta.rosetta.core.chemical.ChemicalManager method) has_resource() (pyrosetta.rosetta.basic.resource_manager.LazyResourceManager method) (pyrosetta.rosetta.basic.resource_manager.ResourceManager method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManager method) has_resource_configuration() (pyrosetta.rosetta.basic.resource_manager.LazyResourceManager method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManager method) has_resource_loader() (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderFactory method) has_resource_locator() (pyrosetta.rosetta.basic.resource_manager.LazyResourceManager method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManager method) has_resource_options() (pyrosetta.rosetta.basic.resource_manager.LazyResourceManager method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManager method) has_resource_tag_by_job_tag() (pyrosetta.rosetta.basic.resource_manager.LazyResourceManager method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManager method) has_resource_with_description() (pyrosetta.rosetta.basic.resource_manager.LazyResourceManager method) (pyrosetta.rosetta.basic.resource_manager.ResourceManager method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManager method) has_restype() (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) has_rna_secstruct_legacy() (in module pyrosetta.rosetta.protocols.rna.denovo.secstruct_legacy) has_sc_orbitals() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) has_segment() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) has_severe_pep_bond_geom_issues() (in module pyrosetta.rosetta.protocols.loops) has_shadow_atoms() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) has_shared_silent_data() (pyrosetta.rosetta.core.io.silent.SilentFileData method) has_silent_in() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) has_stored_constraints() (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsManager method) has_suffix() (in module pyrosetta.rosetta.ObjexxFCL) has_tag() (pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff method) (pyrosetta.rosetta.core.io.silent.SilentFileData method) has_template() (pyrosetta.rosetta.protocols.rna.denovo.libraries.RNA_JumpLibrary method) has_template_pose() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method)

has_top_level_element() (pyrosetta.rosetta.utility.tag.XMLSchemaDefinition method) has_tree() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) has_type() (pyrosetta.rosetta.basic.datacache.DataMap method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerFactory method) has_upper_connect() (pyrosetta.rosetta.core.conformation.Residue method) has_upper_residue() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) has_upstream_only_geomcsts() (pyrosetta.rosetta.protocols.match.Matcher method) has_value() (in module pyrosetta.rosetta.utility.json_spirit) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepLibrary method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) has_variant_type() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) has_virtual_rna_residue_variant_type() (in module pyrosetta.rosetta.core.pose.rna) has_zero_weight() (pyrosetta.rosetta.core.scoring.ScoreFunction method) hASA_patch_energy() (pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential method) hash() (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement method) hash_fingerprint() (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) hash_model() (pyrosetta.rosetta.protocols.sewing.Hasher method) hash_value() (in module pyrosetta.rosetta.protocols.abinitio) (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) HashEdge (class in pyrosetta.rosetta.protocols.sewing) Hasher (class in pyrosetta.rosetta.protocols.sewing) hasPoseExtraScore() (in module pyrosetta.rosetta.core.pose) have_mutated_residue() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) hb_energy() (in module pyrosetta.rosetta.core.scoring.hbonds) hb_energy_deriv() (in module pyrosetta.rosetta.core.scoring.hbonds) hb_energy_deriv_u() (in module pyrosetta.rosetta.core.scoring.hbonds) hb_energy_deriv_u2() (in module pyrosetta.rosetta.core.scoring.hbonds) hb_eval_type() (in module pyrosetta.rosetta.core.scoring.hbonds) hb_eval_type_weight() (in module pyrosetta.rosetta.core.scoring.hbonds) HBAccChemType (class in pyrosetta.rosetta.core.scoring.hbonds) HBDefType (class in pyrosetta.rosetta.protocols.features) hbe_is_BB_type() (in module pyrosetta.rosetta.core.scoring.hbonds) hbe_is_SC_type() (in module pyrosetta.rosetta.core.scoring.hbonds) hbnet_one_body_energies() (in module pyrosetta.rosetta.protocols.hbnet) hbnet_symm_one_body_energies() (in module pyrosetta.rosetta.protocols.hbnet) hbond() (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) hbond_compute_energy() (in module pyrosetta.rosetta.core.scoring.hbonds) hbond_cop() (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) hbond_database() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) hbond_energy_cutoff() (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.residue_selectors.UnsatSelector method) hbond_evaluation_type() (in module pyrosetta.rosetta.core.scoring.hbonds) hbond_exists_in_vector() (in module pyrosetta.rosetta.protocols.hbnet) hbond_net_struct (class in pyrosetta.rosetta.protocols.hbnet) hbond_options() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) hbond_res_struct (class in pyrosetta.rosetta.protocols.hbnet) hbond_weight() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) hbonded() (in module pyrosetta.rosetta.protocols.protein_interface_design) hbonded_atom() (in module pyrosetta.rosetta.protocols.protein_interface_design) HBondEdge (class in pyrosetta.rosetta.protocols.hbnet) HBondFeaturesCreator (class in pyrosetta.rosetta.protocols.features) hbonding_to_res() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) HBondNode (class in pyrosetta.rosetta.protocols.hbnet) HBondParameterFeaturesCreator (class in pyrosetta.rosetta.protocols.features) hbonds() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary method) HBondSet (class in pyrosetta.rosetta.core.scoring.hbonds) HbondsToAtomFilter (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) HbondsToResidueFilter (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) HBondWeightType (class in pyrosetta.rosetta.core.scoring.hbonds) head() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) head_of_queue() (pyrosetta.rosetta.utility.recent_history_queue method) header() (pyrosetta.rosetta.core.io.StructFileRep method) header_from_atom_tree_diff() (in module pyrosetta.rosetta.core.import_pose.atom_tree_diffs) header_information() (pyrosetta.rosetta.core.pose.PDBInfo method) HeaderInformation (class in pyrosetta.rosetta.core.io) HeaderInformation.ExperimentalTechnique (class in pyrosetta.rosetta.core.io) heap_down() (in module pyrosetta.rosetta.protocols.frags) heap_extract() (in module pyrosetta.rosetta.protocols.frags) heap_init() (in module pyrosetta.rosetta.protocols.frags) heap_insert() (in module pyrosetta.rosetta.protocols.frags) heap_replace() (in module pyrosetta.rosetta.protocols.frags) heap_up() (in module pyrosetta.rosetta.protocols.frags) heat_after_cycles() (pyrosetta.rosetta.protocols.moves.MonteCarlo method) heavy_atom_names_match() (in module pyrosetta.rosetta.core.chemical) heavy_atoms_are_within_cutoff() (in module pyrosetta.rosetta.protocols.hbnet) heavy_framework() (pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence method) heavyatom_has_polar_hydrogens() (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) heavyatom_is_an_acceptor() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) HeavyAtomFilter (class in pyrosetta.rosetta.core.chemical) heavyAtoms_end() (pyrosetta.rosetta.core.conformation.Residue method) HeavyAtomWithHydrogensFilter (class in pyrosetta.rosetta.core.chemical) HeavyAtomWithPolarHydrogensFilter (class in pyrosetta.rosetta.core.chemical) HelicalGaussianMover (class in pyrosetta.rosetta.protocols.rbsegment_relax) Helices (class in pyrosetta.rosetta.core.scoring) helices() (pyrosetta.rosetta.core.scoring.SS_Info method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) Helix (class in pyrosetta.rosetta.protocols.fldsgn.topology) helix() (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) helix_fraction() (pyrosetta.rosetta.core.fragment.SecondaryStructure method) helix_id() (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) helix_index() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions method) helix_pairing() (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet method) helix_pairings() (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet method) HelixArchitect (class in pyrosetta.rosetta.protocols.denovo_design.architects) HelixBendFilter (class in pyrosetta.rosetta.protocols.fldsgn.filters) HelixBundleFeaturesCreator (class in pyrosetta.rosetta.protocols.features.helixAssembly) HelixCapFeaturesCreator (class in pyrosetta.rosetta.protocols.features) HelixFromSequence (class in pyrosetta.rosetta.protocols.membrane) HELIXInformation (class in pyrosetta.rosetta.core.io) HELIXInformations() (pyrosetta.rosetta.core.io.StructFileRep method) HelixPairingSet (class in pyrosetta.rosetta.protocols.fldsgn.topology) HelixPerturber (class in pyrosetta.rosetta.protocols.denovo_design.components) HelixRotate (class in pyrosetta.rosetta.protocols.nonlocal) helper() (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) heterogen_formulae() (pyrosetta.rosetta.core.io.StructFileRep method) heterogen_names() (pyrosetta.rosetta.core.io.StructFileRep method) heterogen_synonyms() (pyrosetta.rosetta.core.io.StructFileRep method) HierarchicalDataMap (class in pyrosetta.rosetta.basic.datacache) high_res() (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) high_res_kink_constraint() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) high_temp() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) highest_job_index() (pyrosetta.rosetta.protocols.jd2.JobsContainer method) highest_probability() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config method) highres_reference_energy() (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) highval() (pyrosetta.rosetta.protocols.match.downstream.AtomAngleSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE method) hijack_loop_reading_code_set_loop_line_begin_token() (pyrosetta.rosetta.protocols.loops.PoseNumberedLoopFileReader method) his_tyr_connectivity() (in module pyrosetta.rosetta.protocols.hbnet) history_queue_struct (class in pyrosetta.rosetta.core.pack.interaction_graph) history_size() (pyrosetta.rosetta.utility.recent_history_queue method) hit_list_begin() (pyrosetta.rosetta.protocols.match.Matcher method) hit_list_end() (pyrosetta.rosetta.protocols.match.Matcher method) HitHasher (class in pyrosetta.rosetta.protocols.match) HitNeighborFinder (class in pyrosetta.rosetta.protocols.match) hits() (pyrosetta.rosetta.protocols.match.Matcher method) ho2prime_index() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) hokey_template_workaround() (in module pyrosetta.rosetta.numeric.interpolation.spline) HolesResult (class in pyrosetta.rosetta.core.scoring.packing) host_chain() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) hpatch_score() (pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential method) HPatchEnergy (class in pyrosetta.rosetta.core.pack.interaction_graph) Hpol_index() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) Hpos_apolar() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) Hpos_polar() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) Hpos_polar_sc() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) hr_intersects_hs() (in module pyrosetta.rosetta.numeric.kdtree) HSPairPotential (class in pyrosetta.rosetta.protocols.fldsgn.potentials.sspot) hsv_to_rgb() (in module pyrosetta.rosetta.numeric) ht_for_chitip_atom() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) ht_for_chitip_atoms() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) human_readable_summary() (pyrosetta.rosetta.utility.tag.XMLSchemaDefinition method) hurry() (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) hybridization() (pyrosetta.rosetta.core.chemical.AtomType method) hybridization_rank() (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom method) hydrate_cavities() (in module pyrosetta.rosetta.protocols.hydrate) hydrate_hyfile() (in module pyrosetta.rosetta.protocols.hydrate) hydrate_magnesiums() (in module pyrosetta.rosetta.protocols.magnesium) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) hydrogen_interaction_cutoff2() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) HydrogenAtomFilter (class in pyrosetta.rosetta.core.chemical) HydrogenBondConstraintGenerator (class in pyrosetta.rosetta.protocols.constraint_generator) HydrogenBondInfo (class in pyrosetta.rosetta.protocols.constraint_generator) hydrophobic_constraint_strength() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) HydrophobicityProfileSimilarity (class in pyrosetta.rosetta.protocols.frag_picker.scores) HydrophobicitySimilarity (class in pyrosetta.rosetta.protocols.frag_picker.scores) hyper_tan() (in module pyrosetta.rosetta.numeric.kinematic_closure)