Index – H

H (pyrosetta.rosetta.core.chemical.element.Elements attribute) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.hbDon property) h (pyrosetta.rosetta.protocols.sic_dock.Rose property) H1 (pyrosetta.rosetta.protocols.antibody.CDRNameEnum attribute) h1 (pyrosetta.rosetta.protocols.antibody.CDRNameEnum attribute) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Antibody_Database_Result property) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastResult property) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Results property) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_ResultSet property) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_SubstitutionMatrixResult property) h1() (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairing method) H1_10_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H1_12_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H1_13_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H1_13_10 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H1_13_11 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H1_13_2 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H1_13_3 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H1_13_4 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H1_13_5 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H1_13_6 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H1_13_7 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H1_13_8 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H1_13_9 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H1_13_cis9_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H1_14_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H1_15_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H1_16_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H1_pattern() (pyrosetta.rosetta.protocols.antibody.grafting.RegExManager method) h1_sequence() (pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence method) H2 (pyrosetta.rosetta.protocols.antibody.CDRNameEnum attribute) h2 (pyrosetta.rosetta.protocols.antibody.CDRNameEnum attribute) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Antibody_Database_Result property) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastResult property) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Results property) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_ResultSet property) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_SubstitutionMatrixResult property) h2() (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairing method) H2_10_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H2_10_2 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H2_10_3 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H2_10_4 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H2_10_5 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H2_10_6 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H2_10_7 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H2_10_8 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H2_10_9 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H2_12_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H2_15_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H2_8_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H2_9_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H2_9_2 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H2_9_3 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) h2_sequence() (pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence method) h2o_hbond (pyrosetta.rosetta.core.scoring.ScoreType attribute) h2o_hbond_score_1way() (pyrosetta.rosetta.core.scoring.WaterAdductHBondPotential method) H2O_HBOND_SET (pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType.Enum attribute) h2o_intra (pyrosetta.rosetta.core.scoring.ScoreType attribute) H3 (pyrosetta.rosetta.protocols.antibody.CDRNameEnum attribute) h3 (pyrosetta.rosetta.protocols.antibody.CDRNameEnum attribute) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Antibody_Database_Result property) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastResult property) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Results property) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_ResultSet property) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_SubstitutionMatrixResult property) H3_10_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H3_10_2 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H3_10_3 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H3_10_cis5_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H3_11_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H3_11_2 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H3_12_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H3_12_2 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H3_12_cis9_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H3_13_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H3_13_2 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H3_13_3 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H3_13_cis7_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H3_13_cis8_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H3_14_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H3_14_2 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H3_14_3 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H3_14_4 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H3_14_cis7_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H3_15_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H3_15_2 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H3_16_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H3_16_2 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H3_17_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H3_18_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H3_18_2 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H3_19_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H3_20_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H3_21_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H3_22_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H3_24_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H3_26_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H3_5_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H3_5_2 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H3_6_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H3_7_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H3_7_2 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H3_7_3 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H3_7_cis4_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H3_8_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H3_8_2 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H3_9_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H3_9_2 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) H3_base_library (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler property) 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) H3BaseTypeEnum (class in pyrosetta.rosetta.protocols.antibody) H3BaseTypeEnum_start (pyrosetta.rosetta.protocols.antibody.H3BaseTypeEnum attribute) H3BaseTypeEnum_total (pyrosetta.rosetta.protocols.antibody.H3BaseTypeEnum attribute) H3CterInsert (class in pyrosetta.rosetta.protocols.antibody) H3PerturbCCD (class in pyrosetta.rosetta.protocols.antibody) H3RefineCCD (class in pyrosetta.rosetta.protocols.antibody) H4 (pyrosetta.rosetta.protocols.antibody.CDRNameEnum attribute) h4 (pyrosetta.rosetta.protocols.antibody.CDRNameEnum attribute) H5PyFragmentStoreProvider (class in pyrosetta.protocols.h5_fragment_store_provider) H5StructureStoreProvider (class in pyrosetta.protocols.h5_structure_store_provider) h_ (pyrosetta.rosetta.core.scoring.hbonds.SSWeightParameters property) H_ACCEPTOR (pyrosetta.rosetta.core.chemical.AtomProperty attribute) H_ALA (pyrosetta.rosetta.protocols.match.ProbeRadius attribute) H_ARO (pyrosetta.rosetta.protocols.match.ProbeRadius attribute) H_atom_id() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) H_chain_last_loop (pyrosetta.rosetta.protocols.antibody.CDRNameEnum attribute) h_deriv (pyrosetta.rosetta.core.scoring.hbonds.HBondDerivs property) H_DONOR (pyrosetta.rosetta.core.chemical.AtomProperty attribute) h_ind() (pyrosetta.rosetta.core.scoring.hbonds.HBDerivAssigner method) H_pos() (pyrosetta.rosetta.protocols.match.upstream.OriginalBackboneBuildPoint method) (pyrosetta.rosetta.protocols.match.upstream.ProteinBackboneBuildPoint method) H_SS (pyrosetta.rosetta.protocols.comparative_modeling.features.SSType attribute) HA_atom_id() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) HA_pos() (pyrosetta.rosetta.protocols.match.upstream.OriginalBackboneBuildPoint method) (pyrosetta.rosetta.protocols.match.upstream.ProteinBackboneBuildPoint method) hack_aro (pyrosetta.rosetta.core.scoring.ScoreType attribute) HACK_dump_helices() (in module pyrosetta.rosetta.core.scoring.motif) HACK_dump_helix() (in module pyrosetta.rosetta.core.scoring.motif) hack_fillup_frag_designabilities() (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) HackAroEnergy (class in pyrosetta.rosetta.core.energy_methods) HackAroEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) Hairpin (class in pyrosetta.rosetta.core.scoring) hairpin_list_ (pyrosetta.rosetta.core.scoring.Hairpins property) Hairpins (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) HamiltonianExchange (class in pyrosetta.rosetta.protocols.canonical_sampling) HamiltonianExchangeCreator (class in pyrosetta.rosetta.protocols.canonical_sampling) handle_function_expression() (pyrosetta.rosetta.numeric.expression_parser.BooleanExpressionCreator method) (pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator method) (pyrosetta.rosetta.numeric.expression_parser.SimpleExpressionCreator method) (pyrosetta.rosetta.protocols.optimize_weights.WrappedOptEExpressionCreator method) (pyrosetta.rosetta.protocols.pack_daemon.EntityFuncExpressionCreator method) (pyrosetta.rosetta.protocols.pack_daemon.VectorExpressionCreator method) handle_interrupt() (pyrosetta.rosetta.protocols.jd2.VectorPoseJobDistributor method) handle_mover_tag() (pyrosetta.rosetta.protocols.splice.SpliceIn method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceInTail method) (pyrosetta.rosetta.protocols.splice.SpliceOut method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceOutTail method) handle_structured_xml_error() (in module pyrosetta.rosetta.utility.tag) handle_tail_mover_tag() (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody method) handle_variable_expression() (pyrosetta.rosetta.core.select.residue_selector.SelectorLogicParser method) (pyrosetta.rosetta.numeric.expression_parser.BooleanExpressionCreator method) (pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator method) (pyrosetta.rosetta.numeric.expression_parser.SimpleExpressionCreator method) (pyrosetta.rosetta.protocols.optimize_weights.WrappedOptEExpressionCreator method) (pyrosetta.rosetta.protocols.pack_daemon.EntityFuncExpressionCreator method) (pyrosetta.rosetta.protocols.pack_daemon.VectorExpressionCreator method) handle_xml_error() (in module pyrosetta.rosetta.utility.tag) (pyrosetta.rosetta.utility.tag.XMLErrorHandler method) handle_xml_warning() (in module pyrosetta.rosetta.utility.tag) (pyrosetta.rosetta.utility.tag.XMLErrorHandler method) handles_metric_value() (in module pyrosetta.rosetta.basic) Hankel (class in pyrosetta.rosetta.core.scoring.fiber_diffraction) 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) hard_crossover() (pyrosetta.rosetta.core.scoring.etable.etrie.TrieCountPairGeneric method) HarmonicFunc (class in pyrosetta.rosetta.core.scoring.func) Haro_index() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) Haro_scOrbH (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsLookup attribute) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsLookup.h_type attribute) has() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.basic.datacache.BasicDataCache method) (pyrosetta.rosetta.basic.datacache.ConstDataMap method) (pyrosetta.rosetta.basic.datacache.DataCache_basic_datacache_CacheableData_t method) (pyrosetta.rosetta.basic.datacache.DataCache_CacheableData method) (pyrosetta.rosetta.basic.datacache.DataCache_core_pose_datacache_CacheableObserver_t method) (pyrosetta.rosetta.basic.datacache.DataMap method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableMap method) (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.id.AtomID_Map_AtomID method) (pyrosetta.rosetta.core.id.AtomID_Map_bool method) (pyrosetta.rosetta.core.id.AtomID_Map_bool_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_id_TorsionID_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_scoring_packstat_LR_AtomData_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_scoring_packstat_LR_MP_AtomData_t method) (pyrosetta.rosetta.core.id.AtomID_Map_double_t method) (pyrosetta.rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t method) (pyrosetta.rosetta.core.id.AtomID_Map_Real method) (pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t method) (pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_optimization_DOF_Node_t method) (pyrosetta.rosetta.core.id.AtomID_Map_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.core.id.AtomID_Map_utility_vector1_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.core.id.AtomID_Map_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.core.id.BondID method) (pyrosetta.rosetta.core.id.NamedAtomID_Map_bool_t method) (pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t method) (pyrosetta.rosetta.core.id.NamedAtomID_Map_NamedAtomID method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerLinks 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.cppdb.connection_info method) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.Pharmacophore method) (pyrosetta.rosetta.protocols.loops.Loops method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.NoFailDataMap method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentResidueMap method) (pyrosetta.rosetta.utility.keys.KeyLookup_utility_options_OptionKey_t static method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_AnyOptionKey_utility_options_VariantOption_utility_options_ScalarOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_AnyVectorOptionKey_utility_options_VariantOption_utility_options_VectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_BooleanOptionKey_utility_options_BooleanOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_BooleanVectorOptionKey_utility_options_BooleanVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_FileOptionKey_utility_options_FileOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_FileVectorOptionKey_utility_options_FileVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_IntegerOptionKey_utility_options_IntegerOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_IntegerVectorOptionKey_utility_options_IntegerVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_OptionKey_utility_options_OptionTypes_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_PathOptionKey_utility_options_PathOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_PathVectorOptionKey_utility_options_PathVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_RealOptionKey_utility_options_RealOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_RealVectorOptionKey_utility_options_RealVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_ResidueChainVectorOptionKey_utility_options_ResidueChainVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_StringOptionKey_utility_options_StringOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_StringVectorOptionKey_utility_options_StringVectorOption_t method) (pyrosetta.rosetta.utility.options.OptionCollection method) (pyrosetta.rosetta.utility.thread.MutableCache_const_core_chemical_ResidueTypeSet__star__core_pack_palette_BaseTypeList_t method) has_additional_output() (pyrosetta.rosetta.core.chemical.modifications.ChemistryBase method) (pyrosetta.rosetta.protocols.chemistries.Chemistry method) (pyrosetta.rosetta.protocols.chemistries.PatchChemistry method) (pyrosetta.rosetta.protocols.chemistries.WrappedBaseChemistry method) has_algorithm() (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) has_alias() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) has_another_job() (pyrosetta.rosetta.protocols.rna.setup.RNA_CSA_JobDistributor method) (pyrosetta.rosetta.protocols.rna.setup.RNA_JobDistributor method) (pyrosetta.rosetta.protocols.rna.setup.RNA_MonteCarloJobDistributor method) has_another_pose() (pyrosetta.rosetta.core.import_pose.pose_stream.ExtendedPoseInputStream method) (pyrosetta.rosetta.core.import_pose.pose_stream.LazySilentFilePoseInputStream method) (pyrosetta.rosetta.core.import_pose.pose_stream.MetaPoseInputStream method) (pyrosetta.rosetta.core.import_pose.pose_stream.PDBPoseInputStream method) (pyrosetta.rosetta.core.import_pose.pose_stream.PoseInputStream method) (pyrosetta.rosetta.core.import_pose.pose_stream.SilentFilePoseInputStream method) (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.ScalarOption_T_utility_options_BooleanOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_FileOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_IntegerOptionKey_int_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_PathOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_RealOptionKey_double_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_StringOptionKey_std_string_t method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_BooleanVectorOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_FileVectorOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_IntegerVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_PathVectorOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_RealVectorOptionKey_double_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_ResidueChainVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_StringVectorOptionKey_std_string_t method) has_any_true_selection() (in module pyrosetta.rosetta.core.select.residue_selector) has_aromatic() (in module pyrosetta.rosetta.protocols.constel) has_atom() (pyrosetta.rosetta.core.chemical.AtomTypeSet method) (pyrosetta.rosetta.protocols.frag_picker.CSTalosIO 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_id() (pyrosetta.rosetta.core.pose.toolbox.AtomID_Mapper method) has_atom_info() (pyrosetta.rosetta.core.kinematics.Edge method) has_atom_type() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer method) has_atomistic_energies() (pyrosetta.rosetta.core.energy_methods.AACompositionEnergy method) (pyrosetta.rosetta.core.energy_methods.AARepeatEnergy method) (pyrosetta.rosetta.core.energy_methods.Abego method) (pyrosetta.rosetta.core.energy_methods.ArgCationPiEnergy method) (pyrosetta.rosetta.core.energy_methods.AromaticBackboneRestraintEnergy method) (pyrosetta.rosetta.core.energy_methods.AspartimidePenaltyEnergy method) (pyrosetta.rosetta.core.energy_methods.BranchEnergy method) (pyrosetta.rosetta.core.energy_methods.Burial_v2Energy method) (pyrosetta.rosetta.core.energy_methods.BurialEnergy method) (pyrosetta.rosetta.core.energy_methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.CCS_IMMSEnergy method) (pyrosetta.rosetta.core.energy_methods.CenHBEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairMotifDegreeEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairMotifEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CentroidDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.energy_methods.ChemicalShiftAnisotropyEnergy method) (pyrosetta.rosetta.core.energy_methods.ContactOrderEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextDependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextIndependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingEnergy method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingFAEnergy method) (pyrosetta.rosetta.core.energy_methods.CustomAtomPairEnergy method) (pyrosetta.rosetta.core.energy_methods.D2H_SA_Energy method) (pyrosetta.rosetta.core.energy_methods.DEEREnergy method) (pyrosetta.rosetta.core.energy_methods.DEPC_MS_Energy method) (pyrosetta.rosetta.core.energy_methods.dfire.DFIRE_Energy method) (pyrosetta.rosetta.core.energy_methods.DipolarCouplingEnergy method) (pyrosetta.rosetta.core.energy_methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.energy_methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.energy_methods.DisulfideMatchingEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_DihedralEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.DNAChiEnergy method) (pyrosetta.rosetta.core.energy_methods.DNATorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.DumpTrajectoryEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAllAtomCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAtomwiseEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensEnergy method) (pyrosetta.rosetta.core.energy_methods.EnvEnergy method) (pyrosetta.rosetta.core.energy_methods.EnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.ExactOccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAll method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAro method) (pyrosetta.rosetta.core.energy_methods.FA_GrpElecEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbenvEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbsolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FACTSEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCBEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCGEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPSolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FastDensEnergy method) (pyrosetta.rosetta.core.energy_methods.FastSAXSEnergy method) (pyrosetta.rosetta.core.energy_methods.FiberDiffractionEnergy method) (pyrosetta.rosetta.core.energy_methods.FiberDiffractionEnergyDens method) (pyrosetta.rosetta.core.energy_methods.FreeDOF_Energy method) (pyrosetta.rosetta.core.energy_methods.FullatomDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.GaussianOverlapEnergy method) (pyrosetta.rosetta.core.energy_methods.GenBornEnergy method) (pyrosetta.rosetta.core.energy_methods.GenericBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.GoapEnergy method) (pyrosetta.rosetta.core.energy_methods.HackAroEnergy method) (pyrosetta.rosetta.core.energy_methods.HolesEnergy method) (pyrosetta.rosetta.core.energy_methods.HRF_MSLabelingEnergy method) (pyrosetta.rosetta.core.energy_methods.HRFDynamicsEnergy method) (pyrosetta.rosetta.core.energy_methods.HybridVDW_Energy method) (pyrosetta.rosetta.core.energy_methods.HydroxylTorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.IntermolEnergy method) (pyrosetta.rosetta.core.energy_methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.energy_methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.energy_methods.LK_hack method) (pyrosetta.rosetta.core.energy_methods.LK_PolarNonPolarEnergy method) (pyrosetta.rosetta.core.energy_methods.LoopCloseEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCbetaEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvPenalties method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneLipo method) (pyrosetta.rosetta.core.energy_methods.MgEnergy method) (pyrosetta.rosetta.core.energy_methods.MHCEpitopeEnergy method) (pyrosetta.rosetta.core.energy_methods.MissingEnergy method) (pyrosetta.rosetta.core.energy_methods.MotifDockEnergy method) (pyrosetta.rosetta.core.energy_methods.MPCbetaEnergy method) (pyrosetta.rosetta.core.energy_methods.MPEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.MPHelicalityEnergy method) (pyrosetta.rosetta.core.energy_methods.MPPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.energy_methods.MPSpanAngleEnergy method) (pyrosetta.rosetta.core.energy_methods.MPSpanInsertionEnergy method) (pyrosetta.rosetta.core.energy_methods.MultipoleElecEnergy method) (pyrosetta.rosetta.core.energy_methods.NetChargeEnergy method) (pyrosetta.rosetta.core.energy_methods.NPDHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy_onebody method) (pyrosetta.rosetta.core.energy_methods.OmegaTetherEnergy method) (pyrosetta.rosetta.core.energy_methods.OtherPoseEnergy method) (pyrosetta.rosetta.core.energy_methods.P_AA_Energy method) (pyrosetta.rosetta.core.energy_methods.P_AA_pp_Energy method) (pyrosetta.rosetta.core.energy_methods.P_AA_ss_Energy method) (pyrosetta.rosetta.core.energy_methods.PackStatEnergy method) (pyrosetta.rosetta.core.energy_methods.PairEnergy method) (pyrosetta.rosetta.core.energy_methods.PeptideBondEnergy method) (pyrosetta.rosetta.core.energy_methods.pHEnergy method) (pyrosetta.rosetta.core.energy_methods.PointWaterEnergy method) (pyrosetta.rosetta.core.energy_methods.PoissonBoltzmannEnergy method) (pyrosetta.rosetta.core.energy_methods.ProClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.ProQ_Energy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy2B method) (pyrosetta.rosetta.core.energy_methods.RamaPreProEnergy method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergyNoncanonical method) (pyrosetta.rosetta.core.energy_methods.ResidualDipolarCouplingEnergy method) (pyrosetta.rosetta.core.energy_methods.ResidualDipolarCouplingEnergy_Rohl method) (pyrosetta.rosetta.core.energy_methods.RG_Energy_Fast method) (pyrosetta.rosetta.core.energy_methods.RG_Energy_RNA method) (pyrosetta.rosetta.core.energy_methods.RG_LocalEnergy method) (pyrosetta.rosetta.core.energy_methods.RingClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.RMS_Energy method) (pyrosetta.rosetta.core.energy_methods.RNA_BulgeEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_ChemicalMappingEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_CoarseDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_DataBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FA_ElecEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomStackingEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomVDW_BasePhosphate method) (pyrosetta.rosetta.core.energy_methods.RNA_JR_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_LJ_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_MgPointEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PairwiseLowResolutionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PartitionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_StubCoordinateEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SugarCloseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_TorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_VDW_Energy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResPairDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResStackEnergy method) (pyrosetta.rosetta.core.energy_methods.SA_Energy method) (pyrosetta.rosetta.core.energy_methods.SASAEnergy method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergy method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyCEN method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyFA method) (pyrosetta.rosetta.core.energy_methods.SecondaryStructureEnergy method) (pyrosetta.rosetta.core.energy_methods.SequenceDependentRefEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.SplitUnfoldedTwoBodyEnergy method) (pyrosetta.rosetta.core.energy_methods.SSElementMotifContactEnergy method) (pyrosetta.rosetta.core.energy_methods.StackElecEnergy method) (pyrosetta.rosetta.core.energy_methods.SuckerEnergy method) (pyrosetta.rosetta.core.energy_methods.SugarBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.SurfEnergy method) (pyrosetta.rosetta.core.energy_methods.SurfVolEnergy method) (pyrosetta.rosetta.core.energy_methods.SymmetricLigandEnergy method) (pyrosetta.rosetta.core.energy_methods.TNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.UnfoldedStateEnergy method) (pyrosetta.rosetta.core.energy_methods.VdWTinkerEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductIntraEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterSpecificEnergy method) (pyrosetta.rosetta.core.energy_methods.XtalMLEnergy method) (pyrosetta.rosetta.core.energy_methods.YHHPlanarityEnergy method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenRotDunEnergy method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.ApproximateBuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.lk_dome.LK_DomePackEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.carbon_hbonds.CarbonHBondEnergy method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintsEnergy method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergy method) (pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy method) (pyrosetta.rosetta.core.scoring.interface_.DDPscore method) (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentOneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentOneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondAngleEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondLengthEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntra method) (pyrosetta.rosetta.core.scoring.methods.MMTorsionEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerRefEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy method) (pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.nv.NVscore method) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsScore method) (pyrosetta.rosetta.core.scoring.packing.HolesEnergyRes method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.sym_e.symEnergy method) (pyrosetta.rosetta.core.scoring.vdwaals.VDW_Energy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.membrane.scoring.FaWaterToBilayerEnergy method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSEnergy method) (pyrosetta.rosetta.protocols.nmr.pre.PREEnergy method) (pyrosetta.rosetta.protocols.nmr.rdc.RDCEnergy method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.EnsembleEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainEnvEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainPairEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_Energy method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_Energy_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_Energy_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_Energy_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.ResidualDipolarCouplingEnergyRigidSegments method) (pyrosetta.rosetta.protocols.scoring.methods.saxs.PDDFEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.SpecialRotamerEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.TargetClashEnergy method) (pyrosetta.rosetta.protocols.scoring.VDW_GridEnergy method) has_atomistic_pairwise_energies() (pyrosetta.rosetta.core.energy_methods.AACompositionEnergy method) (pyrosetta.rosetta.core.energy_methods.AARepeatEnergy method) (pyrosetta.rosetta.core.energy_methods.Abego method) (pyrosetta.rosetta.core.energy_methods.ArgCationPiEnergy method) (pyrosetta.rosetta.core.energy_methods.AromaticBackboneRestraintEnergy method) (pyrosetta.rosetta.core.energy_methods.AspartimidePenaltyEnergy method) (pyrosetta.rosetta.core.energy_methods.BranchEnergy method) (pyrosetta.rosetta.core.energy_methods.Burial_v2Energy method) (pyrosetta.rosetta.core.energy_methods.BurialEnergy method) (pyrosetta.rosetta.core.energy_methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.CCS_IMMSEnergy method) (pyrosetta.rosetta.core.energy_methods.CenHBEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairMotifDegreeEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairMotifEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CentroidDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.energy_methods.ChemicalShiftAnisotropyEnergy method) (pyrosetta.rosetta.core.energy_methods.ContactOrderEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextDependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextIndependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingEnergy method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingFAEnergy method) (pyrosetta.rosetta.core.energy_methods.CustomAtomPairEnergy method) (pyrosetta.rosetta.core.energy_methods.D2H_SA_Energy method) (pyrosetta.rosetta.core.energy_methods.DEEREnergy method) (pyrosetta.rosetta.core.energy_methods.DEPC_MS_Energy method) (pyrosetta.rosetta.core.energy_methods.dfire.DFIRE_Energy method) (pyrosetta.rosetta.core.energy_methods.DipolarCouplingEnergy method) (pyrosetta.rosetta.core.energy_methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.energy_methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.energy_methods.DisulfideMatchingEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_DihedralEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.DNAChiEnergy method) (pyrosetta.rosetta.core.energy_methods.DNATorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.DumpTrajectoryEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAllAtomCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAtomwiseEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensEnergy method) (pyrosetta.rosetta.core.energy_methods.EnvEnergy method) (pyrosetta.rosetta.core.energy_methods.EnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.ExactOccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAll method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAro method) (pyrosetta.rosetta.core.energy_methods.FA_GrpElecEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbenvEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbsolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FACTSEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCBEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCGEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPSolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FastDensEnergy method) (pyrosetta.rosetta.core.energy_methods.FastSAXSEnergy method) (pyrosetta.rosetta.core.energy_methods.FiberDiffractionEnergy method) (pyrosetta.rosetta.core.energy_methods.FiberDiffractionEnergyDens method) (pyrosetta.rosetta.core.energy_methods.FreeDOF_Energy method) (pyrosetta.rosetta.core.energy_methods.FullatomDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.GaussianOverlapEnergy method) (pyrosetta.rosetta.core.energy_methods.GenBornEnergy method) (pyrosetta.rosetta.core.energy_methods.GenericBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.GoapEnergy method) (pyrosetta.rosetta.core.energy_methods.HackAroEnergy method) (pyrosetta.rosetta.core.energy_methods.HolesEnergy method) (pyrosetta.rosetta.core.energy_methods.HRF_MSLabelingEnergy method) (pyrosetta.rosetta.core.energy_methods.HRFDynamicsEnergy method) (pyrosetta.rosetta.core.energy_methods.HybridVDW_Energy method) (pyrosetta.rosetta.core.energy_methods.HydroxylTorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.IntermolEnergy method) (pyrosetta.rosetta.core.energy_methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.energy_methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.energy_methods.LK_hack method) (pyrosetta.rosetta.core.energy_methods.LK_PolarNonPolarEnergy method) (pyrosetta.rosetta.core.energy_methods.LoopCloseEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCbetaEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvPenalties method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneLipo method) (pyrosetta.rosetta.core.energy_methods.MgEnergy method) (pyrosetta.rosetta.core.energy_methods.MHCEpitopeEnergy method) (pyrosetta.rosetta.core.energy_methods.MissingEnergy method) (pyrosetta.rosetta.core.energy_methods.MotifDockEnergy method) (pyrosetta.rosetta.core.energy_methods.MPCbetaEnergy method) (pyrosetta.rosetta.core.energy_methods.MPEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.MPHelicalityEnergy method) (pyrosetta.rosetta.core.energy_methods.MPPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.energy_methods.MPSpanAngleEnergy method) (pyrosetta.rosetta.core.energy_methods.MPSpanInsertionEnergy method) (pyrosetta.rosetta.core.energy_methods.MultipoleElecEnergy method) (pyrosetta.rosetta.core.energy_methods.NetChargeEnergy method) (pyrosetta.rosetta.core.energy_methods.NPDHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy_onebody method) (pyrosetta.rosetta.core.energy_methods.OmegaTetherEnergy method) (pyrosetta.rosetta.core.energy_methods.OtherPoseEnergy method) (pyrosetta.rosetta.core.energy_methods.P_AA_Energy method) (pyrosetta.rosetta.core.energy_methods.P_AA_pp_Energy method) (pyrosetta.rosetta.core.energy_methods.P_AA_ss_Energy method) (pyrosetta.rosetta.core.energy_methods.PackStatEnergy method) (pyrosetta.rosetta.core.energy_methods.PairEnergy method) (pyrosetta.rosetta.core.energy_methods.PeptideBondEnergy method) (pyrosetta.rosetta.core.energy_methods.pHEnergy method) (pyrosetta.rosetta.core.energy_methods.PointWaterEnergy method) (pyrosetta.rosetta.core.energy_methods.PoissonBoltzmannEnergy method) (pyrosetta.rosetta.core.energy_methods.ProClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.ProQ_Energy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy2B method) (pyrosetta.rosetta.core.energy_methods.RamaPreProEnergy method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergyNoncanonical method) (pyrosetta.rosetta.core.energy_methods.ResidualDipolarCouplingEnergy method) (pyrosetta.rosetta.core.energy_methods.ResidualDipolarCouplingEnergy_Rohl method) (pyrosetta.rosetta.core.energy_methods.RG_Energy_Fast method) (pyrosetta.rosetta.core.energy_methods.RG_Energy_RNA method) (pyrosetta.rosetta.core.energy_methods.RG_LocalEnergy method) (pyrosetta.rosetta.core.energy_methods.RingClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.RMS_Energy method) (pyrosetta.rosetta.core.energy_methods.RNA_BulgeEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_ChemicalMappingEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_CoarseDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_DataBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FA_ElecEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomStackingEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomVDW_BasePhosphate method) (pyrosetta.rosetta.core.energy_methods.RNA_JR_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_LJ_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_MgPointEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PairwiseLowResolutionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PartitionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_StubCoordinateEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SugarCloseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_TorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_VDW_Energy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResPairDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResStackEnergy method) (pyrosetta.rosetta.core.energy_methods.SA_Energy method) (pyrosetta.rosetta.core.energy_methods.SASAEnergy method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergy method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyCEN method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyFA method) (pyrosetta.rosetta.core.energy_methods.SecondaryStructureEnergy method) (pyrosetta.rosetta.core.energy_methods.SequenceDependentRefEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.SplitUnfoldedTwoBodyEnergy method) (pyrosetta.rosetta.core.energy_methods.SSElementMotifContactEnergy method) (pyrosetta.rosetta.core.energy_methods.StackElecEnergy method) (pyrosetta.rosetta.core.energy_methods.SuckerEnergy method) (pyrosetta.rosetta.core.energy_methods.SugarBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.SurfEnergy method) (pyrosetta.rosetta.core.energy_methods.SurfVolEnergy method) (pyrosetta.rosetta.core.energy_methods.SymmetricLigandEnergy method) (pyrosetta.rosetta.core.energy_methods.TNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.UnfoldedStateEnergy method) (pyrosetta.rosetta.core.energy_methods.VdWTinkerEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductIntraEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterSpecificEnergy method) (pyrosetta.rosetta.core.energy_methods.XtalMLEnergy method) (pyrosetta.rosetta.core.energy_methods.YHHPlanarityEnergy method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenRotDunEnergy method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.ApproximateBuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.lk_dome.LK_DomePackEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.carbon_hbonds.CarbonHBondEnergy method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintsEnergy method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergy method) (pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy method) (pyrosetta.rosetta.core.scoring.interface_.DDPscore method) (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentOneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentOneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondAngleEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondLengthEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntra method) (pyrosetta.rosetta.core.scoring.methods.MMTorsionEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerRefEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy method) (pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.nv.NVscore method) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsScore method) (pyrosetta.rosetta.core.scoring.packing.HolesEnergyRes method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.sym_e.symEnergy method) (pyrosetta.rosetta.core.scoring.vdwaals.VDW_Energy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.membrane.scoring.FaWaterToBilayerEnergy method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSEnergy method) (pyrosetta.rosetta.protocols.nmr.pre.PREEnergy method) (pyrosetta.rosetta.protocols.nmr.rdc.RDCEnergy method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.EnsembleEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainEnvEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainPairEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_Energy method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_Energy_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_Energy_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_Energy_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.ResidualDipolarCouplingEnergyRigidSegments method) (pyrosetta.rosetta.protocols.scoring.methods.saxs.PDDFEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.SpecialRotamerEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.TargetClashEnergy method) (pyrosetta.rosetta.protocols.scoring.VDW_GridEnergy method) has_been_instantiated() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor static method) (pyrosetta.rosetta.protocols.jd2.BOINCJobDistributor static method) (pyrosetta.rosetta.protocols.jd2.FileSystemJobDistributor static method) (pyrosetta.rosetta.protocols.jd2.JobDistributor static method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor static method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor static method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor static method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor static method) (pyrosetta.rosetta.protocols.jd2.ShuffleFileSystemJobDistributor static method) (pyrosetta.rosetta.protocols.jd2.VectorPoseJobDistributor static method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorJobDistributor static method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor static method) has_behavior() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) has_bind (pyrosetta.rosetta.protocols.ligand_docking.ProtLigPair_info property) has_binder() (pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub method) has_bulge() (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing method) has_C_atom() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) has_CA_atom() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) has_cache() (pyrosetta.rosetta.core.energy_methods.PBLifetimeCache 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_chainbreak() (pyrosetta.rosetta.core.util.ChainbreakUtil method) has_chainbreaks_to_close() (pyrosetta.rosetta.protocols.topology_broker.TopologyBroker method) has_chemical_shifts() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) has_clash() (pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelConformer method) has_cluster_for_cdr() (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) has_comment() (pyrosetta.rosetta.core.import_pose.PDBSilentStruct method) (pyrosetta.rosetta.core.io.silent.BinarySilentStruct method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct method) (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.protocols.forge.remodel.LineObject property) has_constraints() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.protocols.abinitio.Template method) (pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet method) (pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet method) has_conventional_residue() (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameters method) has_coordinates() (pyrosetta.rosetta.core.fragment.BBTorsionAndAnglesSRFD method) (pyrosetta.rosetta.core.fragment.BBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) has_custom_variant_types() (pyrosetta.rosetta.core.chemical.ResidueProperties method) has_cut() (pyrosetta.rosetta.core.environment.FoldTreeSketch method) has_data() (pyrosetta.rosetta.core.scoring.epr_deer.DEERDataCache method) (pyrosetta.rosetta.core.simple_metrics.SimpleMetricStruct method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OutputStructureStore method) has_data_int() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) has_data_real() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) has_data_str() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData 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.ScalarOption_T_utility_options_BooleanOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_FileOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_IntegerOptionKey_int_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_PathOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_RealOptionKey_double_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_StringOptionKey_std_string_t method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_BooleanVectorOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_FileVectorOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_IntegerVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_PathVectorOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_RealVectorOptionKey_double_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_ResidueChainVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_StringVectorOptionKey_std_string_t method) has_density() (pyrosetta.rosetta.protocols.loop_grower.DensSkeleton method) has_density_map() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer 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_design_info_ (pyrosetta.rosetta.protocols.forge.remodel.RemodelData property) has_dof() (pyrosetta.rosetta.core.conformation.symmetry.SymDof method) (pyrosetta.rosetta.core.pose.Pose method) has_dof_constraints() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet method) (pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet method) has_domain() (pyrosetta.rosetta.core.pose.toolbox.AtomLevelDomainMap method) has_dy (pyrosetta.rosetta.numeric.interpolation.spline.Point property) has_energy() (pyrosetta.rosetta.core.import_pose.PDBSilentStruct method) (pyrosetta.rosetta.core.io.silent.BinarySilentStruct method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) has_energy_method() (pyrosetta.rosetta.core.scoring.ScoringManager method) has_entry() (pyrosetta.rosetta.protocols.frag_picker.CSTalosIO method) (pyrosetta.rosetta.protocols.frag_picker.PhiPsiTalosIO method) has_evaluator() (pyrosetta.rosetta.protocols.abinitio.HedgeArchive method) (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax method) (pyrosetta.rosetta.protocols.abinitio.IterativeBase method) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid method) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.VarianceStatisticsArchive method) has_exclude_residues_vector() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_Energy_parameters_manager method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_Energy_parameters_manager_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_parameters_manager_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_Energy_parameters_manager_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_Energy_parameters_manager_Ts4 method) has_exclude_residues_vector_changed() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_Energy_parameters_manager method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_Energy_parameters_manager_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_parameters_manager_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_Energy_parameters_manager_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_Energy_parameters_manager_Ts4 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_explicit_Hs() (in module pyrosetta.rosetta.core.chemical.rdkit) has_extra_parameter() (pyrosetta.rosetta.core.chemical.AtomTypeSet method) has_f1_force() (pyrosetta.rosetta.core.scoring.epr_deer.DEERDataCache method) has_f2_force() (pyrosetta.rosetta.core.scoring.epr_deer.DEERDataCache 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) (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) has_free_upper_terminus() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) has_frequencies() (pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDatabase method) has_frequency() (pyrosetta.rosetta.protocols.denovo_design.task_operations.AAFrequencies method) (pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDatabase method) has_generated_residue_type() (pyrosetta.rosetta.core.chemical.ResidueTypeSetCache 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_implicit_Hs() (in module pyrosetta.rosetta.core.chemical.rdkit) has_incomplete_connection() (pyrosetta.rosetta.core.conformation.Residue method) has_incomplete_connections() (in module pyrosetta.rosetta.protocols.ligand_docking) has_inherent_position (pyrosetta.rosetta.core.chemical.carbohydrates.SugarModificationsNomenclatureTableRow property) 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) (pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet method) (pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet method) has_job() (pyrosetta.rosetta.protocols.jd2.JobsContainer method) has_job_previously_been_output() (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryJobQueen method) (pyrosetta.rosetta.protocols.jd3.full_model.FullModelJobQueen method) (pyrosetta.rosetta.protocols.jd3.JobQueen method) (pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueenChecker method) (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsJobQueen method) has_jump() (pyrosetta.rosetta.core.environment.FoldTreeSketch method) has_jump_access() (pyrosetta.rosetta.core.environment.DofPassport method) has_jump_neighbor() (pyrosetta.rosetta.core.environment.FoldTreeSketch.Node method) has_just_simple_cycles() (pyrosetta.rosetta.core.scoring.loop_graph.LoopGraph method) has_label() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) has_lb_function() (pyrosetta.rosetta.numeric.interpolation.spline.CompoundInterpolator method) (pyrosetta.rosetta.numeric.interpolation.spline.Interpolator method) (pyrosetta.rosetta.numeric.interpolation.spline.SimpleInterpolator method) has_low_per_atom_sasa() (pyrosetta.rosetta.protocols.constel.FilterBySASA static method) has_lower_connect() (pyrosetta.rosetta.core.conformation.Residue method) has_lower_residue() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) has_mainchain_bidirectional_linkage_to_child() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) has_mainchain_exocyclic_linkage_to_child() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo 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_methods() (pyrosetta.rosetta.core.pack.interaction_graph.ResidueArrayAnnealingEvaluator method) has_model() (pyrosetta.rosetta.protocols.abinitio.PairingStatEntry method) has_multiple_citations() (pyrosetta.rosetta.basic.citation_manager.CitationCollection 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_ncaa (pyrosetta.rosetta.protocols.forge.remodel.LineObject property) has_neighbor() (pyrosetta.rosetta.core.environment.FoldTreeSketch.Node method) has_next() (pyrosetta.rosetta.cppdb.backend.result method) (pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph method) has_next_level() (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.HierarchicalLevel method) has_node() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree method) (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) has_node_corresponding_to_residue() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) has_non_residue_pair_constraints() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet method) (pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet method) has_nonzero_weight() (pyrosetta.rosetta.core.scoring.DockingScoreFunction method) (pyrosetta.rosetta.core.scoring.MinScoreScoreFunction method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricScoreFunction method) (pyrosetta.rosetta.protocols.flexpack.OtherContextScoreFunction 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.FArray1D_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_ObjexxFCL_FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBIndNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_ObjexxFCL_FArray2D_float__star__t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_ObjexxFCL_ubyte_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2P_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_std_complex_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_std_vector_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_unsigned_int_std_allocator_unsigned_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3P_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_int_t method) (pyrosetta.rosetta.ObjexxFCL.Observer method) (pyrosetta.rosetta.ObjexxFCL.ObserverMulti method) (pyrosetta.rosetta.ObjexxFCL.ObserverSingle method) has_observer_of_type() (in module pyrosetta.rosetta.protocols.network) has_omega() (pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData method) has_open_slaves() (pyrosetta.rosetta.protocols.jd2.SingleFileBuffer method) (pyrosetta.rosetta.protocols.jd2.WriteFileSFB method) has_orbital() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) has_orbital_types() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) HAS_ORBITALS (pyrosetta.rosetta.core.chemical.AtomProperty attribute) has_orientation_and_pleating() (in module pyrosetta.rosetta.core.scoring.dssp) (pyrosetta.rosetta.protocols.jumping.JumpSample method) has_packer_palette() (pyrosetta.rosetta.core.pack.task.TaskFactory method) has_paired_residue() (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing method) has_pairing() (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet method) has_pairings() (pyrosetta.rosetta.protocols.abinitio.Templates method) has_parent_remark() (pyrosetta.rosetta.core.import_pose.PDBSilentStruct method) (pyrosetta.rosetta.core.io.silent.BinarySilentStruct method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct method) (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) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) has_path() (pyrosetta.rosetta.protocols.motifs.Motif method) (pyrosetta.rosetta.protocols.motifs.SingleMotif method) has_peptide_neighbor() (pyrosetta.rosetta.core.environment.FoldTreeSketch.Node method) has_pH_His() (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) has_physical_cut (pyrosetta.rosetta.protocols.environment.claims.JumpElement property) has_physical_Hs() (in module pyrosetta.rosetta.core.chemical.rdkit) has_polymer_dependent_groups() (pyrosetta.rosetta.core.chemical.ResidueType method) has_pore() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle method) (pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry method) has_precomputed_move() (pyrosetta.rosetta.protocols.stepwise.modeler.precomputed.PrecomputedLibraryMover method) has_prefix() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) has_previous() (pyrosetta.rosetta.protocols.legacy_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_proline() (pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet method) has_property() (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.AtomProperties method) (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueProperties method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) has_proton() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D method) (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) has_prox_termini() (in module pyrosetta.rosetta.protocols.constel) has_pseudobonds() (pyrosetta.rosetta.core.scoring.trie.CPDataCorrespondence method) has_range1() (pyrosetta.rosetta.core.conformation.symmetry.SymDof method) has_range1_lower() (pyrosetta.rosetta.core.conformation.symmetry.SymDof method) has_range1_upper() (pyrosetta.rosetta.core.conformation.symmetry.SymDof method) has_range2() (pyrosetta.rosetta.core.conformation.symmetry.SymDof method) has_range2_lower() (pyrosetta.rosetta.core.conformation.symmetry.SymDof method) has_range2_upper() (pyrosetta.rosetta.core.conformation.symmetry.SymDof 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_remark() (pyrosetta.rosetta.protocols.motifs.Motif method) (pyrosetta.rosetta.protocols.motifs.SingleMotif 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) (pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet method) (pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet method) has_residue_selector() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) has_residue_type_set() (pyrosetta.rosetta.core.chemical.ChemicalManager method) has_resnum() (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSamplerComb method) has_resource() (pyrosetta.rosetta.basic.datacache.DataMap method) (pyrosetta.rosetta.basic.resource_manager.ResourceManager method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.NoFailDataMap method) has_resource_in_memory() (pyrosetta.rosetta.basic.resource_manager.ResourceManager method) has_resource_loader() (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderFactory method) has_restype() (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) has_restype_with_name3() (pyrosetta.rosetta.core.chemical.ResidueTypeSetCache method) has_rna_secstruct_legacy() (in module pyrosetta.rosetta.core.pose.rna.secstruct_legacy) has_rotamer_set_for_residue() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSets method) has_sc_orbitals() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) has_score() (pyrosetta.rosetta.protocols.mpi_refinement.MultiObjective method) has_segment() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPairing method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixSheetPairing method) (pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing method) (pyrosetta.rosetta.protocols.denovo_design.components.StrandPairing method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) has_segment_group() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) has_seq_label() (pyrosetta.rosetta.core.environment.SequenceAnnotation method) has_sequence_claimer() (pyrosetta.rosetta.protocols.topology_broker.TopologyBroker 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_silent_struct_type() (pyrosetta.rosetta.core.io.silent.SilentStructFactory method) has_sm_data() (in module pyrosetta.rosetta.core.simple_metrics) has_stored_constraints() (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsManager method) has_subset() (pyrosetta.rosetta.core.select.residue_selector.CachedResidueSubset method) has_subset_prefix() (pyrosetta.rosetta.core.select.residue_selector.CachedResidueSubset 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_task() (pyrosetta.rosetta.protocols.task_operations.STMStoredTask method) has_task_operations() (pyrosetta.rosetta.core.pack.task.TaskFactory method) has_template() (pyrosetta.rosetta.core.import_pose.libraries.RNA_JumpLibrary method) (pyrosetta.rosetta.protocols.abinitio.Templates 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.core.chemical.rotamers.RotamerLibrarySpecificationFactory method) (pyrosetta.rosetta.core.pack.palette.CustomBaseTypePackerPalette method) (pyrosetta.rosetta.core.pack.palette.PackerPaletteFactory method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibraryFactory method) (pyrosetta.rosetta.core.pack.task.operation.ResFilterFactory method) (pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationFactory method) (pyrosetta.rosetta.core.pack.task.operation.TaskOperationFactory method) (pyrosetta.rosetta.core.select.jump_selector.JumpSelectorFactory method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSelectorFactory method) (pyrosetta.rosetta.core.simple_metrics.SimpleMetricFactory method) (pyrosetta.rosetta.protocols.chemistries.ChemistryFactory method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGeneratorFactory method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerFactory method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.ClusterMetricFactory method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.NoFailDataMap method) has_ub_function() (pyrosetta.rosetta.numeric.interpolation.spline.CompoundInterpolator method) (pyrosetta.rosetta.numeric.interpolation.spline.Interpolator method) (pyrosetta.rosetta.numeric.interpolation.spline.SimpleInterpolator 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_valid_moves() (pyrosetta.rosetta.protocols.hybridization.ChunkTrialMover method) has_value() (in module pyrosetta.rosetta.utility.json_spirit) (pyrosetta.rosetta.core.import_pose.libraries.BasePairStepLibrary method) (pyrosetta.rosetta.protocols.denovo_design.components.EnumeratedVectorSelector_utility_vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_std_allocator_std_shared_ptr_const_protocols_denovo_design_components_Segment_t method) (pyrosetta.rosetta.protocols.denovo_design.components.VectorSelector_utility_vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_std_allocator_std_shared_ptr_const_protocols_denovo_design_components_Segment_t method) (pyrosetta.rosetta.protocols.mean_field.AAMatrix method) (pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t method) (pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t method) (pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.utility.deep_copy_vector1_std_shared_ptr_core_chemical_Orbital_t 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) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_BooleanVectorOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_FileVectorOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_IntegerVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_PathVectorOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_RealVectorOptionKey_double_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_ResidueChainVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_StringVectorOptionKey_std_string_t method) has_variant_type() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) (pyrosetta.rosetta.core.conformation.Residue method) has_virtual_rna_residue_variant_type() (in module pyrosetta.rosetta.core.pose.rna) has_waters() (pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo method) (pyrosetta.rosetta.core.scoring.lkball.LKD_ResidueInfo method) has_zero_weight() (pyrosetta.rosetta.core.scoring.DockingScoreFunction method) (pyrosetta.rosetta.core.scoring.MinScoreScoreFunction method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricScoreFunction method) (pyrosetta.rosetta.protocols.flexpack.OtherContextScoreFunction method) hASA_patch_energy() (pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential method) hasAtomBookmark() (pyrosetta.rosetta.RDKit.ROMol method) (pyrosetta.rosetta.RDKit.RWMol method) hasBondBookmark() (pyrosetta.rosetta.RDKit.ROMol method) (pyrosetta.rosetta.RDKit.RWMol method) HasDisulfideFilter (class in pyrosetta.rosetta.protocols.pose_sewing.filters) HasDisulfideFilterCreator (class in pyrosetta.rosetta.protocols.pose_sewing.filters) hash() (pyrosetta.rosetta.protocols.environment.AutoCutData method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement method) (pyrosetta.rosetta.protocols.multistate_design.PosType method) 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method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.RepGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SiteGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationMetaGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGrid method) hash_function() (pyrosetta.rosetta.std.unordered_map_basic_datacache_ResRotPair_float_basic_datacache_ResRotPairHasher_std_equal_to_basic_datacache_ResRotPair_std_allocator_std_pair_const_basic_datacache_ResRotPair_float_t method) 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hbe_dPBAaPES_DNAsepother (pyrosetta.rosetta.core.scoring.hbonds.HBEvalType attribute) hbe_dPBAaPES_DNAsepPM1 (pyrosetta.rosetta.core.scoring.hbonds.HBEvalType attribute) hbe_dPBAaPES_RNAsepother (pyrosetta.rosetta.core.scoring.hbonds.HBEvalType attribute) hbe_dPBAaPES_RNAsepPM1 (pyrosetta.rosetta.core.scoring.hbonds.HBEvalType attribute) hbe_dPBAaRRI_DNAsepother (pyrosetta.rosetta.core.scoring.hbonds.HBEvalType attribute) hbe_dPBAaRRI_DNAsepPM1 (pyrosetta.rosetta.core.scoring.hbonds.HBEvalType attribute) hbe_dPBAaRRI_RNAsepother (pyrosetta.rosetta.core.scoring.hbonds.HBEvalType attribute) hbe_dPBAaRRI_RNAsepPM1 (pyrosetta.rosetta.core.scoring.hbonds.HBEvalType attribute) hbe_dPROTEIN_BB_AMIDEaAROMATIC_HYDROXYLsepother (pyrosetta.rosetta.core.scoring.hbonds.HBEvalType attribute) hbe_dPROTEIN_BB_AMIDEaAROMATIC_HYDROXYLsepPM1 (pyrosetta.rosetta.core.scoring.hbonds.HBEvalType attribute) hbe_dPROTEIN_BB_AMIDEaCARBOXAMIDEsepother (pyrosetta.rosetta.core.scoring.hbonds.HBEvalType attribute) hbe_dPROTEIN_BB_AMIDEaCARBOXAMIDEsepPM1 (pyrosetta.rosetta.core.scoring.hbonds.HBEvalType attribute) hbe_dPROTEIN_BB_AMIDEaCARBOXYLsepother (pyrosetta.rosetta.core.scoring.hbonds.HBEvalType attribute) hbe_dPROTEIN_BB_AMIDEaCARBOXYLsepPM1 (pyrosetta.rosetta.core.scoring.hbonds.HBEvalType attribute) hbe_dPROTEIN_BB_AMIDEaIMIDAZOL_DELTAsepother (pyrosetta.rosetta.core.scoring.hbonds.HBEvalType attribute) hbe_dPROTEIN_BB_AMIDEaIMIDAZOL_DELTAsepPM1 (pyrosetta.rosetta.core.scoring.hbonds.HBEvalType attribute) hbe_dPROTEIN_BB_AMIDEaIMIDAZOL_EPSILONsepother (pyrosetta.rosetta.core.scoring.hbonds.HBEvalType attribute) hbe_dPROTEIN_BB_AMIDEaIMIDAZOL_EPSILONsepPM1 (pyrosetta.rosetta.core.scoring.hbonds.HBEvalType attribute) hbe_dPROTEIN_BB_AMIDEaPROTEIN_BB_AMIDEsepM2turn (pyrosetta.rosetta.core.scoring.hbonds.HBEvalType attribute) hbe_dPROTEIN_BB_AMIDEaPROTEIN_BB_AMIDEsepM3turn (pyrosetta.rosetta.core.scoring.hbonds.HBEvalType attribute) hbe_dPROTEIN_BB_AMIDEaPROTEIN_BB_AMIDEsepM4helix 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attribute) hbe_GENERIC_SP2BB_SR (pyrosetta.rosetta.core.scoring.hbonds.HBEvalType attribute) hbe_GENERIC_SP2BSC_LR (pyrosetta.rosetta.core.scoring.hbonds.HBEvalType attribute) hbe_GENERIC_SP2BSC_SR (pyrosetta.rosetta.core.scoring.hbonds.HBEvalType attribute) hbe_GENERIC_SP2SCSC_LR (pyrosetta.rosetta.core.scoring.hbonds.HBEvalType attribute) hbe_GENERIC_SP2SCSC_SR (pyrosetta.rosetta.core.scoring.hbonds.HBEvalType attribute) hbe_GENERIC_SP3BB_LR (pyrosetta.rosetta.core.scoring.hbonds.HBEvalType attribute) hbe_GENERIC_SP3BB_SR (pyrosetta.rosetta.core.scoring.hbonds.HBEvalType attribute) hbe_GENERIC_SP3BSC_LR (pyrosetta.rosetta.core.scoring.hbonds.HBEvalType attribute) hbe_GENERIC_SP3BSC_SR (pyrosetta.rosetta.core.scoring.hbonds.HBEvalType attribute) hbe_GENERIC_SP3SCSC_LR (pyrosetta.rosetta.core.scoring.hbonds.HBEvalType attribute) hbe_GENERIC_SP3SCSC_SR (pyrosetta.rosetta.core.scoring.hbonds.HBEvalType attribute) hbe_is_BB_type() (in module pyrosetta.rosetta.core.scoring.hbonds) hbe_is_SC_type() (in module pyrosetta.rosetta.core.scoring.hbonds) hbe_MAX (pyrosetta.rosetta.core.scoring.hbonds.HBEvalType attribute) hbe_NONE (pyrosetta.rosetta.core.scoring.hbonds.HBEvalType attribute) hbe_UNKNOWN (pyrosetta.rosetta.core.scoring.hbonds.HBEvalType attribute) hbe_WATERaPROTEIN_BB_AMIDE (pyrosetta.rosetta.core.scoring.hbonds.HBEvalType attribute) HBEnergyList (pyrosetta.rosetta.protocols.sparta.PDB property) HBEvalTuple (class in pyrosetta.rosetta.core.scoring.hbonds) HBEvalType (class in pyrosetta.rosetta.core.scoring.hbonds) HBFadeInterval_from_name() (pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase method) hbgd_AHD (pyrosetta.rosetta.core.scoring.hbonds.HBGeoDimType attribute) hbgd_AHdist (pyrosetta.rosetta.core.scoring.hbonds.HBGeoDimType attribute) hbgd_chi (pyrosetta.rosetta.core.scoring.hbonds.HBGeoDimType attribute) hbgd_cosAHD (pyrosetta.rosetta.core.scoring.hbonds.HBGeoDimType attribute) hbgd_cosBAH (pyrosetta.rosetta.core.scoring.hbonds.HBGeoDimType attribute) hbgd_MAX (pyrosetta.rosetta.core.scoring.hbonds.HBGeoDimType attribute) hbgd_NONE (pyrosetta.rosetta.core.scoring.hbonds.HBGeoDimType attribute) HBGeoDimType (class in pyrosetta.rosetta.core.scoring.hbonds) HBNet (class in pyrosetta.rosetta.protocols.hbnet) hbnet (pyrosetta.rosetta.core.scoring.ScoreType attribute) hbnet_bonus_function_ramping() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) hbnet_energy_ramping_enum_from_string() (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) hbnet_energy_ramping_string_from_enum() (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) hbnet_max_network_size() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) hbnet_one_body_energies() (in module pyrosetta.rosetta.protocols.hbnet) hbnet_symm_one_body_energies() (in module pyrosetta.rosetta.protocols.hbnet) HBNetCreator (class in pyrosetta.rosetta.protocols.hbnet) HBNetEnergy (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy) HBNetEnergyCreator (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy) HBNetEnergyRamp_end_of_list (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergyRamping attribute) HBNetEnergyRamping (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy) HBNetEnergyRampINVALID (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergyRamping attribute) HBNetEnergyRampLinear (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergyRamping attribute) HBNetEnergyRampLogarithmic (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergyRamping attribute) HBNetEnergyRampQuadratic (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergyRamping attribute) HBNetEnergyRampSquareRoot (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergyRamping attribute) HBNetScore (class in pyrosetta.rosetta.protocols.hbnet) HBNetScoreFilterCreator (class in pyrosetta.rosetta.protocols.hbnet) HBNetStapleInterface (class in pyrosetta.rosetta.protocols.hbnet) HBNetStapleInterfaceCreator (class in pyrosetta.rosetta.protocols.hbnet) HBond (class in pyrosetta.rosetta.core.scoring.hbonds) hbond (pyrosetta.rosetta.core.scoring.ScoreType attribute) hbond() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyEdge method) (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) hbond_bb_sc (pyrosetta.rosetta.core.scoring.ScoreType attribute) 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_count (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.DensStructInfo property) hbond_cutoff() (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilter method) hbond_database() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) hbond_derivs_1way() (pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy method) hbond_E_fraction (pyrosetta.rosetta.protocols.analysis.InterfaceData property) hbond_energy() (pyrosetta.rosetta.protocols.pose_metric_calculators.SHOBuriedUnsatisfiedPolarsCalculator method) hbond_energy_comparer() (pyrosetta.rosetta.core.scoring.hbonds.HBond static method) hbond_energy_cutoff() (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric method) (pyrosetta.rosetta.protocols.hbnet.UnsatSelector method) hbond_energy_shift() (pyrosetta.rosetta.core.scoring.hbonds.HBondOptions method) hbond_energy_threshold() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphOptions method) hbond_evaluation_type() (in module pyrosetta.rosetta.core.scoring.hbonds) hbond_exists_in_vector() (in module pyrosetta.rosetta.protocols.hbnet) hbond_graph_from_partial_rotsets() (in module pyrosetta.rosetta.core.pack.hbonds) hbond_intra (pyrosetta.rosetta.core.scoring.ScoreType attribute) hbond_lr_bb (pyrosetta.rosetta.core.scoring.ScoreType attribute) hbond_lr_bb_sc (pyrosetta.rosetta.core.scoring.ScoreType attribute) hbond_method (pyrosetta.rosetta.core.scoring.methods.EnergyMethods attribute) hbond_metric() (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilter method) hbond_options() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNodeData method) (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_ref (pyrosetta.rosetta.core.scoring.ScoreType attribute) hbond_res_data (pyrosetta.rosetta.core.scoring.min_single_data attribute) hbond_respair_data (pyrosetta.rosetta.core.scoring.min_pair_data attribute) hbond_sc (pyrosetta.rosetta.core.scoring.ScoreType attribute) HBOND_SET (pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType.Enum attribute) hbond_set (pyrosetta.rosetta.protocols.hbnet.HBondNetStruct property) hbond_set() (pyrosetta.rosetta.core.energy_methods.ExactOccludedHbondSolEnergy method) hbond_sr_bb (pyrosetta.rosetta.core.scoring.ScoreType attribute) hbond_sr_bb_sc (pyrosetta.rosetta.core.scoring.ScoreType attribute) HBOND_TRIE_COLLECTION (pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType.Enum attribute) hbond_vec (pyrosetta.rosetta.protocols.hbnet.HBondNetStruct property) hbond_wat (pyrosetta.rosetta.core.scoring.ScoreType attribute) hbond_weight() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) hbond_wtd_ (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ReweightableRepEnergy property) HBondAcceptorFilter (class in pyrosetta.rosetta.protocols.ligand_docking) HBondAcceptorFilterCreator (class in pyrosetta.rosetta.protocols.ligand_docking) HBondBonusOptions (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty) HBondCommon (class in pyrosetta.rosetta.protocols.constel) HBondDatabase (class in pyrosetta.rosetta.core.scoring.hbonds) HBondDerivs (class in pyrosetta.rosetta.core.scoring.hbonds) HBondDonorFilter (class in pyrosetta.rosetta.protocols.ligand_docking) HBondDonorFilterCreator (class in pyrosetta.rosetta.protocols.ligand_docking) hbonded() (in module pyrosetta.rosetta.protocols.protein_interface_design) hbonded_atom() (in module pyrosetta.rosetta.protocols.protein_interface_design) HBondEdge (class in pyrosetta.rosetta.core.scoring.hbonds.graph) HBondEnergy (class in pyrosetta.rosetta.core.scoring.hbonds) HBondEnergyCreator (class in pyrosetta.rosetta.core.scoring.hbonds) HBondFeatures (class in pyrosetta.rosetta.protocols.features) HBondFeaturesCreator (class in pyrosetta.rosetta.protocols.features) HBondGraph (class in pyrosetta.rosetta.core.scoring.hbonds.graph) HBondGraphInitializerIG (class in pyrosetta.rosetta.core.pack.hbonds) HBondInfo (class in pyrosetta.rosetta.core.scoring.hbonds.graph) hbonding_to_res() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) HbondMetric (class in pyrosetta.rosetta.core.simple_metrics.per_residue_metrics) HbondMetricCreator (class in pyrosetta.rosetta.core.simple_metrics.per_residue_metrics) HBondNetStruct (class in pyrosetta.rosetta.protocols.hbnet) HBondNode (class in pyrosetta.rosetta.core.scoring.hbonds.graph) HBondOptions (class in pyrosetta.rosetta.core.scoring.hbonds) HBondParameterFeatures (class in pyrosetta.rosetta.protocols.features) HBondParameterFeaturesCreator (class in pyrosetta.rosetta.protocols.features) HBondResStruct (class in pyrosetta.rosetta.protocols.hbnet) hbonds() (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondEdge method) (pyrosetta.rosetta.core.scoring.hbonds.HBondSet method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_JobResultsSummary method) hbonds_list() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyEdgeData method) HBondSelector (class in pyrosetta.rosetta.protocols.residue_selectors) HBondSelectorCreator (class in pyrosetta.rosetta.protocols.residue_selectors) HBondSet (class in pyrosetta.rosetta.core.scoring.hbonds) HbondsToAtomFilter (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) HbondsToAtomFilterCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) HbondsToResidueFilter (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) HbondsToResidueFilterCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) HBondsTrieVsTrieCachedDataContainer (class in pyrosetta.rosetta.core.scoring.hbonds.hbtrie) HBondTypeManager (class in pyrosetta.rosetta.core.scoring.hbonds) HBondWeightType (class in pyrosetta.rosetta.core.scoring.hbonds) HBP_FinalFullatomRefinementMoveGenerator (class in pyrosetta.rosetta.protocols.helical_bundle_predict) HBP_HelixCoilMoveGenerator (class in pyrosetta.rosetta.protocols.helical_bundle_predict) HBP_MoveGenerator (class in pyrosetta.rosetta.protocols.helical_bundle_predict) HBP_SigmoidalTemperatureScheduleGenerator (class in pyrosetta.rosetta.protocols.helical_bundle_predict) HBP_TemperatureScheduleGenerator (class in pyrosetta.rosetta.protocols.helical_bundle_predict) HBPHelix (class in pyrosetta.rosetta.protocols.helical_bundle_predict) HBPHelixAssignments (class in pyrosetta.rosetta.protocols.helical_bundle_predict) HBPHelixParameters (class in pyrosetta.rosetta.protocols.helical_bundle_predict) HBPoly1D_from_name() (pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase method) HBS_POST (pyrosetta.rosetta.core.chemical.VariantType attribute) HBS_PRE (pyrosetta.rosetta.core.chemical.VariantType attribute) HBSeqSep (class in pyrosetta.rosetta.core.scoring.hbonds) HbsPatcher (class in pyrosetta.rosetta.protocols.simple_moves.hbs) hbw_LR_BB (pyrosetta.rosetta.core.scoring.hbonds.HBondWeightType attribute) hbw_LR_BB_SC (pyrosetta.rosetta.core.scoring.hbonds.HBondWeightType attribute) hbw_MAX (pyrosetta.rosetta.core.scoring.hbonds.HBondWeightType attribute) hbw_NONE (pyrosetta.rosetta.core.scoring.hbonds.HBondWeightType attribute) hbw_SC (pyrosetta.rosetta.core.scoring.hbonds.HBondWeightType attribute) hbw_SR_BB (pyrosetta.rosetta.core.scoring.hbonds.HBondWeightType attribute) hbw_SR_BB_SC (pyrosetta.rosetta.core.scoring.hbonds.HBondWeightType attribute) He (pyrosetta.rosetta.core.chemical.element.Elements attribute) head() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) head_item() (pyrosetta.rosetta.utility.heap method) head_of_queue() (pyrosetta.rosetta.utility.recent_history_queue method) HEADER (pyrosetta.rosetta.core.io.pdb.RecordType attribute) 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.CompoundToken (class in pyrosetta.rosetta.core.io) headgroup_type() (pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo method) heap (class in pyrosetta.rosetta.utility) heap_down() (in module pyrosetta.rosetta.protocols.frags) heap_extract() (in module pyrosetta.rosetta.protocols.frags) (pyrosetta.rosetta.utility.heap method) heap_head() (pyrosetta.rosetta.utility.heap method) heap_init() (in module pyrosetta.rosetta.protocols.frags) heap_insert() (in module pyrosetta.rosetta.protocols.frags) (pyrosetta.rosetta.utility.heap method) heap_replace() (in module pyrosetta.rosetta.protocols.frags) (pyrosetta.rosetta.utility.heap method) heap_up() (in module pyrosetta.rosetta.protocols.frags) heat_after_cycles() (pyrosetta.rosetta.protocols.canonical_sampling.BiasedMonteCarlo method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) (pyrosetta.rosetta.protocols.moves.ReplicaExchangeMC method) Heat_ConvergenceCheck (class in pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks) heavy (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyNumbering property) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence property) heavy_atom_names_match() (in module pyrosetta.rosetta.core.chemical) heavy_coords_vector() (pyrosetta.rosetta.core.conformation.UltraLightResidue method) heavy_framework() (pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence method) heavyatom_has_polar_hydrogens() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) heavyatom_heavyatom_energy() (pyrosetta.rosetta.core.scoring.elec.electrie.ElecTrieEvaluator method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEvaluator method) (pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy method) (pyrosetta.rosetta.core.scoring.lkball.lkbtrie.LKBTrieEvaluator method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter method) (pyrosetta.rosetta.core.scoring.vdwaals.VDWTrieEvaluator method) heavyatom_hydrogenatom_energy() (pyrosetta.rosetta.core.scoring.elec.electrie.ElecTrieEvaluator method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEvaluator method) (pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy method) (pyrosetta.rosetta.core.scoring.lkball.lkbtrie.LKBTrieEvaluator method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter method) (pyrosetta.rosetta.core.scoring.vdwaals.VDWTrieEvaluator method) heavyatom_index() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup method) heavyatom_is_an_acceptor() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) HeavyAtomFilter (class in pyrosetta.rosetta.core.chemical) (class in pyrosetta.rosetta.protocols.ligand_docking) HeavyAtomFilterCreator (class in pyrosetta.rosetta.protocols.ligand_docking) HeavyAtomNormalization (class in pyrosetta.rosetta.protocols.qsar.scoring_grid) HeavyAtomWithHydrogensFilter (class in pyrosetta.rosetta.core.chemical) HeavyAtomWithPolarHydrogensFilter (class in pyrosetta.rosetta.core.chemical) HedgeArchive (class in pyrosetta.rosetta.protocols.abinitio) height (pyrosetta.rosetta.core.scoring.sc._PROBE property) helical_substruct_res() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) helical_substructs() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) HelicalBundlePredictApplication (class in pyrosetta.rosetta.protocols.helical_bundle_predict) HelicalBundlePredictApplicationOptions (class in pyrosetta.rosetta.protocols.helical_bundle_predict) HelicalFragment (class in pyrosetta.rosetta.protocols.features.helixAssembly) 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.core.io.pdb.RecordType attribute) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPairing attribute) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPairing.PairingType attribute) (pyrosetta.rosetta.protocols.denovo_design.components.HelixSheetPairing attribute) (pyrosetta.rosetta.protocols.denovo_design.components.HelixSheetPairing.PairingType attribute) (pyrosetta.rosetta.protocols.denovo_design.components.SegmentCounts attribute) (pyrosetta.rosetta.protocols.denovo_design.components.SegmentCounts.SegmentType attribute) (pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing attribute) (pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing.PairingType attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StrandPairing attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StrandPairing.PairingType attribute) helix (pyrosetta.rosetta.protocols.fldsgn.topology.TripletID property) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SecondaryStructureType attribute) helix() (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif method) (pyrosetta.rosetta.protocols.fldsgn.topology.HSSTriplet method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle method) helix_assignment_file() (pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions method) helix_assignment_file_contents() (pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions method) helix_cop() (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle method) helix_cycle() (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif method) helix_cycle_as_string() (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif method) helix_fraction() (pyrosetta.rosetta.core.fragment.SecondaryStructure method) helix_id() (pyrosetta.rosetta.core.scoring.MembraneTopology method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) helix_length() (pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix method) helix_name (pyrosetta.rosetta.core.io.HELIXInformation property) helix_pairing() (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet method) helix_pairings() (pyrosetta.rosetta.protocols.fldsgn.filters.HelixPairingFilter method) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet method) (pyrosetta.rosetta.protocols.parser.BluePrint method) HELIX_SHEET (pyrosetta.rosetta.protocols.denovo_design.components.HelixPairing attribute) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPairing.PairingType attribute) (pyrosetta.rosetta.protocols.denovo_design.components.HelixSheetPairing attribute) (pyrosetta.rosetta.protocols.denovo_design.components.HelixSheetPairing.PairingType attribute) (pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing attribute) (pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing.PairingType attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StrandPairing attribute) (pyrosetta.rosetta.protocols.denovo_design.components.StrandPairing.PairingType attribute) HelixArchitect (class in pyrosetta.rosetta.protocols.denovo_design.architects) HelixArchitectCreator (class in pyrosetta.rosetta.protocols.denovo_design.architects) HelixBendFilter (class in pyrosetta.rosetta.protocols.fldsgn.filters) HelixBendFilterCreator (class in pyrosetta.rosetta.protocols.fldsgn.filters) HelixBundleFeatures (class in pyrosetta.rosetta.protocols.features.helixAssembly) HelixBundleFeaturesCreator (class in pyrosetta.rosetta.protocols.features.helixAssembly) HelixCapFeatures (class in pyrosetta.rosetta.protocols.features) HelixCapFeaturesCreator (class in pyrosetta.rosetta.protocols.features) helixClass (pyrosetta.rosetta.core.io.HELIXInformation property) HelixFromSequence (class in pyrosetta.rosetta.protocols.membrane) HelixFromSequenceCreator (class in pyrosetta.rosetta.protocols.membrane) HelixHelixAngleFilter (class in pyrosetta.rosetta.protocols.simple_filters) HelixHelixAngleFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) helixID (pyrosetta.rosetta.core.io.HELIXInformation property) HELIXInformation (class in pyrosetta.rosetta.core.io) HELIXInformations() (pyrosetta.rosetta.core.io.StructFileRep method) helixjump_picks() (pyrosetta.rosetta.protocols.abinitio.Templates method) HelixKinkFilter (class in pyrosetta.rosetta.protocols.fldsgn.filters) HelixKinkFilterCreator (class in pyrosetta.rosetta.protocols.fldsgn.filters) HelixNCapperMover (class in pyrosetta.rosetta.protocols.helix_capper) HelixPairing (class in pyrosetta.rosetta.protocols.denovo_design.components) (class in pyrosetta.rosetta.protocols.fldsgn.topology) HelixPairing.PairingType (class in pyrosetta.rosetta.protocols.denovo_design.components) HelixPairingFilter (class in pyrosetta.rosetta.protocols.fldsgn.filters) HelixPairingFilterCreator (class in pyrosetta.rosetta.protocols.fldsgn.filters) HelixPairingSet (class in pyrosetta.rosetta.protocols.fldsgn.topology) HelixPerturber (class in pyrosetta.rosetta.protocols.denovo_design.components) HelixScore (class in pyrosetta.rosetta.protocols.sic_dock) HelixSheetPairing (class in pyrosetta.rosetta.protocols.denovo_design.components) HelixSheetPairing.PairingType (class in pyrosetta.rosetta.protocols.denovo_design.components) helper() (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint static method) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraint static method) helper_adds_linker_residue() (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.OctahedralMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.One_Four_BBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.SquarePlanarMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.SquarePyramidalMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TetrahedralMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Thioether_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TrigonalPlanarMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TrigonalPyramidalMetal_Helper method) HEPTOSE (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) HET (pyrosetta.rosetta.core.io.pdb.RecordType attribute) HETATM (pyrosetta.rosetta.core.io.pdb.RecordType attribute) hetero_atom_line() (pyrosetta.rosetta.core.scoring.packstat.CavityBall 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) HETNAM (pyrosetta.rosetta.core.io.pdb.RecordType attribute) HETSYN (pyrosetta.rosetta.core.io.pdb.RecordType attribute) HEXAGONAL (pyrosetta.rosetta.protocols.cryst.SpacegroupSetting attribute) HEXOSE (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) Hf (pyrosetta.rosetta.core.chemical.element.Elements attribute) Hg (pyrosetta.rosetta.core.chemical.element.Elements attribute) HH_helix_end (pyrosetta.rosetta.core.scoring.Helices property) HH_resnum (pyrosetta.rosetta.core.scoring.Helices property) HI_AMBIG (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.QualityClass attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D.QualityClass attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D.QualityClass attribute) HI_NEAR_UNAMBIG (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.QualityClass attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D.QualityClass attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D.QualityClass attribute) HI_UNAMBIG (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.QualityClass attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D.QualityClass attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D.QualityClass attribute) HIERARCHICAL_ADD (pyrosetta.rosetta.basic.ProfTag attribute) HIERARCHICAL_ADD_ELEM_TO_CACHE (pyrosetta.rosetta.basic.ProfTag attribute) HIERARCHICAL_EVALUATE (pyrosetta.rosetta.basic.ProfTag attribute) HIERARCHICAL_FIND (pyrosetta.rosetta.basic.ProfTag attribute) HIERARCHICAL_FIND_ADDRESS (pyrosetta.rosetta.basic.ProfTag attribute) HIERARCHICAL_HYBRID_JD_MPI_SORT_TYPE (class in pyrosetta.rosetta.protocols.cyclic_peptide_predict) HIERARCHICAL_POOL_SIZE (pyrosetta.rosetta.basic.ProfTag attribute) HIERARCHICAL_ROUND (pyrosetta.rosetta.basic.ProfTag attribute) HIERARCHICAL_SORT_ADDRESSES (pyrosetta.rosetta.basic.ProfTag attribute) HierarchicalDataMap (class in pyrosetta.rosetta.basic.datacache) HierarchicalHybridJD_JobResultsSummary (class in pyrosetta.rosetta.protocols.cyclic_peptide_predict) HierarchicalHybridJD_PNearToArbitraryStateSummary (class in pyrosetta.rosetta.protocols.cyclic_peptide_predict) HierarchicalHybridJD_ResultsSummaryBase (class in pyrosetta.rosetta.protocols.cyclic_peptide_predict) HierarchicalHybridJD_RMSDToBestSummary (class in pyrosetta.rosetta.protocols.cyclic_peptide_predict) HierarchicalHybridJD_SASASummary (class in pyrosetta.rosetta.protocols.cyclic_peptide_predict) HierarchicalLevel (class in pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks) HIERARCHY_FIND_ADDRESS (pyrosetta.rosetta.basic.ProfTag attribute) HIERARCHY_GET_NEXT_CANDIDATE (pyrosetta.rosetta.basic.ProfTag attribute) HIERARCHY_RECV_COORDS (pyrosetta.rosetta.basic.ProfTag attribute) HIERARCHY_SEND_COORDS (pyrosetta.rosetta.basic.ProfTag attribute) HIERARCHY_SETUP_TO_RECV (pyrosetta.rosetta.basic.ProfTag attribute) high (pyrosetta.rosetta.protocols.cryst.CheshireCell property) (pyrosetta.rosetta.protocols.make_rot_lib.TorsionRange property) high_res() (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) high_res_angstroms_ (pyrosetta.rosetta.protocols.ligand_docking.LigandArea property) high_res_degrees_ (pyrosetta.rosetta.protocols.ligand_docking.LigandArea property) high_res_kink_constraint() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol method) high_res_outer_cycles() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) high_res_refinement() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) high_temp() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) higher_numbered_node_symmetry_copy_index() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbond 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) highres_score_function() (pyrosetta.rosetta.protocols.moves.MixedMonteCarlo method) HighResDocker (class in pyrosetta.rosetta.protocols.ligand_docking) HighResDockerCreator (class in pyrosetta.rosetta.protocols.ligand_docking) HighResEnsemble (class in pyrosetta.rosetta.protocols.ligand_docking) HighResEnsembleCreator (class in pyrosetta.rosetta.protocols.ligand_docking) 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) Histogram (class in pyrosetta.rosetta.protocols.recces) histogram() (pyrosetta.rosetta.core.scoring.epr_deer.EPRSpinLabel method) histogram_max() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) histogram_min() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) histogram_spacing() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) HistogramCOP_double_double_t (class in pyrosetta.rosetta.numeric.interpolation) histograms() (pyrosetta.rosetta.protocols.simple_moves.DOFHistogramRecorder method) history_queue_struct (class in pyrosetta.rosetta.core.pack.interaction_graph) (class in pyrosetta.rosetta.utility) history_size() (pyrosetta.rosetta.utility.recent_history_queue method) Hit (class in pyrosetta.rosetta.protocols.match) hit() (pyrosetta.rosetta.protocols.match.downstream.TargetRotamerCoords method) HitHasher (class in pyrosetta.rosetta.protocols.match) HitNeighborFinder (class in pyrosetta.rosetta.protocols.match) hits() (pyrosetta.rosetta.protocols.match.Matcher method) hits_potentially_incompatible() (pyrosetta.rosetta.protocols.match.downstream.DownstreamBuilder method) (pyrosetta.rosetta.protocols.match.downstream.LigandConformerBuilder method) (pyrosetta.rosetta.protocols.match.downstream.RigidLigandBuilder method) hits_to_include_with_partial_match() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) (pyrosetta.rosetta.protocols.match.output.WriteUpstreamCoordinateKinemage method) Hmatrices (pyrosetta.rosetta.core.kinematics.jacobian.ModuleType1.screw_construct_struct property) HN_S2 (pyrosetta.rosetta.protocols.sparta.PDB property) Ho (pyrosetta.rosetta.core.chemical.element.Elements attribute) ho2prime_index() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) ho2prime_index_ (pyrosetta.rosetta.core.chemical.rna.RNA_Info property) hoh_ref (pyrosetta.rosetta.core.scoring.ScoreType attribute) hoist_angle_degrees_ (pyrosetta.rosetta.protocols.legacy_sewing.Model property) hokey_template_workaround() (in module pyrosetta.rosetta.numeric.interpolation.spline) holes (pyrosetta.rosetta.core.scoring.ScoreType attribute) holes_decoy (pyrosetta.rosetta.core.scoring.ScoreType attribute) holes_min (pyrosetta.rosetta.core.scoring.ScoreType attribute) holes_min_mean (pyrosetta.rosetta.core.scoring.ScoreType attribute) HOLES_POSE_INFO (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) holes_resl (pyrosetta.rosetta.core.scoring.ScoreType attribute) HolesEnergy (class in pyrosetta.rosetta.core.energy_methods) HolesEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) HolesEnergyRes (class in pyrosetta.rosetta.core.scoring.packing) HolesFilter (class in pyrosetta.rosetta.protocols.simple_filters) HolesFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) HolesParams (class in pyrosetta.rosetta.core.scoring.packing) HolesParamsRes (class in pyrosetta.rosetta.core.scoring.packing) HolesResult (class in pyrosetta.rosetta.core.scoring.packing) HOMO_Tab (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib property) homoFileName (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib property) HomogeneousTransform_Double (class in pyrosetta.rosetta.numeric) HomogeneousTransform_double_t (class in pyrosetta.rosetta.numeric) homooligomer_swap_ (pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringOptions property) hoog_edge_paired() (pyrosetta.rosetta.core.scoring.rna.data.RNA_DMS_LowResolutionPotential method) HOOGSTEEN (pyrosetta.rosetta.core.chemical.rna.BaseEdge attribute) host_chain() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementAuctionMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) hotspot_filter (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags property) hotspot_label() (pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub static method) hotspot_length() (pyrosetta.rosetta.protocols.hotspot_hashing.HotspotStubSet method) HotspotDisjointedFoldTreeMover (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) HotspotDisjointedFoldTreeMoverCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) HotspotHasherMover (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) HotspotHasherMoverCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) HotspotStub (class in pyrosetta.rosetta.protocols.hotspot_hashing) HotspotStubSet (class in pyrosetta.rosetta.protocols.hotspot_hashing) hpairset() (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential method) hpatch (pyrosetta.rosetta.core.scoring.ScoreType attribute) hpatch_score() (pyrosetta.rosetta.core.pack.interaction_graph.SurfacePotential method) HPatchCalculator (class in pyrosetta.rosetta.protocols.pose_metric_calculators) HPatchEnergy (class in pyrosetta.rosetta.core.pack.interaction_graph) HPatchEnergyCreator (class in pyrosetta.rosetta.core.pack.interaction_graph) HPN_CFr (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType attribute) Hpol_bbOrbH (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsLookup attribute) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsLookup.h_type attribute) Hpol_bond_geometry (pyrosetta.rosetta.core.scoring.ScoreType attribute) Hpol_index() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) Hpol_scOrbH (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsLookup attribute) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsLookup.h_type attribute) HPool_RMSD (class in pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks) 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) HRF (pyrosetta.rosetta.core.pose.rna.RNA_ReactivityType attribute) hrf_dynamics (pyrosetta.rosetta.core.scoring.ScoreType attribute) hrf_dynamics_input() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) hrf_ms_labeling (pyrosetta.rosetta.core.scoring.ScoreType attribute) HRF_MSLabelingEnergy (class in pyrosetta.rosetta.core.energy_methods) HRF_MSLabelingEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) HRFDynamicsEnergy (class in pyrosetta.rosetta.core.energy_methods) HRFDynamicsEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) Hs (pyrosetta.rosetta.core.chemical.element.Elements attribute) hs1_dist() (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif method) (pyrosetta.rosetta.protocols.fldsgn.topology.HSSTriplet method) hs1_orient() (pyrosetta.rosetta.protocols.fldsgn.topology.HSSTriplet method) hs2_dist() (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif method) (pyrosetta.rosetta.protocols.fldsgn.topology.HSSTriplet method) hs2_orient() (pyrosetta.rosetta.protocols.fldsgn.topology.HSSTriplet method) hs_angle() (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif method) (pyrosetta.rosetta.protocols.fldsgn.topology.HSSTriplet method) hs_pair (pyrosetta.rosetta.core.scoring.ScoreType attribute) hsheet_dist() (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif method) (pyrosetta.rosetta.protocols.fldsgn.topology.HSSTriplet method) hsheet_elev_angle() (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif method) HSPairPotential (class in pyrosetta.rosetta.protocols.fldsgn.potentials.sspot) hss_triplet() (pyrosetta.rosetta.protocols.fldsgn.topology.HSSTripletSet method) hss_triplet_set() (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential method) hss_triplets() (pyrosetta.rosetta.protocols.fldsgn.topology.HSSTripletSet method) (pyrosetta.rosetta.protocols.parser.BluePrint method) HSSTriplet (class in pyrosetta.rosetta.protocols.fldsgn.topology) HSSTripletFilter (class in pyrosetta.rosetta.protocols.fldsgn.filters) HSSTripletFilterCreator (class in pyrosetta.rosetta.protocols.fldsgn.filters) HSSTripletSet (class in pyrosetta.rosetta.protocols.fldsgn.topology) hsv_to_rgb() (in module pyrosetta.rosetta.numeric) ht() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryTransform method) HT_ang_U1D2 (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalTransform attribute) HT_ang_U2D1 (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalTransform attribute) ht_for_chitip_atom() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) ht_for_chitip_atoms() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) HT_tor_U1D3 (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalTransform attribute) HT_tor_U2D2 (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalTransform attribute) HT_tor_U3D1 (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalTransform attribute) human_readable_summary() (pyrosetta.rosetta.utility.tag.XMLSchemaDefinition method) hurry() (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopRemodel method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) hxl_tors (pyrosetta.rosetta.core.scoring.ScoreType attribute) HYBRID_FA_STANDARD_CENTROID_t (pyrosetta.rosetta.core.chemical.TypeSetMode attribute) HYBRID_MAX (pyrosetta.rosetta.core.chemical.Hybridization attribute) hybrid_vdw (pyrosetta.rosetta.core.scoring.ScoreType attribute) Hybridization (class in pyrosetta.rosetta.core.chemical) hybridization() (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.chemical.orbitals.OrbitalType method) hybridization_rank() (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom method) hybridization_type_from_name() (pyrosetta.rosetta.core.scoring.hbonds.HBondTypeManager static method) hybridize() (pyrosetta.rosetta.protocols.seeded_abinitio.SegmentHybridizer method) HybridizeFoldtreeDynamic (class in pyrosetta.rosetta.protocols.hybridization) HybridizeProtocol (class in pyrosetta.rosetta.protocols.hybridization) HybridizeProtocolCreator (class in pyrosetta.rosetta.protocols.hybridization) HybridVDW_Energy (class in pyrosetta.rosetta.core.energy_methods) HybridVDW_EnergyCreator (class in pyrosetta.rosetta.core.energy_methods) Hydrate (class in pyrosetta.rosetta.protocols.hydrate) hydrate() (pyrosetta.rosetta.protocols.magnesium.MgScanner 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.StepWiseBasicModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) (pyrosetta.rosetta.protocols.stepwise.options.StepWiseBasicOptions method) hydration() (pyrosetta.rosetta.protocols.membrane.scoring.MEnvAtomParams method) hydrogen_interaction (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair property) hydrogen_interaction_cutoff() (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAll method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAro method) (pyrosetta.rosetta.core.energy_methods.RNA_FA_ElecEnergy method) (pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter method) hydrogen_interaction_cutoff2() (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAll method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAro method) (pyrosetta.rosetta.core.energy_methods.NPDHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FA_ElecEnergy method) (pyrosetta.rosetta.core.scoring.elec.electrie.ElecTrieEvaluator method) (pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t method) (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.etable.TableLookupEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEvaluator method) (pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy method) (pyrosetta.rosetta.core.scoring.lkball.lkbtrie.LKBTrieEvaluator method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter method) (pyrosetta.rosetta.core.scoring.vdwaals.VDWTrieEvaluator method) hydrogenatom_heavyatom_energy() (pyrosetta.rosetta.core.scoring.elec.electrie.ElecTrieEvaluator method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEvaluator method) (pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy method) (pyrosetta.rosetta.core.scoring.lkball.lkbtrie.LKBTrieEvaluator method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter method) (pyrosetta.rosetta.core.scoring.vdwaals.VDWTrieEvaluator method) hydrogenatom_hydrogenatom_energy() (pyrosetta.rosetta.core.scoring.elec.electrie.ElecTrieEvaluator method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEvaluator method) (pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy method) (pyrosetta.rosetta.core.scoring.lkball.lkbtrie.LKBTrieEvaluator method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter method) (pyrosetta.rosetta.core.scoring.vdwaals.VDWTrieEvaluator method) HydrogenAtomFilter (class in pyrosetta.rosetta.core.chemical) HydrogenBondConstraintGenerator (class in pyrosetta.rosetta.protocols.constraint_generator) HydrogenBondConstraintGeneratorCreator (class in pyrosetta.rosetta.protocols.constraint_generator) HydrogenBondInfo (class in pyrosetta.rosetta.protocols.constraint_generator) HydrogenBondingAtom (class in pyrosetta.rosetta.protocols.constraint_generator) hydrop_adder (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapParameterOptions property) hydrop_lys_arg_setting (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapParameterOptions property) HYDROPHOBIC (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) hydrophobic_constraint_strength() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) HYDROPHOBIC_SASA (pyrosetta.rosetta.core.scoring.sasa.SasaMethodHPMode attribute) hydrophobic_sasa() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_SASASummary method) hydrophobic_weight() (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapDatabase method) HydrophobicityProfileSimilarity (class in pyrosetta.rosetta.protocols.frag_picker.scores) HydrophobicitySimilarity (class in pyrosetta.rosetta.protocols.frag_picker.scores) hydroxyl_wants_h (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.UnsatCorrectionOptions property) HYDROXYLATION (pyrosetta.rosetta.core.chemical.VariantType attribute) (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric.PTMPredictionMetricModes attribute) HYDROXYLATION1 (pyrosetta.rosetta.core.chemical.VariantType attribute) HYDROXYLATION2 (pyrosetta.rosetta.core.chemical.VariantType attribute) HydroxylTorsionEnergy (class in pyrosetta.rosetta.core.energy_methods) HydroxylTorsionEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) HydroxylTorsionPotential (class in pyrosetta.rosetta.core.scoring) HYDROXYPROLINE_EXCEPTIONS (pyrosetta.rosetta.core.pack.palette.SpecialPackerPaletteBehaviour attribute) hyper_tan() (in module pyrosetta.rosetta.numeric.kinematic_closure) HyperRectangle (class in pyrosetta.rosetta.numeric.kdtree)