Index – L

l (pyrosetta.rosetta.core.scoring.fiber_diffraction.Hankel property) L (pyrosetta.rosetta.protocols.features.RamachandranHash attribute) L() (in module pyrosetta.rosetta.ObjexxFCL.format) l() (pyrosetta.rosetta.core.fragment.FrameList method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections method) (pyrosetta.rosetta.core.scoring.motif.MotifHits method) (pyrosetta.rosetta.core.scoring.motif.ResPairMotifs method) (pyrosetta.rosetta.core.select.residue_selector.ResidueRanges method) (pyrosetta.rosetta.core.select.residue_selector.ResidueVector method) (pyrosetta.rosetta.numeric.Xforms method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.FArray1_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1A_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1A_int_t 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.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_ResultVector method) (pyrosetta.rosetta.protocols.denovo_design.components.BuildPhases 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.NamedSolution method) (pyrosetta.rosetta.protocols.denovo_design.components.NamedSolutions 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.fldsgn.topology.DimerPairings method) (pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface 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.protocols.monte_carlo.AcceptedScores method) (pyrosetta.rosetta.protocols.sewing.hashing.SegmentVector method) (pyrosetta.rosetta.protocols.toolbox.ScoreRmsPoints method) (pyrosetta.rosetta.utility.deep_copy_vector1_std_shared_ptr_core_chemical_Orbital_t method) (pyrosetta.rosetta.utility.vector0_core_conformation_ppo_torsion_bin method) (pyrosetta.rosetta.utility.vector0_core_id_AtomID_Map_bool_t method) (pyrosetta.rosetta.utility.vector0_core_io_AtomInformation method) (pyrosetta.rosetta.utility.vector0_double method) (pyrosetta.rosetta.utility.vector0_float method) (pyrosetta.rosetta.utility.vector0_int method) (pyrosetta.rosetta.utility.vector0_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector0_protocols_flexpack_interaction_graph_FlexbbSparseMatrixIndex method) (pyrosetta.rosetta.utility.vector0_std_list_std_shared_ptr_utility_SimulateMPIMessage_t method) (pyrosetta.rosetta.utility.vector0_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t method) (pyrosetta.rosetta.utility.vector0_std_pair_float_float_t method) (pyrosetta.rosetta.utility.vector0_std_shared_ptr_const_core_select_residue_selector_ResidueSelector_t method) (pyrosetta.rosetta.utility.vector0_std_shared_ptr_const_utility_tag_Tag_t method) (pyrosetta.rosetta.utility.vector0_std_shared_ptr_core_kinematics_tree_Atom_t method) (pyrosetta.rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t method) (pyrosetta.rosetta.utility.vector0_std_shared_ptr_protocols_moves_Mover_t method) (pyrosetta.rosetta.utility.vector0_std_string method) (pyrosetta.rosetta.utility.vector0_unsigned_char method) (pyrosetta.rosetta.utility.vector0_unsigned_long method) (pyrosetta.rosetta.utility.vector0_utility_fixedsizearray0_double_3_t method) (pyrosetta.rosetta.utility.vector0_utility_fixedsizearray0_double_5_t method) (pyrosetta.rosetta.utility.vector0_utility_fixedsizearray0_utility_fixedsizearray0_double_3_3_t method) (pyrosetta.rosetta.utility.vector0_utility_fixedsizearray0_utility_fixedsizearray0_double_5_5_t method) (pyrosetta.rosetta.utility.vector0_utility_fixedsizearray1_double_16_t method) (pyrosetta.rosetta.utility.vector0_utility_vector0_core_io_AtomInformation_std_allocator_core_io_AtomInformation_t method) (pyrosetta.rosetta.utility.vector0_utility_vector0_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector0_utility_vector0_int_std_allocator_int_t method) (pyrosetta.rosetta.utility.vector0_utility_vector0_std_list_std_shared_ptr_utility_SimulateMPIMessage_std_allocator_std_shared_ptr_utility_SimulateMPIMessage_std_allocator_std_list_std_shared_ptr_utility_SimulateMPIMessage_std_allocator_std_shared_ptr_utility_SimulateMPIMessage_t method) (pyrosetta.rosetta.utility.vector0_utility_vector0_std_shared_ptr_const_core_select_residue_selector_ResidueSelector_std_allocator_std_shared_ptr_const_core_select_residue_selector_ResidueSelector_t method) (pyrosetta.rosetta.utility.vector0_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector0_utility_vector1_std_pair_int_int_std_allocator_std_pair_int_int_t method) (pyrosetta.rosetta.utility.vector0_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_basic_citation_manager_AuthorNames method) (pyrosetta.rosetta.utility.vector1_basic_database_schema_generator_Column method) (pyrosetta.rosetta.utility.vector1_basic_database_schema_generator_ForeignKey method) (pyrosetta.rosetta.utility.vector1_basic_database_schema_generator_Index method) (pyrosetta.rosetta.utility.vector1_basic_sampling_orientations_QuatDBMetadata method) (pyrosetta.rosetta.utility.vector1_bool method) (pyrosetta.rosetta.utility.vector1_char method) (pyrosetta.rosetta.utility.vector1_const_utility_vector1_int_std_allocator_int__star_t method) (pyrosetta.rosetta.utility.vector1_core_chemical_AA method) (pyrosetta.rosetta.utility.vector1_core_chemical_Adduct method) (pyrosetta.rosetta.utility.vector1_core_chemical_AtomICoor method) (pyrosetta.rosetta.utility.vector1_core_chemical_AtomType method) (pyrosetta.rosetta.utility.vector1_core_chemical_BondName method) (pyrosetta.rosetta.utility.vector1_core_chemical_io_merge_residue_behavior method) (pyrosetta.rosetta.utility.vector1_core_chemical_MutableResidueConnection method) (pyrosetta.rosetta.utility.vector1_core_chemical_ResConnID method) (pyrosetta.rosetta.utility.vector1_core_chemical_ResidueConnection method) (pyrosetta.rosetta.utility.vector1_core_chemical_ResidueProperty method) (pyrosetta.rosetta.utility.vector1_core_chemical_rings_RingConformer method) (pyrosetta.rosetta.utility.vector1_core_chemical_rings_RingSaturationType method) (pyrosetta.rosetta.utility.vector1_core_chemical_rna_GaussianParameter method) (pyrosetta.rosetta.utility.vector1_core_chemical_rna_PuckerState method) (pyrosetta.rosetta.utility.vector1_core_chemical_VariantType method) (pyrosetta.rosetta.utility.vector1_core_conformation_Atom method) (pyrosetta.rosetta.utility.vector1_core_conformation_PseudoBond method) (pyrosetta.rosetta.utility.vector1_core_conformation_signals_LengthEvent method) (pyrosetta.rosetta.utility.vector1_core_conformation_UltraLightResidue method) (pyrosetta.rosetta.utility.vector1_core_fragment_FragData method) (pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_scores_VallFragmentScore method) (pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_VallResidue method) (pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_VallSection method) (pyrosetta.rosetta.utility.vector1_core_fragment_rna_SYN_ANTI_RESTRICTION method) (pyrosetta.rosetta.utility.vector1_core_id_AtomID method) (pyrosetta.rosetta.utility.vector1_core_id_AtomID_Map_bool_t method) (pyrosetta.rosetta.utility.vector1_core_id_AtomID_Map_core_id_TorsionID_t method) (pyrosetta.rosetta.utility.vector1_core_id_AtomID_Map_std_shared_ptr_core_optimization_DOF_Node_t method) (pyrosetta.rosetta.utility.vector1_core_id_DOF_ID method) (pyrosetta.rosetta.utility.vector1_core_id_NamedAtomID method) (pyrosetta.rosetta.utility.vector1_core_id_TorsionID method) (pyrosetta.rosetta.utility.vector1_core_id_TorsionID_Range method) (pyrosetta.rosetta.utility.vector1_core_io_AtomInformation method) (pyrosetta.rosetta.utility.vector1_core_io_HELIXInformation method) (pyrosetta.rosetta.utility.vector1_core_io_LinkInformation method) (pyrosetta.rosetta.utility.vector1_core_io_ResidueInformation method) (pyrosetta.rosetta.utility.vector1_core_io_SHEETInformation method) (pyrosetta.rosetta.utility.vector1_core_io_silent_SilentEnergy method) (pyrosetta.rosetta.utility.vector1_core_io_SSBondInformation method) (pyrosetta.rosetta.utility.vector1_core_kinematics_AtomWithDOFChange method) (pyrosetta.rosetta.utility.vector1_core_kinematics_Edge method) (pyrosetta.rosetta.utility.vector1_core_kinematics_Jump method) (pyrosetta.rosetta.utility.vector1_core_kinematics_RT method) (pyrosetta.rosetta.utility.vector1_core_kinematics_Stub method) (pyrosetta.rosetta.utility.vector1_core_optimization_DerivCheckDataPoint method) (pyrosetta.rosetta.utility.vector1_core_optimization_DOF_DataPoint method) (pyrosetta.rosetta.utility.vector1_core_pack_annealer_PointDwell method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_1_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_2_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_3_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_4_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_5_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_1_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_2_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_3_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_4_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_5_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_guidance_scoreterms_buried_unsat_penalty_graph_BuriedUnsatPenaltyGraphHbond method) (pyrosetta.rosetta.utility.vector1_core_pack_guidance_scoreterms_buried_unsat_penalty_graph_BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup method) (pyrosetta.rosetta.utility.vector1_core_pack_guidance_scoreterms_sap_BlockParam method) (pyrosetta.rosetta.utility.vector1_core_pack_interaction_graph_DotSphere method) (pyrosetta.rosetta.utility.vector1_core_pack_interaction_graph_exposed_hydrophobic_data method) (pyrosetta.rosetta.utility.vector1_core_pack_interaction_graph_RotamerDots method) (pyrosetta.rosetta.utility.vector1_core_pack_interaction_graph_SparseMatrixIndex method) (pyrosetta.rosetta.utility.vector1_core_pack_rotamer_set_ContinuousRotamerSet method) (pyrosetta.rosetta.utility.vector1_core_pack_scmin_ResidueAtomTreeCollectionMomento method) (pyrosetta.rosetta.utility.vector1_core_pack_task_operation_ResiduePDBIndexIs_ChainPos method) (pyrosetta.rosetta.utility.vector1_core_pack_task_ResidueLevelTask_ method) (pyrosetta.rosetta.utility.vector1_core_pose_PDBInfo_AtomRecord method) (pyrosetta.rosetta.utility.vector1_core_pose_PDBInfo_ResidueRecord method) (pyrosetta.rosetta.utility.vector1_core_pose_Pose method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_Atom_Bin method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_BasePair method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_BaseStack method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_RNA_Datum method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_RNA_Reactivity method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_RNA_SuiteInfo method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_VDW_RepScreenInfo method) (pyrosetta.rosetta.utility.vector1_core_pose_UnrecognizedAtomRecord method) (pyrosetta.rosetta.utility.vector1_core_scoring_bin_transitions_BT_PROPERTIES method) (pyrosetta.rosetta.utility.vector1_core_scoring_CSA method) (pyrosetta.rosetta.utility.vector1_core_scoring_DC method) (pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair method) (pyrosetta.rosetta.utility.vector1_core_scoring_disulfides_DisulfideDerivativeAtom method) (pyrosetta.rosetta.utility.vector1_core_scoring_dssp_Pairing method) (pyrosetta.rosetta.utility.vector1_core_scoring_dssp_StrandPairing method) (pyrosetta.rosetta.utility.vector1_core_scoring_EMapVector method) (pyrosetta.rosetta.utility.vector1_core_scoring_epr_deer_EPRSpinLabel method) (pyrosetta.rosetta.utility.vector1_core_scoring_etable_EtableParamsOnePair method) (pyrosetta.rosetta.utility.vector1_core_scoring_etable_etrie_GenericResidueConnectionData method) (pyrosetta.rosetta.utility.vector1_core_scoring_fiber_diffraction_OneGaussianScattering method) (pyrosetta.rosetta.utility.vector1_core_scoring_GenTorsionParams method) (pyrosetta.rosetta.utility.vector1_core_scoring_Hairpin method) (pyrosetta.rosetta.utility.vector1_core_scoring_hbonds_graph_HBondEdge method) (pyrosetta.rosetta.utility.vector1_core_scoring_hbonds_graph_HBondNode method) (pyrosetta.rosetta.utility.vector1_core_scoring_hbonds_HBEvalTuple method) (pyrosetta.rosetta.utility.vector1_core_scoring_hbonds_HBondWeightType method) (pyrosetta.rosetta.utility.vector1_core_scoring_loop_graph_Loop method) (pyrosetta.rosetta.utility.vector1_core_scoring_loop_graph_LoopCycle method) (pyrosetta.rosetta.utility.vector1_core_scoring_mhc_epitope_energy_AlleleMatrix method) (pyrosetta.rosetta.utility.vector1_core_scoring_motif_MotifHit method) (pyrosetta.rosetta.utility.vector1_core_scoring_motif_ResPairMotif method) (pyrosetta.rosetta.utility.vector1_core_scoring_motif_Xfres method) (pyrosetta.rosetta.utility.vector1_core_scoring_nmr_pcs_PCSSingle method) (pyrosetta.rosetta.utility.vector1_core_scoring_nmr_pre_PRESingle method) (pyrosetta.rosetta.utility.vector1_core_scoring_nmr_rdc_RDCSingle method) (pyrosetta.rosetta.utility.vector1_core_scoring_packing_Ball method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_CavityBall method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_CavityBallCluster method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_LR_AtomData method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_LR_MP_AtomData method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_SimplePDB_Atom method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_Sphere method) (pyrosetta.rosetta.utility.vector1_core_scoring_power_diagram_SAnode method) (pyrosetta.rosetta.utility.vector1_core_scoring_RDC method) (pyrosetta.rosetta.utility.vector1_core_scoring_RDC_Rohl method) (pyrosetta.rosetta.utility.vector1_core_scoring_rna_RNA_Motif method) (pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType method) (pyrosetta.rosetta.utility.vector1_core_scoring_SmallAtNb method) (pyrosetta.rosetta.utility.vector1_core_scoring_SmoothScoreTermCoeffs method) (pyrosetta.rosetta.utility.vector1_core_scoring_SpringParams method) (pyrosetta.rosetta.utility.vector1_core_scoring_tableID method) (pyrosetta.rosetta.utility.vector1_core_select_residue_selector_ResidueRange method) (pyrosetta.rosetta.utility.vector1_core_sequence_Line method) (pyrosetta.rosetta.utility.vector1_core_sequence_SequenceAlignment method) (pyrosetta.rosetta.utility.vector1_double method) (pyrosetta.rosetta.utility.vector1_float method) (pyrosetta.rosetta.utility.vector1_int method) (pyrosetta.rosetta.utility.vector1_long method) (pyrosetta.rosetta.utility.vector1_numeric_CubicPolynomial method) (pyrosetta.rosetta.utility.vector1_numeric_geometry_hashing_Ball method) (pyrosetta.rosetta.utility.vector1_numeric_histograms_TwoDHistogram_unsigned_long_long_t method) (pyrosetta.rosetta.utility.vector1_numeric_HomogeneousTransform_double_t method) (pyrosetta.rosetta.utility.vector1_numeric_interpolation_spline_BicubicSpline method) (pyrosetta.rosetta.utility.vector1_numeric_interpolation_spline_CubicSpline method) (pyrosetta.rosetta.utility.vector1_numeric_interpolation_spline_interp_range method) (pyrosetta.rosetta.utility.vector1_numeric_interpolation_spline_Point method) (pyrosetta.rosetta.utility.vector1_numeric_MultiDimensionalHistogram method) (pyrosetta.rosetta.utility.vector1_numeric_random_WeightedSampler method) (pyrosetta.rosetta.utility.vector1_numeric_RocPoint method) (pyrosetta.rosetta.utility.vector1_numeric_urs_Quat method) (pyrosetta.rosetta.utility.vector1_numeric_xyzMatrix_double_t method) (pyrosetta.rosetta.utility.vector1_numeric_xyzTransform_double_t method) (pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_numeric_xyzVector_float_t method) (pyrosetta.rosetta.utility.vector1_ObjexxFCL_FArray1D_double_t method) (pyrosetta.rosetta.utility.vector1_ObjexxFCL_FArray2D_double_t method) (pyrosetta.rosetta.utility.vector1_ObjexxFCL_FArray2D_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_protocols_abinitio_AlternativePairings method) (pyrosetta.rosetta.utility.vector1_protocols_abinitio_ClassicAbinitio_StageID method) (pyrosetta.rosetta.utility.vector1_protocols_abinitio_PairingStatEntry method) (pyrosetta.rosetta.utility.vector1_protocols_abinitio_StageID method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_AntibodyNumberingSchemeEnum method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_CDRDefinitionEnum method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_CDRNameEnum method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_clusters_CDRClusterEnum method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_clusters_ClusterData method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_design_PDBNumbering method) (pyrosetta.rosetta.utility.vector1_protocols_backbone_moves_local_backbone_mover_Residue method) (pyrosetta.rosetta.utility.vector1_protocols_backrub_BackrubSegment method) (pyrosetta.rosetta.utility.vector1_protocols_branch_angle_BranchCoef1 method) (pyrosetta.rosetta.utility.vector1_protocols_branch_angle_BranchCoef2 method) (pyrosetta.rosetta.utility.vector1_protocols_canonical_sampling_DbTrajectoryRecorder_Frame method) (pyrosetta.rosetta.utility.vector1_protocols_canonical_sampling_TorsionSpec method) (pyrosetta.rosetta.utility.vector1_protocols_cartesian_CartesianAtom method) (pyrosetta.rosetta.utility.vector1_protocols_cartesian_MD_Angle method) (pyrosetta.rosetta.utility.vector1_protocols_cartesian_MD_Bond method) (pyrosetta.rosetta.utility.vector1_protocols_cartesian_MD_HarmonicDihedral method) (pyrosetta.rosetta.utility.vector1_protocols_cluster_DataPoint method) (pyrosetta.rosetta.utility.vector1_protocols_cluster_Exemplar method) (pyrosetta.rosetta.utility.vector1_protocols_constraints_additional_ConstraintEvaluator method) (pyrosetta.rosetta.utility.vector1_protocols_contact_map_Contact method) (pyrosetta.rosetta.utility.vector1_protocols_cyclic_peptide_PSM_StubMode method) (pyrosetta.rosetta.utility.vector1_protocols_denovo_design_components_BondInfo method) (pyrosetta.rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution method) (pyrosetta.rosetta.utility.vector1_protocols_denovo_design_components_StructureSlice method) (pyrosetta.rosetta.utility.vector1_protocols_features_TaskOperationFeatures_Taskop_id_name_factory_ method) (pyrosetta.rosetta.utility.vector1_protocols_fold_from_loops_utils_NubSegment method) (pyrosetta.rosetta.utility.vector1_protocols_forge_build_Interval method) (pyrosetta.rosetta.utility.vector1_protocols_frag_picker_LazySortedVector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_protocols_frag_picker_CompareTotalScore_t method) (pyrosetta.rosetta.utility.vector1_protocols_helical_bundle_BPC_Parameters method) (pyrosetta.rosetta.utility.vector1_protocols_hotspot_hashing_VectorPair method) (pyrosetta.rosetta.utility.vector1_protocols_hybridization_detailedControlsTagSetting method) (pyrosetta.rosetta.utility.vector1_protocols_indexed_structure_store_BackboneStub method) (pyrosetta.rosetta.utility.vector1_protocols_jd2_archive_Batch method) (pyrosetta.rosetta.utility.vector1_protocols_jd3_chunk_library_ChunkLibraryPreliminaryLarvalJob method) (pyrosetta.rosetta.utility.vector1_protocols_jd3_dag_node_managers_ResultElements method) (pyrosetta.rosetta.utility.vector1_protocols_jd3_full_model_FullModelPreliminaryLarvalJob method) (pyrosetta.rosetta.utility.vector1_protocols_jd3_standard_PreliminaryLarvalJob method) (pyrosetta.rosetta.utility.vector1_protocols_jumping_DisulfPairing method) (pyrosetta.rosetta.utility.vector1_protocols_jumping_JumpSelector_JumpWeightDef method) (pyrosetta.rosetta.utility.vector1_protocols_jumping_JumpSetup_JumpDef method) (pyrosetta.rosetta.utility.vector1_protocols_jumping_ResiduePairJumpSetup_JumpDef method) (pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewAtom method) (pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewResidue method) (pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewSegment method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_AtomProperties method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_GADockStageParams method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_Pharmacophore method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_ReweightableRepEnergy method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_TorsionDistrParams method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_TorsionType method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ligand_options_InterfaceInfo method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ProtLigPair_info method) (pyrosetta.rosetta.utility.vector1_protocols_loop_grower_LoopPartialSolution method) (pyrosetta.rosetta.utility.vector1_protocols_loop_grower_LoopPartialSolutionStore method) (pyrosetta.rosetta.utility.vector1_protocols_loop_grower_ResTorsions method) (pyrosetta.rosetta.utility.vector1_protocols_loop_grower_SheetPositions method) (pyrosetta.rosetta.utility.vector1_protocols_loops_Loop method) (pyrosetta.rosetta.utility.vector1_protocols_loops_LoopFromFileData method) (pyrosetta.rosetta.utility.vector1_protocols_loops_Loops method) (pyrosetta.rosetta.utility.vector1_protocols_loops_SerializedLoop method) (pyrosetta.rosetta.utility.vector1_protocols_make_rot_lib_CentroidRotNum method) (pyrosetta.rosetta.utility.vector1_protocols_make_rot_lib_RotData method) (pyrosetta.rosetta.utility.vector1_protocols_make_rot_lib_TorsionRange method) (pyrosetta.rosetta.utility.vector1_protocols_match_Hit method) (pyrosetta.rosetta.utility.vector1_protocols_match_match_dspos1 method) (pyrosetta.rosetta.utility.vector1_protocols_match_ProbeRadius method) (pyrosetta.rosetta.utility.vector1_protocols_match_upstream_BuildSet method) (pyrosetta.rosetta.utility.vector1_protocols_match_upstream_hit method) (pyrosetta.rosetta.utility.vector1_protocols_match_upstream_SampleStrategyData method) (pyrosetta.rosetta.utility.vector1_protocols_md_Constraint method) (pyrosetta.rosetta.utility.vector1_protocols_md_MDscheduleData method) (pyrosetta.rosetta.utility.vector1_protocols_mean_field_AAMatrix method) (pyrosetta.rosetta.utility.vector1_protocols_mean_field_jagged_array_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_protocols_mean_field_RotMatrix method) (pyrosetta.rosetta.utility.vector1_protocols_membrane_SpanInfo method) (pyrosetta.rosetta.utility.vector1_protocols_monte_carlo_AcceptedScores method) (pyrosetta.rosetta.utility.vector1_protocols_motif_grafting_movers_motif2scaffold_indexes method) (pyrosetta.rosetta.utility.vector1_protocols_moves_TrialCounter method) (pyrosetta.rosetta.utility.vector1_protocols_mpi_refinement_MethodParams method) (pyrosetta.rosetta.utility.vector1_protocols_multistate_design_SingleStateEntityData method) (pyrosetta.rosetta.utility.vector1_protocols_nonlocal_Chunk method) (pyrosetta.rosetta.utility.vector1_protocols_optimize_weights_WeightRangeConstraint method) (pyrosetta.rosetta.utility.vector1_protocols_pack_daemon_StructureFileNames method) (pyrosetta.rosetta.utility.vector1_protocols_pdbinfo_manipulations_SequenceSpecification method) (pyrosetta.rosetta.utility.vector1_protocols_pmut_scan_Mutant method) (pyrosetta.rosetta.utility.vector1_protocols_pmut_scan_MutationData method) (pyrosetta.rosetta.utility.vector1_protocols_pose_creation_MergePDBMover_Overlap method) (pyrosetta.rosetta.utility.vector1_protocols_pose_creation_SliceToMiniProteinMover_Chunk method) (pyrosetta.rosetta.utility.vector1_protocols_pose_metric_calculators_EnergiesData method) (pyrosetta.rosetta.utility.vector1_protocols_protein_interface_design_movers_SecretionOptimizationMover_mutt method) (pyrosetta.rosetta.utility.vector1_protocols_protein_interface_design_movers_SecretionOptimizationMover_tm_region method) (pyrosetta.rosetta.utility.vector1_protocols_protein_interface_design_movers_VLBInstruction method) (pyrosetta.rosetta.utility.vector1_protocols_protein_interface_design_Transformation method) (pyrosetta.rosetta.utility.vector1_protocols_qsar_ColorGradient method) (pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBResidueRange method) (pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBSegment method) (pyrosetta.rosetta.utility.vector1_protocols_recces_Histogram method) (pyrosetta.rosetta.utility.vector1_protocols_relax_DatabaseRelaxScript method) (pyrosetta.rosetta.utility.vector1_protocols_rigid_Partner method) (pyrosetta.rosetta.utility.vector1_protocols_rosetta_scripts_ParsedProtocol_ParsedProtocolStep method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsDataCenter method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsDataLanthanide method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsEnergyParameter method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsGridSearchParameter method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsInputLine method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs_PCS_data_per_lanthanides method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs_PCS_line_data method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs1_PCS_data_per_lanthanides_Ts1 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs1_PCS_line_data_Ts1 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs2_PCS_data_per_lanthanides_Ts2 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs2_PCS_line_data_Ts2 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs3_PCS_data_per_lanthanides_Ts3 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs3_PCS_line_data_Ts3 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs4_PCS_data_per_lanthanides_Ts4 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs4_PCS_line_data_Ts4 method) (pyrosetta.rosetta.utility.vector1_protocols_seeded_abinitio_SegmentSpec method) (pyrosetta.rosetta.utility.vector1_protocols_sewing_data_storage_ContactDescription method) (pyrosetta.rosetta.utility.vector1_protocols_sewing_data_storage_LigandDescription method) (pyrosetta.rosetta.utility.vector1_protocols_simple_filters_Quat method) (pyrosetta.rosetta.utility.vector1_protocols_simple_filters_RegionalConnections method) (pyrosetta.rosetta.utility.vector1_protocols_simple_filters_ResidueDepthFrag method) (pyrosetta.rosetta.utility.vector1_protocols_simple_moves_IonizableResidue method) (pyrosetta.rosetta.utility.vector1_protocols_simple_moves_LoggedFragmentMover_Item method) (pyrosetta.rosetta.utility.vector1_protocols_simple_moves_TorsionPerturbType method) (pyrosetta.rosetta.utility.vector1_protocols_simple_moves_WaterRot method) (pyrosetta.rosetta.utility.vector1_protocols_splice_BBDofs method) (pyrosetta.rosetta.utility.vector1_protocols_splice_ResidueBBDofs method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_modeler_protein_MainChainTorsionSet method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_modeler_rna_Combine_Tags_Info method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_modeler_rna_phosphate_PhosphateMove method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_monte_carlo_mover_Attachment method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_monte_carlo_mover_StepWiseMove method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_sampler_copy_dofs_ResidueAlternativeSet method) (pyrosetta.rosetta.utility.vector1_protocols_toolbox_match_enzdes_util_CstResInteractions method) (pyrosetta.rosetta.utility.vector1_protocols_toolbox_match_enzdes_util_ExternalGeomSampler method) (pyrosetta.rosetta.utility.vector1_protocols_toolbox_match_enzdes_util_ResInteractions method) (pyrosetta.rosetta.utility.vector1_protocols_toolbox_match_enzdes_util_SingleConstraint method) (pyrosetta.rosetta.utility.vector1_protocols_toolbox_ScoreRmsPoint method) (pyrosetta.rosetta.utility.vector1_protocols_trajectory_DbTrajectoryWriter_Frame method) (pyrosetta.rosetta.utility.vector1_short method) (pyrosetta.rosetta.utility.vector1_signed_char method) (pyrosetta.rosetta.utility.vector1_std__Rb_tree_const_iterator_protocols_match_downstream_hit_t method) (pyrosetta.rosetta.utility.vector1_std__Rb_tree_const_iterator_protocols_match_upstream_hit_t method) (pyrosetta.rosetta.utility.vector1_std_array_int_3_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_pair_std_shared_ptr_const_protocols_match_downstream_SecMatchResiduePairEvaluator_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_pair_unsigned_long_std_shared_ptr_const_numeric_expression_parser_Expression_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_pair_unsigned_long_std_shared_ptr_protocols_pack_daemon_NPDPropCalculator_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_pair_unsigned_long_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_shared_ptr_const_core_pack_task_ResfileCommand_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_shared_ptr_protocols_match_downstream_DownstreamAlgorithm_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_shared_ptr_protocols_match_downstream_DownstreamBuilder_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_list_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_char_double_std_less_char_std_allocator_std_pair_const_char_double_t method) (pyrosetta.rosetta.utility.vector1_std_map_core_chemical_AA_utility_vector1_double_std_allocator_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_std_map_protocols_jumping_cstType_unsigned_long_std_less_protocols_jumping_cstType_std_allocator_std_pair_const_protocols_jumping_cstType_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_protocols_jumping_dofType_unsigned_long_std_less_protocols_jumping_dofType_std_allocator_std_pair_const_protocols_jumping_dofType_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_shared_ptr_const_core_conformation_Residue_double_std_less_std_shared_ptr_const_core_conformation_Residue_std_allocator_std_pair_const_std_shared_ptr_const_core_conformation_Residue_double_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_bool_std_less_std_string_std_allocator_std_pair_const_std_string_bool_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_core_id_NamedAtomID_std_less_std_string_std_allocator_std_pair_const_std_string_core_id_NamedAtomID_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_core_io_pdb_Field_std_less_std_string_std_allocator_std_pair_const_std_string_core_io_pdb_Field_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_numeric_xyzVector_double_std_less_std_string_std_allocator_std_pair_const_std_string_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_unsigned_long_std_less_std_string_std_allocator_std_pair_const_std_string_unsigned_long_t method) 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(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.FArray3_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_std_complex_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_std_vector_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_utility_vector1_unsigned_int_std_allocator_unsigned_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3A_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.FArray4_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4_unsigned_char_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.FArray5_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_int_t method) L1_10_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) L1_10_2 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) L1_11_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) L1_11_2 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) L1_11_3 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) L1_12_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) L1_12_2 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) L1_12_3 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) L1_13_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) L1_13_2 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) L1_14_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) L1_14_2 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) L1_15_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) L1_15_2 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) L1_16_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) L1_17_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) L1_pattern() (pyrosetta.rosetta.protocols.antibody.grafting.RegExManager method) l1_sequence() (pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence method) L1ScoringScheme (class in pyrosetta.rosetta.core.sequence) L2 (pyrosetta.rosetta.protocols.antibody.CDRNameEnum attribute) l2 (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) l2() (pyrosetta.rosetta.ObjexxFCL.FArray2_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBIndNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_ObjexxFCL_FArray2D_float__star__t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_ObjexxFCL_ubyte_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2A_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2A_float_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.FArray3_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_std_complex_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_std_vector_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_utility_vector1_unsigned_int_std_allocator_unsigned_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3A_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.FArray4_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4_unsigned_char_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.FArray5_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_int_t method) L2_12_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) L2_12_2 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) L2_8_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) L2_8_2 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) L2_8_3 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) L2_8_4 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) L2_8_5 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) l2_sequence() (pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence method) L3 (pyrosetta.rosetta.protocols.antibody.CDRNameEnum attribute) l3 (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) l3() (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_std_complex_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_std_vector_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_utility_vector1_unsigned_int_std_allocator_unsigned_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3A_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.FArray4_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4_unsigned_char_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.FArray5_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_int_t method) L3_10_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) L3_10_cis7_8_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) L3_10_cis8_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) L3_11_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) L3_11_cis7_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) L3_12_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) L3_13_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) L3_7_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) L3_8_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) L3_8_2 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) L3_8_cis6_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) L3_9_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) L3_9_2 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) L3_9_cis6_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) L3_9_cis7_1 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) L3_9_cis7_2 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) L3_9_cis7_3 (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterEnum attribute) L3_pattern() (pyrosetta.rosetta.protocols.antibody.grafting.RegExManager method) l3_sequence() (pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence method) L4 (pyrosetta.rosetta.protocols.antibody.CDRNameEnum attribute) l4 (pyrosetta.rosetta.protocols.antibody.CDRNameEnum attribute) l4() (pyrosetta.rosetta.ObjexxFCL.FArray4_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4_unsigned_char_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.FArray5_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_int_t method) l5() (pyrosetta.rosetta.ObjexxFCL.FArray5_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_int_t method) l_ (pyrosetta.rosetta.core.scoring.hbonds.SSWeightParameters property) L_AA (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) L_chain_last_loop (pyrosetta.rosetta.protocols.antibody.CDRNameEnum attribute) L_CHIRALITY (pyrosetta.rosetta.protocols.simple_moves.chiral.Chirality attribute) l_initialized() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) l_no_notify() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) L_RNA (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) L_SS (pyrosetta.rosetta.protocols.comparative_modeling.features.SSType attribute) L_SUGAR (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) La (pyrosetta.rosetta.core.chemical.element.Elements attribute) LA3_COORDINATION (pyrosetta.rosetta.core.chemical.VariantType attribute) label (pyrosetta.rosetta.core.pose.PDBInfo.ResidueRecord property) (pyrosetta.rosetta.protocols.environment.claims.JumpElement property) (pyrosetta.rosetta.protocols.environment.claims.ResidueElement property) label() (pyrosetta.rosetta.core.environment.LocalPosition method) (pyrosetta.rosetta.core.kinematics.Edge method) (pyrosetta.rosetta.core.scoring.epr_deer.EPRSpinLabel method) (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) (pyrosetta.rosetta.protocols.abinitio.abscript.StructPerturberCM method) (pyrosetta.rosetta.protocols.environment.claims.JumpClaim method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (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.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) (pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer method) (pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.ClaimerMessage method) (pyrosetta.rosetta.protocols.topology_broker.claims.SequenceClaim method) (pyrosetta.rosetta.protocols.topology_broker.claims.SymmetryClaim method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer method) (pyrosetta.rosetta.protocols.topology_broker.CoordConstraintClaimer method) (pyrosetta.rosetta.protocols.topology_broker.CutBiasClaimer method) (pyrosetta.rosetta.protocols.topology_broker.DensityScoringClaimer method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FibrilModelingClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FoldandDockClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.LoopFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer method) (pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts2 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts3 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts4 method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer.CM_SuggestFixResidue method) (pyrosetta.rosetta.protocols.topology_broker.SequenceClaimer method) (pyrosetta.rosetta.protocols.topology_broker.StartStructClaimer method) (pyrosetta.rosetta.protocols.topology_broker.SuggestValueMessage method) (pyrosetta.rosetta.protocols.topology_broker.SymmetryClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TMHTopologySamplerClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer method) label_accessor (pyrosetta.bindings.pose.PoseResidueLabelMaskAccessor attribute) label_atom() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) label_atom_name() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) label_atom_type() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) label_energy() (pyrosetta.rosetta.protocols.moves.PyMOLMover method) label_everything() (pyrosetta.rosetta.core.scoring.epr_deer.EPRSpinLabel method) label_insertion() (pyrosetta.rosetta.protocols.indexed_structure_store.movers.DirectSegmentLookupMover method) label_loop() (pyrosetta.rosetta.protocols.pose_length_moves.PossibleLoop method) label_resonance() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) label_resonance_id() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) label_tolerance() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) label_types() (pyrosetta.rosetta.core.scoring.epr_deer.DEERDataCache method) label_with_index() (in module pyrosetta.rosetta.core.chemical.rdkit) labeled_residues() (pyrosetta.rosetta.core.scoring.epr_deer.DEERDataCache method) LabelPoseFromResidueSelectorMover (class in pyrosetta.rosetta.protocols.fold_from_loops.movers) LabelPoseFromResidueSelectorMoverCreator (class in pyrosetta.rosetta.protocols.fold_from_loops.movers) LabelResonance (class in pyrosetta.rosetta.protocols.noesy_assign) labels (pyrosetta.rosetta.core.scoring.packstat.PosePackData property) labels() (pyrosetta.rosetta.core.scoring.epr_deer.DEERDataCache method) LACTYL_SUGAR (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) lambda (pyrosetta.rosetta.protocols.antibody.LightChainTypeEnum attribute) lambda() (pyrosetta.rosetta.core.optimization.CMAES_Minimizer method) lambda6 (pyrosetta.rosetta.protocols.antibody.LightChainTypeEnum attribute) LAMBDA_ATOM (pyrosetta.rosetta.core.chemical.GreekDistance attribute) lambda_memory() (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBDesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover method) (pyrosetta.rosetta.protocols.mean_field.MeanField method) LAMBEGO_IO (class in pyrosetta.rosetta.protocols.frag_picker) LAMBEGO_Similarity (class in pyrosetta.rosetta.protocols.frag_picker.scores) landing_domain() (pyrosetta.rosetta.core.scoring.loop_graph.Loop method) landing_pos() (pyrosetta.rosetta.core.scoring.loop_graph.Loop method) laplacian_offset_ (pyrosetta.rosetta.protocols.electron_density.DensityGridSearchOptions property) (pyrosetta.rosetta.protocols.electron_density.PoseSphericalSamplesOptions property) (pyrosetta.rosetta.protocols.electron_density.SelectDensityPointsOptions property) large_fragments() (pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub method) LargeFragWeight (class in pyrosetta.rosetta.protocols.topology_broker.weights) LargeNstructJobInputter (class in pyrosetta.rosetta.protocols.jd2) LargeNstructJobInputterCreator (class in pyrosetta.rosetta.protocols.jd2) LARGER (pyrosetta.rosetta.protocols.enzdes.ValueEvaluator attribute) (pyrosetta.rosetta.protocols.enzdes.ValueEvaluator.CompareMode attribute) largest_continuous_atom_map() (in module pyrosetta.rosetta.protocols.legacy_sewing) largest_ddg() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover method) largest_possible_sequence_sep() (pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet method) largestTargetPocketVolume() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) LarvalJob (class in pyrosetta.rosetta.protocols.jd3) last (pyrosetta.CD property) last() (pyrosetta.rosetta.utility.graph.DirectedEdgeList method) (pyrosetta.rosetta.utility.graph.EdgeList method) last_accept() (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) last_accepted() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) last_accepted_pose() (pyrosetta.rosetta.protocols.canonical_sampling.BiasedMonteCarlo method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.DualMonteCarlo method) (pyrosetta.rosetta.protocols.moves.MixedMonteCarlo method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) (pyrosetta.rosetta.protocols.moves.ReplicaExchangeMC method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) last_accepted_score() (pyrosetta.rosetta.protocols.canonical_sampling.BiasedMonteCarlo method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.DualMonteCarlo method) (pyrosetta.rosetta.protocols.moves.MixedMonteCarlo method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) (pyrosetta.rosetta.protocols.moves.ReplicaExchangeMC method) last_accepted_scores() (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) LAST_ADD_OR_DELETE_CHOICE (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.MoveType attribute) last_angle() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) last_apply_failed() (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelix method) last_assignment() (pyrosetta.rosetta.protocols.pack_daemon.PackDaemon method) last_atomdesc (pyrosetta.rosetta.core.scoring.rna.chemical_shift.atomitem attribute) LAST_ATTACHMENT_TYPE (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AttachmentType attribute) last_attempted_mover_idx() (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol method) last_backbone_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) last_batch_id() (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager method) (pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager method) last_beta2_aa (pyrosetta.rosetta.core.chemical.AA attribute) last_beta3_aa (pyrosetta.rosetta.core.chemical.AA attribute) last_carbon_in_ring() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) LAST_CENTROID_START (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax attribute) (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax.IterationStage attribute) (pyrosetta.rosetta.protocols.abinitio.IterativeBase attribute) (pyrosetta.rosetta.protocols.abinitio.IterativeBase.IterationStage attribute) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid attribute) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid.IterationStage attribute) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom attribute) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom.IterationStage attribute) last_closure_cycles() (pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover method) last_closure_success() (pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover method) last_controlling_chi() (pyrosetta.rosetta.core.chemical.ResidueType method) last_D_aa (pyrosetta.rosetta.core.chemical.AA attribute) last_DNA_aa (pyrosetta.rosetta.core.chemical.AA attribute) last_end_atom_name() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) last_ind_assigned() (pyrosetta.rosetta.protocols.mean_field.ResHashMap method) last_independent_residue() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) last_index() (in module pyrosetta.rosetta.ObjexxFCL) last_inner_score_delta_over_temperature() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.enzdes.PredesignPerturbMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDeterministicSpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbRandomJumpMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.BBConRotMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.topology_broker.RigidBodyRandomTMHMover method) last_insert_id() (pyrosetta.rosetta.cppdb.statement method) last_inserted_frag_begin() (pyrosetta.rosetta.protocols.frags.TorsionFragmentMover method) last_job_for_input_source_id() (pyrosetta.rosetta.protocols.jd3.JobTracker method) last_jobs_for_inputs_sources() (pyrosetta.rosetta.protocols.jd3.JobTracker method) last_key() (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList method) last_move() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) last_move_succeeded() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) last_mutation() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) last_nchi() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) last_nonempty_bin() (pyrosetta.rosetta.core.scoring.saxs.DistanceHistogram method) last_oligourea (pyrosetta.rosetta.core.chemical.AA attribute) last_proposal_density_ratio() (pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.ClearCompositionConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.AbrelaxMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptLoopCloserCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptStageMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.ConstraintPreparer method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentJumpCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.RigidChunkCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.StagePreparer method) (pyrosetta.rosetta.protocols.abinitio.abscript.StructPerturberCM method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.DoubleLayerKinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.KinematicTaskControl method) (pyrosetta.rosetta.protocols.abinitio.LoopJumpFoldCst method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.abinitio.Protocol method) (pyrosetta.rosetta.protocols.abinitio.ResolutionSwitcher method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.PackStatMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyModelerProtocol method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CDRsMinPackMin method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.GraftCDRLoopsProtocol method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.H3PerturbCCD method) (pyrosetta.rosetta.protocols.antibody.H3RefineCCD method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRamp method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRampLegacy method) (pyrosetta.rosetta.protocols.antibody.LHSnugFitLegacy method) (pyrosetta.rosetta.protocols.antibody.RefineBetaBarrel method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol method) (pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backbone_moves.RandomizeBBByRamaPrePro method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.backrub.BackrubProtocol method) (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.AsyncMPITemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy method) (pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.WTEBiasEnergy method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.carbohydrates.TautomerizeAnomerMover method) (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) (pyrosetta.rosetta.protocols.cluster.AssignToClustersMover method) (pyrosetta.rosetta.protocols.cluster.ClusterBase method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints_Simple method) (pyrosetta.rosetta.protocols.cluster.GatherPosesMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ExtraThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.LoopRelaxThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.PartialThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.RecoverSideChainsMover method) (pyrosetta.rosetta.protocols.comparative_modeling.StealLigandMover method) (pyrosetta.rosetta.protocols.comparative_modeling.StealSideChainsMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMover method) (pyrosetta.rosetta.protocols.constraint_movers.ClearConstraintsMover method) (pyrosetta.rosetta.protocols.constraint_movers.ConstraintSetMover method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.constraint_movers.ResidueTypeConstraintMover method) (pyrosetta.rosetta.protocols.contact_map.ContactMap method) (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) (pyrosetta.rosetta.protocols.cryst.CrystRMS method) (pyrosetta.rosetta.protocols.cryst.DockLatticeMover method) (pyrosetta.rosetta.protocols.cryst.FitBfactorsMover method) (pyrosetta.rosetta.protocols.cryst.LoadDensityMapMover method) (pyrosetta.rosetta.protocols.cryst.MakeLatticeMover method) (pyrosetta.rosetta.protocols.cryst.MakeLayerMover method) (pyrosetta.rosetta.protocols.cryst.RecomputeDensityMapMover method) (pyrosetta.rosetta.protocols.cryst.ReportGradientsMover method) (pyrosetta.rosetta.protocols.cryst.SetCrystWeightMover method) (pyrosetta.rosetta.protocols.cryst.SetRefinementOptionsMover method) (pyrosetta.rosetta.protocols.cryst.TagPoseWithRefinementStatsMover method) (pyrosetta.rosetta.protocols.cryst.UpdateCrystInfo method) (pyrosetta.rosetta.protocols.cryst.UpdateSolventMover method) (pyrosetta.rosetta.protocols.cutoutdomain.CutOutDomain method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrankshaftFlipMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateAngleConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateDistanceConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepRigidBodyPermutationMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutations method) (pyrosetta.rosetta.protocols.ddg.ddGMover method) (pyrosetta.rosetta.protocols.denovo_design.components.VLBProtected method) (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetPoseSecstructFromStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover method) (pyrosetta.rosetta.protocols.design_opt.Supercharge method) (pyrosetta.rosetta.protocols.dna.DesignProteinBackboneAroundDNA method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker method) (pyrosetta.rosetta.protocols.dna.SeparateDnaFromNonDna method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingHighRes method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) (pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.DockMCMCycle method) (pyrosetta.rosetta.protocols.docking.DockMCMProtocol method) (pyrosetta.rosetta.protocols.docking.DockMinMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.EnsureExclusivelySharedJumpMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.InterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMover method) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparately method) (pyrosetta.rosetta.protocols.docking.SidechainMinMover method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.domain_assembly.AddAssemblyConstraints method) (pyrosetta.rosetta.protocols.domain_assembly.AssembleLinkerMover method) (pyrosetta.rosetta.protocols.domain_assembly.CombineChainsMover method) (pyrosetta.rosetta.protocols.domain_assembly.PostDockAssemblyScorer method) (pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetricsMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DensityZscores method) (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.SetupForDensityScoringMover method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.environment.ClientMover method) (pyrosetta.rosetta.protocols.environment.CoMTrackerCM method) (pyrosetta.rosetta.protocols.environment.EnvMover method) (pyrosetta.rosetta.protocols.environment.ScriptCM method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.BackboneSampler method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.PredesignPerturbMover method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.BluePrintBDR method) (pyrosetta.rosetta.protocols.fldsgn.CircularPermutation method) (pyrosetta.rosetta.protocols.fldsgn.MatchResiduesMover method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetAACompositionPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetSecStructEnergies method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.flexpack.FlexPacker method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingAbInitio method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingLowRes method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocol method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMover method) (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) (pyrosetta.rosetta.protocols.forge.components.BDR method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.constraints.NtoCConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.RemoveRemodelCsts method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLigandHandler method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentMover method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingLowResRefinement method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingProtocol method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelix method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceProbeMover method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceSurfaceProbe method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionPerturbation method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionSampler method) (pyrosetta.rosetta.protocols.hybridization.CartesianHybridize method) (pyrosetta.rosetta.protocols.hybridization.CartesianSampler method) (pyrosetta.rosetta.protocols.hybridization.ChunkTrialMover method) (pyrosetta.rosetta.protocols.hybridization.DomainAssembly method) (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol method) (pyrosetta.rosetta.protocols.hybridization.InsertChunkMover method) (pyrosetta.rosetta.protocols.hybridization.MRMover method) (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentSmoothTrialMover method) (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentTrialMover method) (pyrosetta.rosetta.protocols.hydrate.Hydrate method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.indel.IndelOptimizationMover method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.DirectSegmentLookupMover method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.SegmentSequenceProfileMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAddStartnodeFragments method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyEnumerateAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGivenPathAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGreedyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyMonteCarloAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogen method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogens method) (pyrosetta.rosetta.protocols.ligand_docking.CompoundTranslate method) (pyrosetta.rosetta.protocols.ligand_docking.ComputeLigandRDF method) (pyrosetta.rosetta.protocols.ligand_docking.FinalMinimizer method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDock method) (pyrosetta.rosetta.protocols.ligand_docking.GrowLigand method) (pyrosetta.rosetta.protocols.ligand_docking.HighResDocker method) (pyrosetta.rosetta.protocols.ligand_docking.HighResEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculator method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDesign method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDockProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeBackbone method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeLigand method) (pyrosetta.rosetta.protocols.ligand_docking.ProtLigEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformers method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.Rotate method) (pyrosetta.rosetta.protocols.ligand_docking.Rotates method) (pyrosetta.rosetta.protocols.ligand_docking.SlideTogether method) (pyrosetta.rosetta.protocols.ligand_docking.StartFrom method) (pyrosetta.rosetta.protocols.ligand_docking.TetherLigand method) (pyrosetta.rosetta.protocols.ligand_docking.Transform method) (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.Translate method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.ligand_docking.WriteLigandMolFile method) (pyrosetta.rosetta.protocols.loop_build.LoopBuildMover method) (pyrosetta.rosetta.protocols.loop_build.LoopmodelWrapper method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_grower.FragmentExtension method) (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) (pyrosetta.rosetta.protocols.loop_grower.SheetSampler method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibrary method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loophash.Mover_LoopHashRefine method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.loops.FoldTreeFromLoops method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopCM method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial method) (pyrosetta.rosetta.protocols.magnesium.MgHydrater method) (pyrosetta.rosetta.protocols.magnesium.MgMinimizer method) (pyrosetta.rosetta.protocols.magnesium.MgMonteCarlo method) (pyrosetta.rosetta.protocols.magnesium.MgOrbitalFrameFinder method) (pyrosetta.rosetta.protocols.magnesium.MgScanner method) (pyrosetta.rosetta.protocols.magnesium.MgWaterHydrogenPacker method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover method) (pyrosetta.rosetta.protocols.match.MatcherMover method) (pyrosetta.rosetta.protocols.matdes.ExtractSubposeMover method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) (pyrosetta.rosetta.protocols.matdes.SchemePlaceMotifsMover method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover method) (pyrosetta.rosetta.protocols.medal.MedalExchangeMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanConstraint method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanTermZConstraint method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AqueousPoreFinder method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMover method) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMover method) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMover method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.membrane_benchmark.MembraneEnergyLandscapeSampler method) (pyrosetta.rosetta.protocols.membrane_benchmark.PeptideOrientationMover method) (pyrosetta.rosetta.protocols.metal_interface.RemoveMetalConnectionsMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover method) (pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.GreenPacker method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.TaskAwareSymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloRecover method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloReset method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloTest method) (pyrosetta.rosetta.protocols.monte_carlo.ResetBaselineMover method) (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover method) (pyrosetta.rosetta.protocols.motifs.MotifDnaPacker method) (pyrosetta.rosetta.protocols.moves.ChangeFoldTreeMover method) (pyrosetta.rosetta.protocols.moves.CompositionMover method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.DsspMover method) (pyrosetta.rosetta.protocols.moves.FilterMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IfMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.JumpOutMover method) (pyrosetta.rosetta.protocols.moves.MCShowMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.MoveMapMover method) (pyrosetta.rosetta.protocols.moves.Mover method) (pyrosetta.rosetta.protocols.moves.MoverApplyingMover method) (pyrosetta.rosetta.protocols.moves.MoverContainer method) (pyrosetta.rosetta.protocols.moves.MoverForPoseList method) (pyrosetta.rosetta.protocols.moves.NullMover method) (pyrosetta.rosetta.protocols.moves.PDBDumpMover method) (pyrosetta.rosetta.protocols.moves.ProfilerMover method) (pyrosetta.rosetta.protocols.moves.PyMOLMover method) (pyrosetta.rosetta.protocols.moves.RampingMover method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.StructureRestrictor method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.moves.WhileMover method) (pyrosetta.rosetta.protocols.mpi_refinement.StructAvrgMover method) (pyrosetta.rosetta.protocols.ncbb.NcbbDockDesignProtocol method) (pyrosetta.rosetta.protocols.ncbb.oop.OopCreatorMover method) (pyrosetta.rosetta.protocols.ncbb.oop.OopDockDesignProtocol method) (pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMover method) (pyrosetta.rosetta.protocols.ncbb.SecStructFinder method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover method) (pyrosetta.rosetta.protocols.network.UIMover method) (pyrosetta.rosetta.protocols.nmr.ParaNMRScoreMover method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover method) (pyrosetta.rosetta.protocols.nmr.pre.PREMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover method) (pyrosetta.rosetta.protocols.pb_potential.SetupPoissonBoltzmannPotential method) (pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences method) (pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMover method) (pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover method) (pyrosetta.rosetta.protocols.pose_creation.MakePolyXMover method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMover method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBMover method) (pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMover method) (pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover method) (pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModeling method) (pyrosetta.rosetta.protocols.pose_length_moves.ConnectChainsMover method) (pyrosetta.rosetta.protocols.pose_length_moves.FixAllLoopsMover method) (pyrosetta.rosetta.protocols.pose_length_moves.InsertResMover method) (pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloser method) (pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.BlockwiseAnalysisMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.OmnibusDisulfideAnalysisLabelerMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddSidechainConstraintsToHotspots method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BackrubDDMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DisulfideMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNativeResiduePreCycle method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNonNativeResiduePreCycle method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotDisjointedFoldTreeMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotHasherMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopFinder method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLine method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopRemodel method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.MapHotspot method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (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.PlaceOnLoop method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PrepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetupHotspotConstraintsLoopsMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetupHotspotConstraintsMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ShoveResidueMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SpinMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SubroutineMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TryRotamers method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMover method) (pyrosetta.rosetta.protocols.qsar.qsarMover method) (pyrosetta.rosetta.protocols.qsar.RenderGridsToKinemage method) (pyrosetta.rosetta.protocols.quantum_annealing.ExternalPackerResultLoader method) (pyrosetta.rosetta.protocols.rbsegment_relax.AutoRBMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.IdealizeHelicesMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.RBSegmentRelaxImpl method) (pyrosetta.rosetta.protocols.recces.RECCES_Mover method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Any method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Comb method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Loop method) (pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_MultiSuite method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_OneJump method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Sugar method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Suite method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence method) (pyrosetta.rosetta.protocols.recon_design.MSDMover method) (pyrosetta.rosetta.protocols.relax.AcceptToBestMover method) (pyrosetta.rosetta.protocols.relax.AtomCoordinateCstMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.relax.FastRelax method) (pyrosetta.rosetta.protocols.relax.LocalRelax method) (pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover method) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMover method) (pyrosetta.rosetta.protocols.relax.membrane.MPRangeRelaxMover method) (pyrosetta.rosetta.protocols.relax.MiniRelax method) (pyrosetta.rosetta.protocols.relax.RangeRelaxMover method) (pyrosetta.rosetta.protocols.relax.RelaxProtocolBase method) (pyrosetta.rosetta.protocols.relax.RepeatProteinRelax method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDeterministicSpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMotionMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbRandomJumpMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RollMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyCM method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoMasterMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoProtocolMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.denovo.output.RNA_FragmentMonteCarloOutputter method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo method) (pyrosetta.rosetta.protocols.rna.movers.ERRASER2Protocol method) (pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Coarsify method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Decoarsify method) (pyrosetta.rosetta.protocols.rna.movers.RNA_DeNovoOptimizer method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (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) (pyrosetta.rosetta.protocols.rosetta_scripts.AdditionalOutputWrapper method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultipleOutputWrapper method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultiplePoseMover method) (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryMover method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.seeded_abinitio.CAcstGenerator method) (pyrosetta.rosetta.protocols.seeded_abinitio.CloseFold method) (pyrosetta.rosetta.protocols.seeded_abinitio.CoordinateCst method) (pyrosetta.rosetta.protocols.seeded_abinitio.DefineMovableLoops method) (pyrosetta.rosetta.protocols.seeded_abinitio.GrowPeptides method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedFoldTree method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedSetupMover method) (pyrosetta.rosetta.protocols.seeded_abinitio.SegmentHybridizer method) (pyrosetta.rosetta.protocols.seeded_abinitio.SwapSegment method) (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentFileGeneratorMover method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) (pyrosetta.rosetta.protocols.simple_ddg.ddG method) (pyrosetta.rosetta.protocols.simple_filters.EvaluatedTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.a3b_hbs.A3BHbsPatcher method) (pyrosetta.rosetta.protocols.simple_moves.AddCavitiesMover method) (pyrosetta.rosetta.protocols.simple_moves.AddChainMover method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraint method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMover method) (pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover method) (pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.BBConRotMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.chiral.ChiralMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover method) (pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyDofMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeclareBond method) (pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DME_FilterMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover method) (pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfile method) (pyrosetta.rosetta.protocols.simple_moves.FavorSymmetricSequence method) (pyrosetta.rosetta.protocols.simple_moves.FoldTreeFromMotif method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.hbs.HbsPatcher method) (pyrosetta.rosetta.protocols.simple_moves.LoadPDBMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.LoggedFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.MissingDensityToJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopDPuckMinusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopDPuckPlusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPatcher method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPuckMinusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPuckPlusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopRandomPuckMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopRandomSmallMover method) (pyrosetta.rosetta.protocols.simple_moves.PDBReloadMover method) (pyrosetta.rosetta.protocols.simple_moves.PeptideStapleMover method) (pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.ProlineFixMover method) (pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.RepeatPropagationMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.ReportXYZ method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ResetFoldTree method) (pyrosetta.rosetta.protocols.simple_moves.ResetFullModelInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.ResTypeFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities method) (pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover method) (pyrosetta.rosetta.protocols.simple_moves.SaveSequenceToCommentsMover method) (pyrosetta.rosetta.protocols.simple_moves.ScoreMover method) (pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.StructProfileMover method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TailsScoreMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionSetMover method) (pyrosetta.rosetta.protocols.simple_moves.triazolamer.TriazolamerMover method) (pyrosetta.rosetta.protocols.simple_moves.triazolamer.TriazolamerRandomSmallMover method) (pyrosetta.rosetta.protocols.simple_moves.Tumble method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.VirtualRootMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.splice.AlignEndsMover method) (pyrosetta.rosetta.protocols.splice.RBInMover method) (pyrosetta.rosetta.protocols.splice.RBOutMover method) (pyrosetta.rosetta.protocols.splice.RotLibOut method) (pyrosetta.rosetta.protocols.splice.Splice method) (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) (pyrosetta.rosetta.protocols.splice.TailSegmentMover method) (pyrosetta.rosetta.protocols.star.StarAbinitio method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.SideChainCopier method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.polar_hydrogens.PolarHydrogenPacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.precomputed.PrecomputedLibraryMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_MultiPoseCloser method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge.BulgeApplyMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge.BulgeUnApplyMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.o2prime.O2PrimePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarInstantiateMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarVirtualizeMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarJustInTimeInstantiator method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSamplerFromStringList method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseConnectionSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseMinimizer method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseModeler method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.FromScratchMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.ResampleMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMasterMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.StepWiseMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.CopyDofStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueListStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.input_streams.InputStreamStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.jump.JumpStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinBetaAntiParallelStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinFragmentStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinMainChainStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueAlternatives method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueList method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_NucleosideStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneDOF method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneTorsion method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValue method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValueComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerRingConformer method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedComb method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) (pyrosetta.rosetta.protocols.surface_docking.CentroidRelaxMover method) (pyrosetta.rosetta.protocols.surface_docking.FullatomRelaxMover method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceDockingProtocol method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceOrientMover method) (pyrosetta.rosetta.protocols.switches.GraftSwitchMover method) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockBaseProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymInterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymSidechainMinMover method) (pyrosetta.rosetta.protocols.symmetry.DetectSymmetry method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricPoseMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSequenceSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingInitialPerturbation method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.testing.BenchmarkBuildRotamersMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus method) (pyrosetta.rosetta.protocols.topology_broker.RigidBodyRandomTMHMover method) (pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolMover method) (pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) last_received_from() (pyrosetta.rosetta.protocols.loophash.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Sampler method) (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax method) (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax_and_PostRescore method) (pyrosetta.rosetta.protocols.wum.DatabaseEntryWorkUnit method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) (pyrosetta.rosetta.protocols.wum.WorkUnit_Wait method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) last_residue() (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) (pyrosetta.rosetta.protocols.topology_broker.claims.BBClaim method) (pyrosetta.rosetta.protocols.topology_broker.claims.CutClaim method) (pyrosetta.rosetta.protocols.topology_broker.claims.DofClaim method) (pyrosetta.rosetta.protocols.topology_broker.claims.JumpClaim method) (pyrosetta.rosetta.protocols.topology_broker.claims.LegacyRootClaim method) (pyrosetta.rosetta.protocols.topology_broker.claims.SequenceClaim method) (pyrosetta.rosetta.protocols.topology_broker.claims.SymmetryClaim method) last_residue_enzyme() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) last_residue_index() (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) last_residue_substrate() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) last_row_reached (pyrosetta.rosetta.cppdb.backend.result attribute) (pyrosetta.rosetta.cppdb.backend.result.next_row attribute) last_run_successful() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) last_score() (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) last_section() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary method) last_segment_id() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) last_slide_good() (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) LAST_STAGE (pyrosetta.rosetta.protocols.abinitio.StageID attribute) last_start_atom_name() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) last_symmetry_mirror() (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) last_symmetry_repeats() (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) last_tested_scores() (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) LAST_TYPE (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameterType attribute) last_uniform() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) last_withinrot() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) lastcol (pyrosetta.rosetta.core.scoring.packstat.SimplePDB_Atom property) lastRes (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib property) launch_atom() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) layer() (pyrosetta.rosetta.core.select.util.SelectResiduesByLayer method) layer_residues() (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation method) LayerDesignOperation (class in pyrosetta.rosetta.protocols.flxbb) LayerDesignOperation.LayerOperationType (class in pyrosetta.rosetta.protocols.flxbb) LayerDesignOperation.LayerSpecificationType (class in pyrosetta.rosetta.protocols.flxbb) LayerDesignOperationCreator (class in pyrosetta.rosetta.protocols.flxbb) LayerSelector (class in pyrosetta.rosetta.core.select.residue_selector) LayerSelectorCreator (class in pyrosetta.rosetta.core.select.residue_selector) lazy_ig() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) LazyEdge (class in pyrosetta.rosetta.core.pack.interaction_graph) LazyInteractionGraph (class in pyrosetta.rosetta.core.pack.interaction_graph) LazyNode (class in pyrosetta.rosetta.core.pack.interaction_graph) LazySilentFileJobInputter (class in pyrosetta.rosetta.protocols.jd2) LazySilentFileJobInputterCreator (class in pyrosetta.rosetta.protocols.jd2) LazySilentFilePoseInputStream (class in pyrosetta.rosetta.core.import_pose.pose_stream) LazySortedVector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_protocols_frag_picker_CompareByScoreCombination_t (class in pyrosetta.rosetta.protocols.frag_picker) LazySortedVector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_protocols_frag_picker_CompareTotalScore_t (class in pyrosetta.rosetta.protocols.frag_picker) lb (pyrosetta.rosetta.numeric.interpolation.spline.interp_range property) lb() (pyrosetta.rosetta.core.scoring.constraints.BoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc method) lbfgs_iteration_data (class in pyrosetta.rosetta.core.optimization) LD_types (pyrosetta.rosetta.protocols.forge.remodel.RemodelData property) (pyrosetta.rosetta.protocols.forge.remodel.RemodelWorkingSet property) lddt() (in module pyrosetta.rosetta.core.scoring) lDDT_Calculator (class in pyrosetta.rosetta.core.scoring) LeapIndex (class in pyrosetta.rosetta.protocols.loophash) leave_as_is() (pyrosetta.rosetta.protocols.task_operations.DatabaseThread method) lec_order (pyrosetta.rosetta.core.scoring.fiber_diffraction.Hankel property) LeeRichards (class in pyrosetta.rosetta.core.scoring.packstat) left (pyrosetta.rosetta.core.sequence.AlignMove attribute) (pyrosetta.rosetta.protocols.forge.build.Interval property) left() (pyrosetta.rosetta.numeric.ClusteringTreeNode method) left_ (pyrosetta.rosetta.core.pack.dunbrack.BBIndNRChiSample_float_t property) left_cdf() (pyrosetta.rosetta.core.scoring.Ramachandran2B method) left_cdf_for_torsion_bin() (pyrosetta.rosetta.core.scoring.Ramachandran2B method) left_child() (pyrosetta.rosetta.numeric.kdtree.KDNode method) left_handed() (pyrosetta.rosetta.protocols.fldsgn.topology.HSSTriplet method) left_justified() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) left_justify() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) left_multiply_by() (pyrosetta.rosetta.numeric.Quaternion_double_t method) left_multiply_by_inverse_of() (pyrosetta.rosetta.numeric.Quaternion_double_t method) LEFT_PAREN (pyrosetta.rosetta.numeric.expression_parser.TokenType attribute) left_skip (pyrosetta.rosetta.protocols.forge.build.CountFromLeft property) left_stub_atoms() (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) legacy (pyrosetta.rosetta.core.scoring.sasa.SasaRadii attribute) legacy() (pyrosetta.rosetta.protocols.hbnet.UnsatSelector method) legacy_assembly_mover_ct_namer() (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMover static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyEnumerateAssemblyMover static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGivenPathAssemblyMover static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGreedyAssemblyMover static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyMonteCarloAssemblyMover static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover static method) legacy_global_requirements_ct_namer() (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyRequirementFactory static method) legacy_global_requirements_group_name() (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyRequirementFactory static method) legacy_intra_segment_requirements_ct_namer() (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyRequirementFactory static method) legacy_intra_segment_requirements_group_name() (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyRequirementFactory static method) legacy_saved_pose_or_input() (in module pyrosetta.rosetta.protocols.rosetta_scripts) legacy_turner_mode() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) LegacyAddStartnodeFragments (class in pyrosetta.rosetta.protocols.legacy_sewing) LegacyAddStartnodeFragmentsCreator (class in pyrosetta.rosetta.protocols.legacy_sewing) LegacyAppendAssemblyMover (class in pyrosetta.rosetta.protocols.legacy_sewing) LegacyAppendAssemblyMoverCreator (class in pyrosetta.rosetta.protocols.legacy_sewing) LegacyAssemblyConstraintsMover (class in pyrosetta.rosetta.protocols.legacy_sewing) LegacyAssemblyConstraintsMoverCreator (class in pyrosetta.rosetta.protocols.legacy_sewing) LegacyAssemblyMover (class in pyrosetta.rosetta.protocols.legacy_sewing) LegacyAssemblyScoreFunction (class in pyrosetta.rosetta.protocols.legacy_sewing.scoring) LegacyAssemblyScorer (class in pyrosetta.rosetta.protocols.legacy_sewing.scoring) LegacyBlosumScorer (class in pyrosetta.rosetta.protocols.legacy_sewing.scoring) LegacyCalciumMotifScorer (class in pyrosetta.rosetta.protocols.legacy_sewing.scoring) LegacyClashScorer (class in pyrosetta.rosetta.protocols.legacy_sewing.scoring) LegacyEnumerateAssemblyMover (class in pyrosetta.rosetta.protocols.legacy_sewing) LegacyEnumerateAssemblyMoverCreator (class in pyrosetta.rosetta.protocols.legacy_sewing) LegacyGivenPathAssemblyMover (class in pyrosetta.rosetta.protocols.legacy_sewing) LegacyGivenPathAssemblyMoverCreator (class in pyrosetta.rosetta.protocols.legacy_sewing) LegacyGlobalLengthRequirement (class in pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements) LegacyGlobalLengthRequirementCreator (class in pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements) LegacyGlobalRequirement (class in pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements) LegacyGlobalRequirementCreator (class in pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements) LegacyGreedyAssemblyMover (class in pyrosetta.rosetta.protocols.legacy_sewing) LegacyGreedyAssemblyMoverCreator (class in pyrosetta.rosetta.protocols.legacy_sewing) LegacyInterModelMotifScorer (class in pyrosetta.rosetta.protocols.legacy_sewing.scoring) LegacyIntraSegmentRequirement (class in pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements) LegacyIntraSegmentRequirementCreator (class in pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements) LegacyKicSampler (class in pyrosetta.rosetta.protocols.loop_modeling.samplers) LegacyKicSamplerCreator (class in pyrosetta.rosetta.protocols.loop_modeling.samplers) LegacyLeapIndex (class in pyrosetta.rosetta.protocols.loophash) LegacyMonteCarloAssemblyMover (class in pyrosetta.rosetta.protocols.legacy_sewing) LegacyMonteCarloAssemblyMoverCreator (class in pyrosetta.rosetta.protocols.legacy_sewing) LegacyMotifScorer (class in pyrosetta.rosetta.protocols.legacy_sewing.scoring) LegacyPartnerMotifScorer (class in pyrosetta.rosetta.protocols.legacy_sewing.scoring) LegacyReadNativeRotamersFile (class in pyrosetta.rosetta.protocols.legacy_sewing) LegacyReadNativeRotamersFileCreator (class in pyrosetta.rosetta.protocols.legacy_sewing) LegacyReadRepeatNativeRotamersFile (class in pyrosetta.rosetta.protocols.legacy_sewing) LegacyReadRepeatNativeRotamersFileCreator (class in pyrosetta.rosetta.protocols.legacy_sewing) LegacyRepeatAssemblyMover (class in pyrosetta.rosetta.protocols.legacy_sewing) LegacyRepeatAssemblyMoverCreator (class in pyrosetta.rosetta.protocols.legacy_sewing) LegacyRequirementFactory (class in pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements) LegacyRequirementSet (class in pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements) LegacyResidueRetentionRequirement (class in pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements) LegacyResidueRetentionRequirementCreator (class in pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements) LegacyRootClaim (class in pyrosetta.rosetta.protocols.topology_broker.claims) LegacyRootClaim.ClaimRight (class in pyrosetta.rosetta.protocols.topology_broker.claims) LegacySegmentDsspRequirement (class in pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements) LegacySegmentDsspRequirementCreator (class in pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements) LegacySegmentLengthRequirement (class in pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements) LegacySegmentLengthRequirementCreator (class in pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements) legal() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) (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) legal_check() (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) legal_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) legal_default_check() (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) legal_default_report() (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) legal_default_size() (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 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) legal_default_value() (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 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) legal_limits_report() (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) legal_report() (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) legal_size() (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 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) legal_size_report() (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) legal_specs_report() (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) legal_string() (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) legal_value() (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 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) Legendre() (pyrosetta.rosetta.numeric.fourier.SO3coeffs method) LeGrand (pyrosetta.rosetta.core.scoring.sasa.SasaMethodEnum attribute) LeGrandSasa (class in pyrosetta.rosetta.core.scoring.sasa) len() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) len_h_ (pyrosetta.rosetta.core.scoring.hbonds.SSWeightParameters property) len_l_ (pyrosetta.rosetta.core.scoring.hbonds.SSWeightParameters property) len_trim() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) len_trim_whitespace() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) length (pyrosetta.rosetta.core.io.HELIXInformation property) (pyrosetta.rosetta.core.io.LinkInformation property) (pyrosetta.rosetta.core.io.SSBondInformation property) (pyrosetta.rosetta.protocols.antibody.clusters.ClusterData property) (pyrosetta.rosetta.protocols.cartesian.MD_Angle property) (pyrosetta.rosetta.protocols.cartesian.MD_Bond property) length() (pyrosetta.rosetta.core.environment.SequenceAnnotation method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.scoring.sc.Atom method) (pyrosetta.rosetta.core.sequence.AnnotatedSequence method) (pyrosetta.rosetta.core.sequence.ChemicalShiftSequence method) (pyrosetta.rosetta.core.sequence.CompositeSequence method) (pyrosetta.rosetta.core.sequence.Sequence method) (pyrosetta.rosetta.core.sequence.SequenceAlignment method) (pyrosetta.rosetta.core.sequence.SequenceCoupling method) (pyrosetta.rosetta.core.sequence.SequenceProfile method) (pyrosetta.rosetta.numeric.IntervalSet_Double method) (pyrosetta.rosetta.numeric.IntervalSet_double_t method) (pyrosetta.rosetta.numeric.xyzTriple_unsigned_long_t method) (pyrosetta.rosetta.numeric.xyzVector_double_t method) (pyrosetta.rosetta.numeric.xyzVector_float_t method) (pyrosetta.rosetta.numeric.xyzVector_int_t method) (pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.FArray1_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1A_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1A_int_t 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_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) (pyrosetta.rosetta.protocols.fldsgn.topology.Helix method) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base method) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand method) (pyrosetta.rosetta.protocols.forge.build.Interval method) (pyrosetta.rosetta.protocols.jd2.SingleFileBuffer method) (pyrosetta.rosetta.protocols.jd2.WriteFileSFB method) (pyrosetta.rosetta.protocols.loophash.BackboneSegment method) (pyrosetta.rosetta.protocols.loops.Loop method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange method) (pyrosetta.rosetta.protocols.topology_broker.claims.SequenceClaim method) (pyrosetta.rosetta.RDGeom.Point method) (pyrosetta.rosetta.RDGeom.Point3D method) length_change (pyrosetta.rosetta.core.conformation.signals.LengthEvent property) length_dependent_srbb() (pyrosetta.rosetta.core.scoring.hbonds.HBondOptions method) length_dependent_srbb_highscale() (pyrosetta.rosetta.core.scoring.hbonds.HBondOptions method) length_dependent_srbb_lowscale() (pyrosetta.rosetta.core.scoring.hbonds.HBondOptions method) length_dependent_srbb_maxlength() (pyrosetta.rosetta.core.scoring.hbonds.HBondOptions method) length_dependent_srbb_minlength() (pyrosetta.rosetta.core.scoring.hbonds.HBondOptions method) LENGTH_EVENT_COLLECTOR (pyrosetta.rosetta.core.pose.datacache.CacheableObserverType attribute) length_normalized_distance() (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster method) length_parameters() (pyrosetta.rosetta.core.energy_methods.ResidueCartBondedParameters method) length_squared() (pyrosetta.rosetta.core.scoring.sc.Atom method) (pyrosetta.rosetta.numeric.xyzTriple_unsigned_long_t method) (pyrosetta.rosetta.numeric.xyzVector_double_t method) (pyrosetta.rosetta.numeric.xyzVector_float_t method) (pyrosetta.rosetta.numeric.xyzVector_int_t method) (pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1A_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1A_int_t 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_unsigned_long_t method) length_tolerance() (pyrosetta.rosetta.numeric.NumericTraits_double_t static method) (pyrosetta.rosetta.numeric.NumericTraits_float_t static method) (pyrosetta.rosetta.numeric.NumericTraits_long_double_t static method) length_type() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) LengthEvent (class in pyrosetta.rosetta.core.conformation.signals) LengthEvent.Tag (class in pyrosetta.rosetta.core.conformation.signals) LengthEventCollector (class in pyrosetta.rosetta.core.pose.datacache) LengthGen (class in pyrosetta.rosetta.core.fragment.picking_old.vall.gen) LengthInResiduesRequirement (class in pyrosetta.rosetta.protocols.sewing.requirements) LengthInResiduesRequirementCreator (class in pyrosetta.rosetta.protocols.sewing.requirements) lengths_shifts() (pyrosetta.rosetta.protocols.denovo_design.components.SheetDB method) lengthSq() (pyrosetta.rosetta.RDGeom.Point method) (pyrosetta.rosetta.RDGeom.Point3D method) let_rigid_body_jumps_move() (in module pyrosetta.rosetta.protocols.rna.denovo) level (pyrosetta.rosetta.basic.TracerOptions property) level() (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.HierarchicalLevel method) level_2_grid_coord() (pyrosetta.rosetta.protocols.canonical_sampling.AsyncMPITemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) level_radius() (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.HierarchicalLevel method) level_size() (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.HierarchicalLevel method) levels (pyrosetta.rosetta.basic.TracerOptions property) lex_position() (pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMover method) LexicographicalIterator (class in pyrosetta.rosetta.utility) lge() (in module pyrosetta.rosetta.ObjexxFCL) lgt() (in module pyrosetta.rosetta.ObjexxFCL) LHRepulsiveRamp (class in pyrosetta.rosetta.protocols.antibody) LHRepulsiveRampLegacy (class in pyrosetta.rosetta.protocols.antibody) LHSnugFitLegacy (class in pyrosetta.rosetta.protocols.antibody) Li (pyrosetta.rosetta.core.chemical.element.Elements attribute) lib() (pyrosetta.rosetta.protocols.sparta.Sparta method) LIB_FULL_PATH (pyrosetta.rosetta.basic.ProfTag attribute) lib_full_path() (in module pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.HierarchicalLevel method) Librarian_core_fragment_picking_old_vall_scores_VallFragmentScore_core_fragment_picking_old_vall_eval_VallFragmentEval_core_fragment_picking_old_vall_gen_VallFragmentGen_core_fragment_picking_old_vall_VallLibrary_t (class in pyrosetta.rosetta.core.fragment.picking_old.concepts) Librarian_VallFragmentScore_VallFragmentEval_VallFragmentGen_VallLibrary (class in pyrosetta.rosetta.core.fragment.picking_old.concepts) library() (pyrosetta.rosetta.protocols.frags.FragLib method) (pyrosetta.rosetta.protocols.motifs.MotifLibrary method) Library_core_fragment_picking_old_vall_VallSections_t (class in pyrosetta.rosetta.core.fragment.picking_old.concepts) library_name() (pyrosetta.rosetta.core.chemical.rotamers.BasicRotamerLibrarySpecification static method) (pyrosetta.rosetta.core.chemical.rotamers.CenrotRotamerLibrarySpecification static method) (pyrosetta.rosetta.core.chemical.rotamers.DunbrackRotamerLibrarySpecification static method) (pyrosetta.rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification static method) (pyrosetta.rosetta.core.chemical.rotamers.PDBRotamerLibrarySpecification static method) (pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification static method) library_size() (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.Mutate1Randomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer method) Library_VallSections (class in pyrosetta.rosetta.core.fragment.picking_old.concepts) lig_chain (pyrosetta.rosetta.protocols.ligand_docking.ProtLigPair_info property) lig_dens (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.DensStructInfo property) lig_num_unsatisfied (pyrosetta.rosetta.protocols.hbnet.HBondNetStruct property) lig_rigid_body_confs() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver method) lig_state_list (pyrosetta.rosetta.protocols.hbnet.HBondNetStruct property) LIGAND (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) (pyrosetta.rosetta.protocols.denovo_design.components.SegmentCounts attribute) (pyrosetta.rosetta.protocols.denovo_design.components.SegmentCounts.SegmentType attribute) ligand (pyrosetta.rosetta.protocols.sewing.data_storage.PolymericType attribute) ligand() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) ligand_area_ct_namer() (pyrosetta.rosetta.protocols.ligand_docking.LigandAreaLoader static method) ligand_atom (pyrosetta.rosetta.protocols.ligand_docking.rdf.AtomPairData property) (pyrosetta.rosetta.protocols.sewing.data_storage.LigandContact property) (pyrosetta.rosetta.protocols.sewing.hashing.IdealContact property) ligand_atom_charge (pyrosetta.rosetta.protocols.ligand_docking.rdf.AtomPairData property) ligand_atom_coords (pyrosetta.rosetta.protocols.ligand_docking.rdf.AtomPairData property) ligand_atom_id (pyrosetta.rosetta.protocols.ligand_docking.rdf.AtomPairData property) ligand_atom_index (pyrosetta.rosetta.protocols.sewing.hashing.LigandCoordInfo property) ligand_atom_name (pyrosetta.rosetta.protocols.sewing.data_storage.ContactDescription property) ligand_atom_num (pyrosetta.rosetta.protocols.sewing.data_storage.ContactDescription property) ligand_atom_type (pyrosetta.rosetta.protocols.ligand_docking.rdf.AtomPairData property) ligand_contacts (pyrosetta.rosetta.protocols.sewing.data_storage.LigandDescription property) ligand_coord_files (pyrosetta.rosetta.protocols.sewing.data_storage.LigandDescription property) ligand_coords (pyrosetta.rosetta.protocols.sewing.data_storage.LigandDescription property) ligand_id (pyrosetta.rosetta.protocols.sewing.data_storage.LigandDescription property) ligand_ids() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) Ligand_info (class in pyrosetta.rosetta.protocols.ligand_docking) ligand_residue() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) ligand_resno() (pyrosetta.rosetta.protocols.enzdes.EnzdesConstraintReporter method) ligand_resnum (pyrosetta.rosetta.protocols.sewing.data_storage.LigandDescription property) ligand_resnum_string (pyrosetta.rosetta.protocols.sewing.data_storage.LigandDescription property) ligand_rg() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) ligand_rot() (pyrosetta.rosetta.protocols.simple_moves.WaterRotsDB method) ligand_selector (pyrosetta.rosetta.protocols.sewing.data_storage.LigandDescription property) ligand_subtag_ct_namer() (pyrosetta.rosetta.protocols.sewing.hashing.LigandBindingResPlacer static method) ligand_typename() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) ligand_xyz() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) LigandAligner (class in pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) LigandArea (class in pyrosetta.rosetta.protocols.ligand_docking) LigandAreaLoader (class in pyrosetta.rosetta.protocols.ligand_docking) LigandAreaLoaderCreator (class in pyrosetta.rosetta.protocols.ligand_docking) LigandAssemblyRequirement (class in pyrosetta.rosetta.protocols.sewing.requirements) LigandAssemblyScorer (class in pyrosetta.rosetta.protocols.sewing.scoring) LigandBaseProtocol (class in pyrosetta.rosetta.protocols.ligand_docking) LigandBindingAssemblyMover (class in pyrosetta.rosetta.protocols.sewing.movers) LigandBindingAssemblyMoverCreator (class in pyrosetta.rosetta.protocols.sewing.movers) LigandBindingResPlacer (class in pyrosetta.rosetta.protocols.sewing.hashing) LigandClashRequirement (class in pyrosetta.rosetta.protocols.sewing.requirements) LigandClashRequirementCreator (class in pyrosetta.rosetta.protocols.sewing.requirements) LigandConformer (class in pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) (class in pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) LigandConformerBuilder (class in pyrosetta.rosetta.protocols.match.downstream) LigandContact (class in pyrosetta.rosetta.protocols.sewing.data_storage) LigandCoordInfo (class in pyrosetta.rosetta.protocols.sewing.hashing) LigandDescription (class in pyrosetta.rosetta.protocols.sewing.data_storage) LigandDesign (class in pyrosetta.rosetta.protocols.ligand_docking) LigandDesignCreator (class in pyrosetta.rosetta.protocols.ligand_docking) LigandDockProtocol (class in pyrosetta.rosetta.protocols.ligand_docking) LigandMetalContactSelector (class in pyrosetta.rosetta.protocols.residue_selectors) LigandMetalContactSelectorCreator (class in pyrosetta.rosetta.protocols.residue_selectors) LigandMinusProteinPlus (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBase attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBase.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction.FunctionSign attribute) LigandMotifSearch (class in pyrosetta.rosetta.protocols.motifs) ligandname (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.DensStructInfo property) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.StructInfo property) LigandPlusProteinMinus (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBase attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBase.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction.FunctionSign attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction attribute) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction.FunctionSign attribute) LigandPropertyScore (class in pyrosetta.rosetta.protocols.qsar.scoring_grid) LigandPropertyScoreCreator (class in pyrosetta.rosetta.protocols.qsar.scoring_grid) LigandResidue (class in pyrosetta.rosetta.protocols.sewing.data_storage) ligands_subtag_ct_namer() (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentFileGeneratorMover static method) ligandscore (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.DensStructInfo property) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.StructInfo property) LigandScorer (class in pyrosetta.rosetta.protocols.sewing.scoring) LigandScorerCreator (class in pyrosetta.rosetta.protocols.sewing.scoring) LigandSegment (class in pyrosetta.rosetta.protocols.sewing.data_storage) LigBurialFilter (class in pyrosetta.rosetta.protocols.enzdes) LigBurialFilterCreator (class in pyrosetta.rosetta.protocols.enzdes) ligchis (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ChiInfo property) LigDSasaFilter (class in pyrosetta.rosetta.protocols.enzdes) LigDSasaFilterCreator (class in pyrosetta.rosetta.protocols.enzdes) light (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyNumbering property) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence property) light_chain_type_enum_to_string() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) light_chain_type_is_present() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) light_chain_type_string_to_enum() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) light_framework() (pyrosetta.rosetta.protocols.antibody.grafting.AntibodySequence method) light_type (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Antibody_Database_Result property) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastResult property) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_SubstitutionMatrixResult property) LightChainTypeEnum (class in pyrosetta.rosetta.protocols.antibody) LightChainTypeEnum_start (pyrosetta.rosetta.protocols.antibody.LightChainTypeEnum attribute) LightChainTypeEnum_total (pyrosetta.rosetta.protocols.antibody.LightChainTypeEnum attribute) lightning() (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintOptions method) LigInterfaceEnergyFilter (class in pyrosetta.rosetta.protocols.enzdes) LigInterfaceEnergyFilterCreator (class in pyrosetta.rosetta.protocols.enzdes) limit() (pyrosetta.rosetta.core.scoring.func.TopOutFunc method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ConstraintInfo method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.wum.SilentStructStore method) limit_cluster_size (pyrosetta.rosetta.protocols.toolbox.ClusterOptions property) limit_clusters_ (pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringOptions property) limit_groups() (pyrosetta.rosetta.protocols.cluster.ClusterBase method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter method) limit_groupsize() (pyrosetta.rosetta.protocols.cluster.ClusterBase method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter method) (pyrosetta.rosetta.protocols.toolbox.ClusterBase method) (pyrosetta.rosetta.protocols.toolbox.ClusterPhilStyle method) limit_ig_setup_threads() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) limit_rotamer_set() (in module pyrosetta.rosetta.protocols.multistate_design) limit_structures_per_cluster_ (pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringOptions property) limit_to_positions() (pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperation method) limit_total_structures() (pyrosetta.rosetta.protocols.cluster.ClusterBase method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter method) LimitAromaChi2_RotamerSetOperation (class in pyrosetta.rosetta.protocols.task_operations) LimitAromaChi2Operation (class in pyrosetta.rosetta.protocols.task_operations) LimitAromaChi2OperationCreator (class in pyrosetta.rosetta.protocols.task_operations) LimitHitsPerRotamerFilter (class in pyrosetta.rosetta.protocols.match.output) lin_isc (pyrosetta.rosetta.protocols.peptide_deriver.DerivedPeptideEntry property) lin_pose (pyrosetta.rosetta.protocols.peptide_deriver.DerivedPeptideEntry property) Line (class in pyrosetta.rosetta.core.sequence) line (pyrosetta.rosetta._xmlNode property) line() (pyrosetta.rosetta.core.conformation.membrane.EXCN_Illegal_Arguments method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane_Bounds method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_MembraneFoldTree method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_NonMembrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Resource_Definition method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_VirtualRsd method) (pyrosetta.rosetta.core.environment.EXCN_Env_Exception method) (pyrosetta.rosetta.core.environment.EXCN_FTSketchGraph method) (pyrosetta.rosetta.core.id.EXCN_AtomNotFound method) (pyrosetta.rosetta.core.kinematics.EXCN_InvalidFoldTree method) (pyrosetta.rosetta.core.pack.task.ResfileReaderException method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculatorException method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.EXCN_CalcFailed method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.EXCN_InitFailed method) (pyrosetta.rosetta.core.simple_metrics.metrics.EXCN_CalcFailed method) (pyrosetta.rosetta.core.simple_metrics.metrics.EXCN_InitFailed method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_cdr_detection_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_cdr_undefined_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_grafting_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_invalid_cdr_region_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_json_cdr_detection_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_numbering_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_scs_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_unexpected_region_length_ method) (pyrosetta.rosetta.protocols.antibody.grafting.Grafting_Base_Exception method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.EXCN_Heat_Converged method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.EXCN_Pool_Converged method) (pyrosetta.rosetta.protocols.constraint_generator.EXCN_RemoveCstsFailed method) (pyrosetta.rosetta.protocols.denovo_design.architects.EXCN_PreFilterFailed method) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_Fold method) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_PoseInconsistent method) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_RemarksNotPresent method) (pyrosetta.rosetta.protocols.denovo_design.connection.EXCN_ConnectionSetupFailed method) (pyrosetta.rosetta.protocols.denovo_design.movers.EXCN_FilterFailed method) (pyrosetta.rosetta.protocols.denovo_design.movers.EXCN_NothingToFold method) (pyrosetta.rosetta.protocols.environment.EXCN_Env_Passport method) (pyrosetta.rosetta.protocols.environment.EXCN_Env_Security_Exception method) (pyrosetta.rosetta.protocols.forge.remodel.EXCN_RemoveCstsFailed method) (pyrosetta.rosetta.protocols.jd2.archive.EXCN_Archive method) (pyrosetta.rosetta.protocols.jd2.JD2Failure method) (pyrosetta.rosetta.protocols.loophash.EXCN_bbdb_Merge_Failed method) (pyrosetta.rosetta.protocols.loophash.EXCN_DB_IO_Failed method) (pyrosetta.rosetta.protocols.loophash.EXCN_Invalid_Hashmap method) (pyrosetta.rosetta.protocols.loophash.EXCN_No_Extra_Data_To_Write method) (pyrosetta.rosetta.protocols.loophash.EXCN_Wrong_DB_Format method) (pyrosetta.rosetta.protocols.loops.EXCN_Loop_not_closed method) (pyrosetta.rosetta.protocols.moves.EXCN_Converged method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_AssignmentNotFound method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_FileFormat method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_NoesyAssign method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_UnknownAtomname method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_UnknownResonance method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_CalcFailed method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_InitFailed method) (pyrosetta.rosetta.protocols.topology_broker.EXCN_FailedBroking method) (pyrosetta.rosetta.protocols.topology_broker.EXCN_FilterFailed method) (pyrosetta.rosetta.protocols.topology_broker.EXCN_Input method) (pyrosetta.rosetta.protocols.topology_broker.EXCN_TopologyBroker method) (pyrosetta.rosetta.protocols.topology_broker.EXCN_Unknown method) (pyrosetta.rosetta.utility.excn.BadInput method) (pyrosetta.rosetta.utility.excn.Exception method) (pyrosetta.rosetta.utility.excn.FileNotFound method) (pyrosetta.rosetta.utility.excn.IOError method) (pyrosetta.rosetta.utility.excn.KeyError method) (pyrosetta.rosetta.utility.excn.NullPointerError method) (pyrosetta.rosetta.utility.excn.RangeError method) (pyrosetta.rosetta.utility.excn.RosettaScriptsOptionError method) (pyrosetta.rosetta.utility.excn.UserCorrectableIssue method) (pyrosetta.rosetta.utility.graph.EXCN_Stop_BFS method) line_to_design() (pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover method) LINEAR (pyrosetta.rosetta.numeric.interpolation.CatmullRomSplineBoundaryType attribute) linear (pyrosetta.rosetta.protocols.canonical_sampling.InterpolationType attribute) linear_branch_conn (pyrosetta.rosetta.core.scoring.ScoreType attribute) linear_chainbreak (pyrosetta.rosetta.core.scoring.ScoreType attribute) linear_chainbreak() (in module pyrosetta.rosetta.protocols.denovo_design) (in module pyrosetta.rosetta.protocols.forge.methods) linear_chainbreak_weight() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) linear_interpolate() (in module pyrosetta.rosetta.core.scoring.constraints) linear_vector_of_results() (pyrosetta.rosetta.protocols.jd3.dag_node_managers.NodeManagerStorageMatrix method) LinearBranchEnergy (class in pyrosetta.rosetta.core.energy_methods) LinearBranchEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) LinearChainbreakEnergy (class in pyrosetta.rosetta.core.energy_methods) LinearChainbreakEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) LinearFunc (class in pyrosetta.rosetta.protocols.moves) LinearFunction (class in pyrosetta.rosetta.numeric.interpolation.spline) linearize_fold_tree() (in module pyrosetta.rosetta.core.kinematics) LinearMemEdge (class in pyrosetta.rosetta.core.pack.interaction_graph) LinearMemNode (class in pyrosetta.rosetta.core.pack.interaction_graph) LinearMemoryInteractionGraph (class in pyrosetta.rosetta.core.pack.interaction_graph) LinearPenaltyFunction (class in pyrosetta.rosetta.core.scoring.func) LineMinimizationAlgorithm (class in pyrosetta.rosetta.core.optimization) linenum() (pyrosetta.rosetta.core.pose.RID_FileSource method) LineObject (class in pyrosetta.rosetta.protocols.forge.remodel) Link (class in pyrosetta.rosetta.utility.signals) LINK (pyrosetta.rosetta.core.io.pdb.RecordType attribute) link_cutoff_ (pyrosetta.rosetta.protocols.pose_sewing.filters.CSSettings property) link_in_vector() (in module pyrosetta.rosetta.core.io) link_map() (pyrosetta.rosetta.core.io.StructFileRep method) link_to() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment static method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSegment static method) link_torsion_vectors() (pyrosetta.rosetta.core.optimization.MinimizerMap method) (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap method) link_vectors() (pyrosetta.rosetta.core.optimization.DOF_Node method) link_vertex_to_generators() (in module pyrosetta.rosetta.core.scoring.power_diagram) LINKAGE_NA (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType attribute) linkage_notation() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) linkage_type (pyrosetta.rosetta.core.scoring.carbohydrates.CHIDihedralSamplingData property) LinkageConformerData (class in pyrosetta.rosetta.core.chemical.carbohydrates) LinkageConformerMover (class in pyrosetta.rosetta.protocols.carbohydrates) LinkageConformerMoverCreator (class in pyrosetta.rosetta.protocols.carbohydrates) linker_count2score() (in module pyrosetta.rosetta.protocols.sic_dock) linker_name() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) LinkerScore (class in pyrosetta.rosetta.protocols.sic_dock) linkExemplarsThroughSolvent() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) LinkInformation (class in pyrosetta.rosetta.core.io) LinkResidues (class in pyrosetta.rosetta.protocols.task_operations) LinkResiduesCreator (class in pyrosetta.rosetta.protocols.task_operations) LinkUnit (class in pyrosetta.rosetta.utility.signals) linmem_ig() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) linmem_ig_history_size() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) linmin_deriv_cutoff() (pyrosetta.rosetta.core.optimization.MinimizerOptions method) LIPID (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) lipid_composition_name() (pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo method) lipid_composition_name_long() (pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo method) LipidBurial() (pyrosetta.rosetta.core.scoring.MembraneTopology method) LipidExposure() (pyrosetta.rosetta.core.scoring.MembraneTopology method) LipidMemGrid (class in pyrosetta.rosetta.protocols.qsar.scoring_grid) LipidMemGridCreator (class in pyrosetta.rosetta.protocols.qsar.scoring_grid) LipoDefined() (pyrosetta.rosetta.core.scoring.MembraneTopology method) LIST (pyrosetta.rosetta.protocols.cluster.calibur.ADJ_LIST_MODE attribute) list() (pyrosetta.rosetta.core.scoring.Hairpins method) list_allowable_mutations() (pyrosetta.rosetta.protocols.constel.SingResCnlCrea static method) list_amino_acid_options() (in module pyrosetta.rosetta.protocols.multistate_design) list_attributes() (pyrosetta.rosetta.core.import_pose.options.RNA_BasicOptions static method) (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions static method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions static method) (pyrosetta.rosetta.core.import_pose.options.RNA_MinimizerOptions static method) list_const_protocols_match_Hit__star__t (class in pyrosetta.rosetta.std) list_core_id_AtomID_t (class in pyrosetta.rosetta.std) list_core_io_rcsb_ExperimentalTechnique_t (class in pyrosetta.rosetta.std) list_core_scoring_custom_pair_distance_atoms_and_func_struct_t (class in pyrosetta.rosetta.std) list_core_scoring_power_diagram_PDvertex__star__t (class in pyrosetta.rosetta.std) list_cycpep_rigid_body_permutation_mover_modes() (in module pyrosetta.rosetta.protocols.cyclic_peptide) list_dir() (in module pyrosetta.rosetta.utility.file) list_double_t (class in pyrosetta.rosetta.std) list_filters() (pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects method) list_int_t (class in pyrosetta.rosetta.std) list_movers() (pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects method) list_numeric_xyzVector_double_t (class in pyrosetta.rosetta.std) list_options_read() (pyrosetta.rosetta.basic.random.RandomGeneratorSettings static method) (pyrosetta.rosetta.core.import_pose.ImportPoseOptions static method) (pyrosetta.rosetta.core.import_pose.options.RNA_BasicOptions static method) (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions static method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions static method) (pyrosetta.rosetta.core.import_pose.options.RNA_MinimizerOptions static method) (pyrosetta.rosetta.core.import_pose.RNA_DeNovoSetup static method) (pyrosetta.rosetta.core.io.StructFileReaderOptions static method) (pyrosetta.rosetta.core.io.StructFileRepOptions static method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfile static method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents static method) (pyrosetta.rosetta.core.pack.task.PackerTask static method) (pyrosetta.rosetta.core.pack.task.PackerTask_ static method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask static method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ static method) (pyrosetta.rosetta.core.scoring.DockingScoreFunction static method) (pyrosetta.rosetta.core.scoring.etable.EtableOptions static method) (pyrosetta.rosetta.core.scoring.hbonds.HBondOptions static method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions static method) (pyrosetta.rosetta.core.scoring.MinScoreScoreFunction static method) (pyrosetta.rosetta.core.scoring.ScoreFunction static method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricScoreFunction static method) (pyrosetta.rosetta.protocols.dna.DesignProteinBackboneAroundDNA static method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign static method) (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker static method) (pyrosetta.rosetta.protocols.flexpack.OtherContextScoreFunction static method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack static method) (pyrosetta.rosetta.protocols.jd3.chunk_library_inputters.ChunkLibraryInputterCreator method) (pyrosetta.rosetta.protocols.jd3.chunk_library_inputters.ChunkLibraryInputterFactory method) (pyrosetta.rosetta.protocols.jd3.chunk_library_inputters.PDBChunkLibraryInputter static method) (pyrosetta.rosetta.protocols.jd3.chunk_library_inputters.PDBChunkLibraryInputterCreator method) (pyrosetta.rosetta.protocols.jd3.full_model_inputters.FullModelInputterCreator method) (pyrosetta.rosetta.protocols.jd3.full_model_inputters.FullModelInputterFactory method) (pyrosetta.rosetta.protocols.jd3.full_model_inputters.PDBFullModelInputter static method) (pyrosetta.rosetta.protocols.jd3.full_model_inputters.PDBFullModelInputterCreator method) (pyrosetta.rosetta.protocols.jd3.full_model_inputters.SilentFileFullModelInputter static method) (pyrosetta.rosetta.protocols.jd3.full_model_inputters.SilentFileFullModelInputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_inputters.PDBPoseInputter static method) (pyrosetta.rosetta.protocols.jd3.pose_inputters.PDBPoseInputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputterFactory method) (pyrosetta.rosetta.protocols.jd3.pose_inputters.SilentFilePoseInputter static method) (pyrosetta.rosetta.protocols.jd3.pose_inputters.SilentFilePoseInputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.DeNovoSilentFilePoseOutputter static method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.DeNovoSilentFilePoseOutputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputter static method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputter static method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputter static method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SecondaryPoseOutputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputter static method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputterCreator method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover static method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy static method) (pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover static method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PrepackMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover static method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoProtocolMover static method) (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser static method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseBasicModelerOptions static method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions static method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.options.StepWiseMoveSelectorOptions static method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions static method) (pyrosetta.rosetta.protocols.stepwise.options.StepWiseBasicOptions static method) (pyrosetta.rosetta.protocols.testing.BenchmarkBuildRotamersMover static method) list_outputter_options_read() (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputterFactory method) list_pools() (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector method) list_protocols_match_Hit_t (class in pyrosetta.rosetta.std) list_protocols_multistage_rosetta_scripts_mover_or_filter_t (class in pyrosetta.rosetta.std) list_protocols_pockets_spherical_coor_triplet_t (class in pyrosetta.rosetta.std) list_RDKit_Atom__star__t (class in pyrosetta.rosetta.std) list_RDKit_Bond__star__t (class in pyrosetta.rosetta.std) list_read_options() (pyrosetta.rosetta.core.io.silent.SilentFileOptions static method) (pyrosetta.rosetta.core.scoring.ScoreFunctionFactory static method) list_read_options_in_get_score_function() (in module pyrosetta.rosetta.core.scoring) list_read_options_in_get_score_function_legacy() (in module pyrosetta.rosetta.core.scoring) list_residue_selectors() (pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects method) list_sasa_method_hp_modes() (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa static method) (pyrosetta.rosetta.core.scoring.sasa.SasaMethod static method) list_score_functions() (pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects method) list_secondary_outputter_options_read() (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputterFactory method) list_simple_metrics() (pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects method) list_std_pair_double_core_pose_rna_BasePair_t (class in pyrosetta.rosetta.std) list_std_pair_double_core_pose_rna_BaseStack_t (class in pyrosetta.rosetta.std) list_std_pair_unsigned_long_double_t (class in pyrosetta.rosetta.std) list_std_pair_unsigned_long_unsigned_long_t (class in pyrosetta.rosetta.std) list_std_set_std_string_t (class in pyrosetta.rosetta.std) list_std_shared_ptr_const_core_chemical_ResidueType_t (class in pyrosetta.rosetta.std) list_std_shared_ptr_const_core_conformation_Residue_t (class in pyrosetta.rosetta.std) list_std_shared_ptr_const_core_pack_task_operation_ResLvlTaskOperation_t (class in pyrosetta.rosetta.std) list_std_shared_ptr_const_core_pack_task_ResfileCommand_t (class in pyrosetta.rosetta.std) list_std_shared_ptr_const_core_scoring_methods_EnergyMethod_t (class in pyrosetta.rosetta.std) list_std_shared_ptr_const_protocols_jd3_chunk_library_inputters_ChunkLibraryInputterCreator_t (class in pyrosetta.rosetta.std) list_std_shared_ptr_const_protocols_jd3_full_model_inputters_FullModelInputterCreator_t (class in pyrosetta.rosetta.std) list_std_shared_ptr_const_protocols_jd3_pose_inputters_PoseInputterCreator_t (class in pyrosetta.rosetta.std) list_std_shared_ptr_const_protocols_jd3_pose_outputters_PoseOutputterCreator_t (class in pyrosetta.rosetta.std) list_std_shared_ptr_const_protocols_jd3_pose_outputters_SecondaryPoseOutputterCreator_t (class in pyrosetta.rosetta.std) list_std_shared_ptr_const_utility_tag_Tag_t (class in pyrosetta.rosetta.std) list_std_shared_ptr_const_utility_tag_XMLSchemaParticle_t (class in pyrosetta.rosetta.std) list_std_shared_ptr_core_conformation_Residue_t (class in pyrosetta.rosetta.std) list_std_shared_ptr_core_io_silent_SilentStruct_t (class in pyrosetta.rosetta.std) list_std_shared_ptr_core_optimization_DOF_Node_t (class in pyrosetta.rosetta.std) list_std_shared_ptr_core_pack_interaction_graph_AnnealableGraphBase_t (class in pyrosetta.rosetta.std) list_std_shared_ptr_core_pack_rotamer_set_RotamerOperation_t (class in pyrosetta.rosetta.std) list_std_shared_ptr_core_pack_task_operation_TaskOperation_std_allocator_std_shared_ptr_core_pack_task_operation_TaskOperation_t (in module pyrosetta.rosetta.std) list_std_shared_ptr_core_pack_task_operation_TaskOperation_t (class in pyrosetta.rosetta.std) list_std_shared_ptr_core_scoring_PDvertex_t (class in pyrosetta.rosetta.std) list_std_shared_ptr_core_scoring_power_diagram_PDvertex_t (class in pyrosetta.rosetta.std) list_std_shared_ptr_protocols_environment_claims_EnvClaim_t (class in pyrosetta.rosetta.std) list_std_shared_ptr_protocols_jd3_deallocation_DeallocationMessage_t (class in pyrosetta.rosetta.std) list_std_shared_ptr_protocols_jd3_LarvalJob_t (class in pyrosetta.rosetta.std) list_std_shared_ptr_protocols_jd3_output_OutputSpecification_t (class in pyrosetta.rosetta.std) list_std_shared_ptr_protocols_jd3_pose_outputters_SecondaryPoseOutputter_t (class in pyrosetta.rosetta.std) list_std_shared_ptr_protocols_match_downstream_DownstreamAlgorithm_t (class in pyrosetta.rosetta.std) list_std_shared_ptr_protocols_match_downstream_DownstreamBuilder_t (class in pyrosetta.rosetta.std) list_std_shared_ptr_protocols_noesy_assign_CrossPeak_t (class in pyrosetta.rosetta.std) list_std_shared_ptr_protocols_noesy_assign_PeakAssignment_t (class in pyrosetta.rosetta.std) list_std_shared_ptr_protocols_toolbox_Node_t (class in pyrosetta.rosetta.std) list_std_shared_ptr_utility_SimulateMPIMessage_t (class in pyrosetta.rosetta.std) list_std_string_t (class in pyrosetta.rosetta.std) list_task_operations() (pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects method) list_unsigned_long_t (class in pyrosetta.rosetta.std) list_utility_keys_VariantKey_utility_options_OptionKey_t (class in pyrosetta.rosetta.std) list_utility_tag_XMLSchemaAttribute_t (class in pyrosetta.rosetta.std) list_utility_tag_XMLSchemaSimpleSubelementList_ElementSummary_t (class in pyrosetta.rosetta.std) list_utility_vector1_double_std_allocator_double_t (class in pyrosetta.rosetta.std) list_utility_vector1_unsigned_long_std_allocator_unsigned_long_t (class in pyrosetta.rosetta.std) listAdjacentLists() (pyrosetta.rosetta.protocols.cluster.calibur.Clustering method) listen() (pyrosetta.network.rosetta_udp_to_tcp_bridge.PR_UDPServer method) listener_tag_to_name() (in module pyrosetta.rosetta.basic.mpi) listener_tags (class in pyrosetta.rosetta.basic.mpi) LITE (pyrosetta.rosetta.protocols.cluster.calibur.ADJ_LIST_MODE attribute) LITERAL (pyrosetta.rosetta.numeric.expression_parser.TokenType attribute) literal_value() (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTValue method) LiteralExpression (class in pyrosetta.rosetta.numeric.expression_parser) LiteralToken (class in pyrosetta.rosetta.numeric.expression_parser) live() (pyrosetta.rosetta.core.scoring.PDvertex method) (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) LJ (pyrosetta.rosetta.core.scoring.sasa.SasaRadii attribute) lj_cutoff() (pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) lj_hbond_hdis (pyrosetta.rosetta.core.scoring.etable.EtableOptions property) lj_hbond_OH_donor_dis (pyrosetta.rosetta.core.scoring.etable.EtableOptions property) lj_minimum (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair property) lj_r12_coeff (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair property)

lj_r6_coeff (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair property) lj_radius() (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.chemical.MMAtomType method) (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) lj_radius_sq() (pyrosetta.rosetta.core.chemical.MMAtomType method) lj_sigma() (pyrosetta.rosetta.core.scoring.etable.MembEtable method) lj_slope_intercept() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) lj_switch_dis2sigma (pyrosetta.rosetta.core.scoring.etable.EtableOptions property) lj_switch_dis2sigma() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) lj_switch_intercept (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair property) lj_switch_slope (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair property) lj_three_bond_radius() (pyrosetta.rosetta.core.chemical.MMAtomType method) lj_three_bond_radius_sq() (pyrosetta.rosetta.core.chemical.MMAtomType method) lj_three_bond_wdepth() (pyrosetta.rosetta.core.chemical.MMAtomType method) lj_use_hbond_radii() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) lj_use_lj_deriv_slope() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) lj_use_water_radii() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) lj_val_at_minimum (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair property) lj_water_dis() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) lj_water_hdis() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) lj_wdepth() (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.chemical.MMAtomType method) (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) ljatr() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) ljatr_cubic_poly_parameters (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair property) ljatr_cubic_poly_xhi (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair property) ljatr_cubic_poly_xlo (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair property) ljatr_final_weight (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair property) ljrep() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) ljrep_extra_repulsion (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair property) ljrep_from_negcrossing (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair property) ljrep_linear_ramp_d2_cutoff (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair property) ljust() (in module pyrosetta.rosetta.ObjexxFCL) lk_ball (pyrosetta.rosetta.core.scoring.ScoreType attribute) lk_ball() (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) lk_ball_bridge (pyrosetta.rosetta.core.scoring.ScoreType attribute) lk_ball_bridge2 (pyrosetta.rosetta.core.scoring.ScoreType attribute) lk_ball_bridge_uncpl (pyrosetta.rosetta.core.scoring.ScoreType attribute) lk_ball_bridge_uncpl2 (pyrosetta.rosetta.core.scoring.ScoreType attribute) LK_BALL_INFO (pyrosetta.rosetta.core.conformation.residue_datacache.ResidueDataCacheIndex attribute) lk_ball_iso (pyrosetta.rosetta.core.scoring.ScoreType attribute) LK_BALL_POSE_INFO (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) LK_BALL_ROTAMER_SET_INFO (pyrosetta.rosetta.core.conformation.RotamerSetCacheableDataType.Enum attribute) lk_ball_wtd (pyrosetta.rosetta.core.scoring.ScoreType attribute) lk_ball_wtd_ (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ReweightableRepEnergy property) LK_BallEnergy (class in pyrosetta.rosetta.core.scoring.lkball) LK_BallEnergyCreator (class in pyrosetta.rosetta.core.scoring.lkball) lk_coeff1 (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair property) lk_coeff2 (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair property) lk_costheta (pyrosetta.rosetta.core.scoring.ScoreType attribute) lk_dgfree() (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) lk_dgrefce() (pyrosetta.rosetta.core.scoring.etable.MembEtable method) lk_dome (pyrosetta.rosetta.core.scoring.ScoreType attribute) lk_dome_bridge (pyrosetta.rosetta.core.scoring.ScoreType attribute) lk_dome_bridge_uncpl (pyrosetta.rosetta.core.scoring.ScoreType attribute) LK_DOME_INFO (pyrosetta.rosetta.core.conformation.residue_datacache.ResidueDataCacheIndex attribute) lk_dome_iso (pyrosetta.rosetta.core.scoring.ScoreType attribute) lk_dome_pack (pyrosetta.rosetta.core.scoring.ScoreType attribute) LK_DomeEnergy (class in pyrosetta.rosetta.core.scoring.lkball) LK_DomeEnergyCreator (class in pyrosetta.rosetta.core.scoring.lkball) LK_DomeHelper (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.lk_dome) LK_DomePackEnergy (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.lk_dome) LK_DomePackEnergyCreator (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.lk_dome) lk_frac_sigmoid() (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) LK_hack (class in pyrosetta.rosetta.core.energy_methods) lk_hack (pyrosetta.rosetta.core.scoring.ScoreType attribute) LK_hackCreator (class in pyrosetta.rosetta.core.energy_methods) lk_inv_lambda2() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) lk_lambda() (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) lk_min_dis2sigma() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) lk_min_dis2sigma_value (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair property) lk_nonpolar (pyrosetta.rosetta.core.scoring.ScoreType attribute) lk_nonpolar_intra_RNA (pyrosetta.rosetta.core.scoring.ScoreType attribute) lk_polar (pyrosetta.rosetta.core.scoring.ScoreType attribute) lk_polar_intra_RNA (pyrosetta.rosetta.core.scoring.ScoreType attribute) LK_POLARNONPOLAR_NBLIST (pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType.Enum attribute) lk_PolarNonPolar_pair_nblist (pyrosetta.rosetta.core.scoring.min_pair_data attribute) LK_PolarNonPolarEnergy (class in pyrosetta.rosetta.core.energy_methods) LK_PolarNonPolarEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) lk_volume() (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) lkb_max_dis() (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) lkb_max_dis2() (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) lkb_res_data (pyrosetta.rosetta.core.scoring.min_single_data attribute) LKB_ResidueInfo (class in pyrosetta.rosetta.core.scoring.lkball) LKB_ResiduesInfo (class in pyrosetta.rosetta.core.scoring.lkball) lkb_respair_data (pyrosetta.rosetta.core.scoring.min_pair_data attribute) LKB_TRIE_COLLECTION (pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType.Enum attribute) lkball_method (pyrosetta.rosetta.core.scoring.methods.EnergyMethods attribute) lkball_nblist (pyrosetta.rosetta.core.scoring.min_pair_data attribute) LKBallDatabase (class in pyrosetta.rosetta.core.scoring.lkball) LKBAtom (class in pyrosetta.rosetta.core.scoring.lkball.lkbtrie) lkbr_score (pyrosetta.rosetta.core.scoring.lkball.ScoredBridgingWater property) lkbr_uncpl_score (pyrosetta.rosetta.core.scoring.lkball.ScoredBridgingWater property) lkbrinfo (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.PlaceableRotamer property) LKBTrieEvaluator (class in pyrosetta.rosetta.core.scoring.lkball.lkbtrie) LKD_ResidueInfo (class in pyrosetta.rosetta.core.scoring.lkball) lkd_respair_data (pyrosetta.rosetta.core.scoring.min_pair_data attribute) lkdome_nblist (pyrosetta.rosetta.core.scoring.min_pair_data attribute) LKHBondInfo (class in pyrosetta.rosetta.core.scoring.hbonds.graph) lle() (in module pyrosetta.rosetta.ObjexxFCL) llt() (in module pyrosetta.rosetta.ObjexxFCL) lm_control_struct (class in pyrosetta.rosetta.numeric.nls) lm_enorm() (in module pyrosetta.rosetta.numeric.nls) lm_index() (pyrosetta.rosetta.numeric.fourier.SO3coeffs method) lm_printout_std() (in module pyrosetta.rosetta.numeric.nls) lm_status_struct (class in pyrosetta.rosetta.numeric.nls) ln() (in module pyrosetta.rosetta.core.scoring.epr_deer) LnExpression (class in pyrosetta.rosetta.protocols.pack_daemon) load() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) (pyrosetta.rosetta.protocols.make_rot_lib.RotData method) (pyrosetta.rosetta.utility.options.OptionCollection method) load_and_hash_fragmentStore() (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStoreManager method) load_bin_params() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionCalculator method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) load_binary() (pyrosetta.rosetta.protocols.cluster.APCluster method) load_build_position_data() (in module pyrosetta.rosetta.protocols.motifs) load_cdr_design_data() (pyrosetta.rosetta.protocols.antibody.AntibodyDatabaseManager method) load_cdr_design_data_for_cdrs() (pyrosetta.rosetta.protocols.antibody.AntibodyDatabaseManager method) load_cdr_pose() (pyrosetta.rosetta.protocols.antibody.AntibodyDatabaseManager method) load_cdr_poses() (pyrosetta.rosetta.protocols.antibody.AntibodyDatabaseManager method) load_cdr_sequences() (pyrosetta.rosetta.protocols.antibody.AntibodyDatabaseManager method) load_checkpoint() (in module pyrosetta.rosetta.protocols.dna) load_checkpoint_file() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) load_component_weights() (in module pyrosetta.rosetta.protocols.optimize_weights) load_conformation() (pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeatures method) (pyrosetta.rosetta.protocols.features.ResidueConformationFeatures method) load_csv() (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorPreLoaded method) load_custom_electrons() (pyrosetta.rosetta.core.scoring.epr_deer.EPRSpinLabel method) load_data() (pyrosetta.rosetta.protocols.chemistries.ChemistryLoader method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoader method) (pyrosetta.rosetta.protocols.ligand_docking.LigandAreaLoader method) (pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoader method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerLoader method) (pyrosetta.rosetta.protocols.parser.ConstraintGeneratorLoader method) (pyrosetta.rosetta.protocols.parser.DatabaseSessionLoader method) (pyrosetta.rosetta.protocols.parser.DataLoader method) (pyrosetta.rosetta.protocols.parser.FragSetLoader method) (pyrosetta.rosetta.protocols.parser.JumpSelectorLoader method) (pyrosetta.rosetta.protocols.parser.MonteCarloLoader method) (pyrosetta.rosetta.protocols.parser.MoveMapFactoryLoader method) (pyrosetta.rosetta.protocols.parser.PackerPaletteLoader method) (pyrosetta.rosetta.protocols.parser.ResidueSelectorLoader method) (pyrosetta.rosetta.protocols.parser.ResLvlTaskOperationLoader method) (pyrosetta.rosetta.protocols.parser.ScoreFunctionLoader method) (pyrosetta.rosetta.protocols.parser.SimpleMetricLoader method) (pyrosetta.rosetta.protocols.parser.TaskOperationLoader method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoader method) load_database() (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorPreLoaded method) load_db() (pyrosetta.rosetta.protocols.loophash.LoopHashLibrary method) load_decoys() (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.ArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.VarianceStatisticsArchive method) load_density() (pyrosetta.rosetta.protocols.loop_grower.DensSkeleton method) load_dist_table() (pyrosetta.rosetta.protocols.noesy_assign.CovalentCompliance method) load_dna_design_defs_from_file() (in module pyrosetta.rosetta.protocols.dna) load_dna_design_defs_from_options() (in module pyrosetta.rosetta.protocols.dna) load_dna_design_defs_from_strings() (in module pyrosetta.rosetta.protocols.dna) load_edge_file() (pyrosetta.rosetta.protocols.sewing.hashing.EdgeMapGenerator method) load_factor() (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) (pyrosetta.rosetta.std.unordered_map_std_pair_char_char_int_core_sequence_CharPairHash_std_equal_to_std_pair_char_char_std_allocator_std_pair_const_std_pair_char_char_int_t method) (pyrosetta.rosetta.std.unordered_map_unsigned_long_numeric_MathMatrix_float_t method) load_fasta_from_rcsb() (in module pyrosetta.toolbox.rcsb) load_ff() (pyrosetta.rosetta.core.scoring.saxs.FormFactorManager method) load_ff_from_db() (pyrosetta.rosetta.core.scoring.saxs.FormFactorManager method) load_filter_bin_params() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) load_fragment_lookup() (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStoreManager method) load_fragment_store() (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStoreManager method) load_from_checkpoint() (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceIn method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceInTail method) load_from_rcsb() (in module pyrosetta.toolbox.rcsb) load_grouped_fragment_store() (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStoreManager method) LOAD_HIERARCHY (pyrosetta.rosetta.basic.ProfTag attribute) load_initial_conformers() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) load_into_pose() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterFeatures method) (pyrosetta.rosetta.protocols.features.AtomAtomPairFeatures method) (pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeatures method) (pyrosetta.rosetta.protocols.features.AtomTypesFeatures method) (pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeatures method) (pyrosetta.rosetta.protocols.features.ChargeChargeFeatures method) (pyrosetta.rosetta.protocols.features.DdGFeatures method) (pyrosetta.rosetta.protocols.features.FeaturesReporter method) (pyrosetta.rosetta.protocols.features.GeometricSolvationFeatures method) (pyrosetta.rosetta.protocols.features.HBondFeatures method) (pyrosetta.rosetta.protocols.features.HBondParameterFeatures method) (pyrosetta.rosetta.protocols.features.helixAssembly.ConcurrencyTest method) (pyrosetta.rosetta.protocols.features.helixAssembly.HelixBundleFeatures method) (pyrosetta.rosetta.protocols.features.HelixCapFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) (pyrosetta.rosetta.protocols.features.JobDataFeatures method) (pyrosetta.rosetta.protocols.features.LoopAnchorFeatures method) (pyrosetta.rosetta.protocols.features.ModelFeatures method) (pyrosetta.rosetta.protocols.features.OrbitalsFeatures method) (pyrosetta.rosetta.protocols.features.PairFeatures method) (pyrosetta.rosetta.protocols.features.PdbDataFeatures method) (pyrosetta.rosetta.protocols.features.PoseCommentsFeatures method) (pyrosetta.rosetta.protocols.features.PoseConformationFeatures method) (pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeatures method) (pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeatures method) (pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeatures method) (pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeatures method) (pyrosetta.rosetta.protocols.features.ProteinRMSDFeatures method) (pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeatures method) (pyrosetta.rosetta.protocols.features.RadiusOfGyrationFeatures method) (pyrosetta.rosetta.protocols.features.ResidueBurialFeatures method) (pyrosetta.rosetta.protocols.features.ResidueConformationFeatures method) (pyrosetta.rosetta.protocols.features.ResidueFeatures method) (pyrosetta.rosetta.protocols.features.ResidueGridScoresFeatures method) (pyrosetta.rosetta.protocols.features.ResidueScoresFeatures method) (pyrosetta.rosetta.protocols.features.ResidueSecondaryStructureFeatures method) (pyrosetta.rosetta.protocols.features.ResidueTotalScoresFeatures method) (pyrosetta.rosetta.protocols.features.ResidueTypesFeatures method) (pyrosetta.rosetta.protocols.features.RotamerBoltzmannWeightFeatures method) (pyrosetta.rosetta.protocols.features.RotamerFeatures method) (pyrosetta.rosetta.protocols.features.RotamerRecoveryFeatures method) (pyrosetta.rosetta.protocols.features.RuntimeFeatures method) (pyrosetta.rosetta.protocols.features.SaltBridgeFeatures method) (pyrosetta.rosetta.protocols.features.ScoreFunctionFeatures method) (pyrosetta.rosetta.protocols.features.ScoreTypeFeatures method) (pyrosetta.rosetta.protocols.features.ScreeningFeatures method) (pyrosetta.rosetta.protocols.features.SecondaryStructureSegmentFeatures method) (pyrosetta.rosetta.protocols.features.SimpleMetricFeatures method) (pyrosetta.rosetta.protocols.features.SmotifFeatures method) (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFeatures method) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeatures method) (pyrosetta.rosetta.protocols.features.StructureFeatures method) (pyrosetta.rosetta.protocols.features.StructureScoresFeatures method) (pyrosetta.rosetta.protocols.features.TaskOperationFeatures method) (pyrosetta.rosetta.protocols.features.TotalScoreFeatures method) (pyrosetta.rosetta.protocols.features.TrajectoryMapFeatures method) (pyrosetta.rosetta.protocols.features.UnrecognizedAtomFeatures method) (pyrosetta.rosetta.protocols.features.WaterFeatures method) load_json_file() (pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences method) load_larmord_neighbor_atoms() (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftPotential method) load_larmord_parameters() (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftPotential method) load_larmord_reference_shifts() (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftPotential method) load_larmord_weights() (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftPotential method) load_lib() (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.HPool_RMSD method) load_loop_definitions() (in module pyrosetta.rosetta.protocols.loops.loops_definers) load_matrix() (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorMatrix method) load_mergeddb() (pyrosetta.rosetta.protocols.loophash.LoopHashLibrary method) load_options_from_file() (pyrosetta.rosetta.utility.options.OptionCollection method) load_options_from_file_exception() (pyrosetta.rosetta.utility.options.OptionCollection method) load_options_from_option_system() (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) load_options_from_stream() (pyrosetta.rosetta.utility.options.OptionCollection method) load_pdb_id_from_file() (pyrosetta.rosetta.protocols.frag_picker.AllowPdbIdFilter method) (pyrosetta.rosetta.protocols.frag_picker.DenyPdbIdFilter method) (pyrosetta.rosetta.protocols.frag_picker.PdbIdChunkFilter method) load_pdb_segments_from_pose_comments() (in module pyrosetta.rosetta.protocols.splice) (pyrosetta.rosetta.protocols.splice.Splice method) (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) load_perturber_bin_params() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) load_pose() (pyrosetta.rosetta.protocols.features.ProteinSilentReport method) load_pose_allocate_memory() (pyrosetta.rosetta.protocols.hybridization.TMalign method) load_poses() (in module pyrosetta.rosetta.protocols.simple_filters) load_prehashed_fragmentStore() (pyrosetta.rosetta.protocols.indexed_structure_store.SSHashedFragmentStore method) load_pssm() (pyrosetta.rosetta.protocols.analysis.simple_metrics.SequenceRecoveryMetric method) load_pssm_data() (pyrosetta.rosetta.protocols.protein_interface_design.ReportPSSMDifferences method) load_s_and_l() (in module pyrosetta.rosetta.protocols.jobdist) (in module pyrosetta.rosetta.protocols.stepwise.setup) load_silent_file() (pyrosetta.rosetta.protocols.toolbox.KClusterData method) load_silent_files() (pyrosetta.rosetta.protocols.toolbox.KClusterData method) load_store() (pyrosetta.protocols.h5_structure_store_provider.H5StructureStoreProvider method) (pyrosetta.rosetta.protocols.indexed_structure_store.DirStructureStoreBackend method) (pyrosetta.rosetta.protocols.indexed_structure_store.JSONStructureStoreBackend method) (pyrosetta.rosetta.protocols.indexed_structure_store.SilentStructureStoreBackend method) (pyrosetta.rosetta.protocols.indexed_structure_store.StructureStoreProvider method) load_structure_store() (pyrosetta.rosetta.protocols.indexed_structure_store.StructureStoreManager method) load_tag() (pyrosetta.rosetta.protocols.features.StructureFeatures method) load_templates_from_pdbs() (pyrosetta.rosetta.protocols.antibody.Ab_TemplateInfo method) load_trial_number_from_checkpoint() (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) load_unboundrot() (in module pyrosetta.rosetta.core.pack.dunbrack) loadable_driver (class in pyrosetta.rosetta.cppdb.backend) LoadDensityMapMover (class in pyrosetta.rosetta.protocols.cryst) LoadDensityMapMoverCreator (class in pyrosetta.rosetta.protocols.cryst) LoadedProbabilitiesMetric (class in pyrosetta.rosetta.core.simple_metrics.per_residue_metrics) LoadedProbabilitiesMetricCreator (class in pyrosetta.rosetta.core.simple_metrics.per_residue_metrics) loader_map() (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderFactory method) (pyrosetta.rosetta.protocols.parser.DataLoaderFactory method) loader_name() (pyrosetta.rosetta.protocols.chemistries.ChemistryLoader static method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoader static method) (pyrosetta.rosetta.protocols.ligand_docking.LigandAreaLoader static method) (pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoader static method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerLoader static method) (pyrosetta.rosetta.protocols.parser.ConstraintGeneratorLoader static method) (pyrosetta.rosetta.protocols.parser.DatabaseSessionLoader static method) (pyrosetta.rosetta.protocols.parser.FragSetLoader static method) (pyrosetta.rosetta.protocols.parser.JumpSelectorLoader static method) (pyrosetta.rosetta.protocols.parser.MonteCarloLoader static method) (pyrosetta.rosetta.protocols.parser.MoveMapFactoryLoader static method) (pyrosetta.rosetta.protocols.parser.PackerPaletteLoader static method) (pyrosetta.rosetta.protocols.parser.ResidueSelectorLoader static method) (pyrosetta.rosetta.protocols.parser.ResLvlTaskOperationLoader static method) (pyrosetta.rosetta.protocols.parser.ScoreFunctionLoader static method) (pyrosetta.rosetta.protocols.parser.SimpleMetricLoader static method) (pyrosetta.rosetta.protocols.parser.TaskOperationLoader static method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoader static method) loader_type() (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderCreator method) (pyrosetta.rosetta.core.conformation.symmetry.SymmDataLoaderCreator method) (pyrosetta.rosetta.core.fragment.FragmentSetLoaderCreator method) (pyrosetta.rosetta.core.import_pose.PoseResourceLoaderCreator method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoaderCreator method) (pyrosetta.rosetta.protocols.loops.LoopsFileLoaderCreator method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceVectorLoaderCreator method) loadFiberDiffractionData() (pyrosetta.rosetta.core.scoring.fiber_diffraction.FiberDiffraction method) loadGDB() (pyrosetta.rosetta.protocols.sparta.GDB method) loadPDB() (pyrosetta.rosetta.protocols.sparta.PDB method) loadPDB_Entry() (pyrosetta.rosetta.protocols.sparta.PDB method) loadPDBFromList() (pyrosetta.rosetta.protocols.cluster.calibur.PreloadedPDB method) LoadPDBMover (class in pyrosetta.rosetta.protocols.simple_moves) LoadPDBMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) loadSilentFile() (pyrosetta.rosetta.protocols.cluster.calibur.PreloadedPDB method) LoadUnboundRotMover (class in pyrosetta.rosetta.protocols.simple_moves) LoadUnboundRotMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) LoadVarSolDistSasaCalculatorMover (class in pyrosetta.rosetta.protocols.vardist_solaccess) LoadVarSolDistSasaCalculatorMoverCreator (class in pyrosetta.rosetta.protocols.vardist_solaccess) loadWeightBias3() (pyrosetta.rosetta.protocols.sparta.ANN method) loadWeights() (pyrosetta.rosetta.protocols.sparta.ANN method) local2global() (pyrosetta.rosetta.core.kinematics.Stub method) local_atom_id() (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomInfo method) local_atom_id_A() (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondInfo method) local_atom_id_D() (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondInfo method) local_atom_id_H() (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondInfo method) local_coord_matrix() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) local_coords (pyrosetta.rosetta.protocols.sewing.hashing.LigandCoordInfo property) local_distviol_cutoff_ (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters property) local_distviol_cutoff_buffer_ (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters property) local_distviol_global_buffer_ (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters property) local_distviol_global_factor_ (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters property) local_distviol_range_ (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters property) local_name() (pyrosetta.rosetta.utility.file.FileName method) local_nstruct() (pyrosetta.rosetta.protocols.design_opt.Supercharge method) local_perturb() (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionSampler method) local_pos1() (pyrosetta.rosetta.protocols.topology_broker.claims.JumpClaim method) local_pos2() (pyrosetta.rosetta.protocols.topology_broker.claims.JumpClaim method) local_position() (pyrosetta.rosetta.protocols.topology_broker.claims.BBClaim method) (pyrosetta.rosetta.protocols.topology_broker.claims.LegacyRootClaim method) local_positions() (pyrosetta.rosetta.protocols.environment.claims.EnvLabelSelector method) local_redock_only() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) local_result_id (pyrosetta.rosetta.protocols.jd3.dag_node_managers.ResultElements property) local_rotamer_id() (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode method) local_rotid_for_rotamer() (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) local_rotid_for_rotamer_on_moltenres() (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) local_rotid_start_for_moltenres_in_bbconf() (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) local_segments() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) local_variable() (pyrosetta.rosetta.protocols.pack_daemon.IterativeVectorExpression method) LocalBackboneMover (class in pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover) LocalBackboneMoverCreator (class in pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover) LocalCoordinateConstraint (class in pyrosetta.rosetta.core.scoring.constraints) LocalCoordinateConstraintCreator (class in pyrosetta.rosetta.core.scoring.constraints) locale (class in pyrosetta.rosetta.std) locale._Impl (class in pyrosetta.rosetta.std) locale.id (class in pyrosetta.rosetta.std) LocalInserter (class in pyrosetta.rosetta.protocols.loophash) LocalInserter_SimpleMin (class in pyrosetta.rosetta.protocols.loophash) LocalPosition (class in pyrosetta.rosetta.core.environment) LocalRelax (class in pyrosetta.rosetta.protocols.relax) LocalRelaxCreator (class in pyrosetta.rosetta.protocols.relax) locate_bcl() (in module pyrosetta.rosetta.core.chemical.bcl) locate_resource_stream() (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocator method) locate_rosetta_database() (in module pyrosetta.rosetta.core.init) location() (pyrosetta.rosetta.numeric.kdtree.KDNode method) (pyrosetta.rosetta.numeric.kdtree.KDPoint method) location_in_parent_node() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNode method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.SingleResidueInvrotTarget method) locator_map() (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorFactory method) locator_tag() (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocator method) locator_type() (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorCreator method) lock() (pyrosetta.rosetta.std.weak_ptr_basic_datacache_CacheableData_t method) (pyrosetta.rosetta.std.weak_ptr_const_basic_datacache_HierarchicalDataMap_t method) (pyrosetta.rosetta.std.weak_ptr_const_core_chemical_AtomTypeSet_t method) (pyrosetta.rosetta.std.weak_ptr_const_core_chemical_ElementSet_t method) (pyrosetta.rosetta.std.weak_ptr_const_core_chemical_MMAtomTypeSet_t method) (pyrosetta.rosetta.std.weak_ptr_const_core_chemical_ResidueType_t method) (pyrosetta.rosetta.std.weak_ptr_const_core_chemical_ResidueTypeSet_t method) (pyrosetta.rosetta.std.weak_ptr_const_core_conformation_Conformation_t method) (pyrosetta.rosetta.std.weak_ptr_const_core_environment_EnvCore_t method) (pyrosetta.rosetta.std.weak_ptr_const_core_environment_FoldTreeSketch_Node_t method) (pyrosetta.rosetta.std.weak_ptr_const_core_kinematics_AtomTree_t method) (pyrosetta.rosetta.std.weak_ptr_const_core_scoring_etable_Etable_t method) (pyrosetta.rosetta.std.weak_ptr_const_core_scoring_etable_MembEtable_t method) (pyrosetta.rosetta.std.weak_ptr_const_protocols_environment_Environment_t method) (pyrosetta.rosetta.std.weak_ptr_const_protocols_enzdes_EnzdesFlexBBProtocol_t method) (pyrosetta.rosetta.std.weak_ptr_const_protocols_enzdes_SecondaryMatchProtocol_t method) (pyrosetta.rosetta.std.weak_ptr_const_protocols_flexpack_rotamer_set_FlexbbRotamerSets_t method) (pyrosetta.rosetta.std.weak_ptr_const_protocols_forge_build_BuildInstruction_t method) (pyrosetta.rosetta.std.weak_ptr_const_protocols_jd3_JGJobNode_t method) (pyrosetta.rosetta.std.weak_ptr_const_protocols_loops_loop_closure_kinematic_closure_KinematicMover_t method) (pyrosetta.rosetta.std.weak_ptr_const_protocols_toolbox_match_enzdes_util_EnzConstraintIO_t method) (pyrosetta.rosetta.std.weak_ptr_const_protocols_toolbox_match_enzdes_util_EnzConstraintParameters_t method) (pyrosetta.rosetta.std.weak_ptr_const_protocols_toolbox_match_enzdes_util_InvrotTreeNodeBase_t method) (pyrosetta.rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyBroker_t method) (pyrosetta.rosetta.std.weak_ptr_const_protocols_topology_broker_TopologyClaimer_t method) (pyrosetta.rosetta.std.weak_ptr_const_utility_tag_Tag_t method) (pyrosetta.rosetta.std.weak_ptr_core_chemical_ResidueType_t method) (pyrosetta.rosetta.std.weak_ptr_core_conformation_Conformation_t method) (pyrosetta.rosetta.std.weak_ptr_core_conformation_parametric_Parameter_t method) (pyrosetta.rosetta.std.weak_ptr_core_conformation_parametric_Parameters_t method) (pyrosetta.rosetta.std.weak_ptr_core_conformation_parametric_ParametersSet_t method) (pyrosetta.rosetta.std.weak_ptr_core_conformation_parametric_ParametrizationCalculator_t method) (pyrosetta.rosetta.std.weak_ptr_core_conformation_Residue_t method) (pyrosetta.rosetta.std.weak_ptr_core_environment_FoldTreeSketch_Node_t method) (pyrosetta.rosetta.std.weak_ptr_core_kinematics_tree_Atom_t method) (pyrosetta.rosetta.std.weak_ptr_core_pose_Pose_t method) (pyrosetta.rosetta.std.weak_ptr_core_pose_reference_pose_ReferencePose_t method) (pyrosetta.rosetta.std.weak_ptr_core_pose_reference_pose_ReferencePoseSet_t method) (pyrosetta.rosetta.std.weak_ptr_numeric_ClusteringTreeNode_t method) (pyrosetta.rosetta.std.weak_ptr_protocols_abinitio_Templates_t method) (pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t method) (pyrosetta.rosetta.std.weak_ptr_protocols_environment_Environment_t method) (pyrosetta.rosetta.std.weak_ptr_protocols_flexpack_rotamer_set_FlexbbRotamerSets_t method) (pyrosetta.rosetta.std.weak_ptr_protocols_forge_components_VarLengthBuild_t method) (pyrosetta.rosetta.std.weak_ptr_protocols_frag_picker_FragmentPicker_t method) (pyrosetta.rosetta.std.weak_ptr_protocols_frag_picker_VallChunk_t method) (pyrosetta.rosetta.std.weak_ptr_protocols_frag_picker_VallProvider_t method) (pyrosetta.rosetta.std.weak_ptr_protocols_helical_bundle_BackboneGridSamplerHelper_t method) (pyrosetta.rosetta.std.weak_ptr_protocols_helical_bundle_BundleGridSamplerHelper_t method) (pyrosetta.rosetta.std.weak_ptr_protocols_jd2_JobInputter_t method) (pyrosetta.rosetta.std.weak_ptr_protocols_jd3_JGJobNode_t method) (pyrosetta.rosetta.std.weak_ptr_protocols_jd3_JGResultNode_t method) (pyrosetta.rosetta.std.weak_ptr_protocols_loops_loop_mover_refine_LoopMover_Refine_CCD_t method) (pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t method) (pyrosetta.rosetta.std.weak_ptr_protocols_noesy_assign_Resonance_t method) (pyrosetta.rosetta.std.weak_ptr_protocols_optimize_weights_WrapperOptEMultifunc_t method) (pyrosetta.rosetta.std.weak_ptr_protocols_toolbox_match_enzdes_util_EnzConstraintIO_t method) (pyrosetta.rosetta.std.weak_ptr_protocols_toolbox_match_enzdes_util_InvrotTreeNodeBase_t method) (pyrosetta.rosetta.std.weak_ptr_protocols_topology_broker_TopologyBroker_t method) (pyrosetta.rosetta.std.weak_ptr_protocols_topology_broker_TopologyClaimer_t method) (pyrosetta.rosetta.std.weak_ptr_protocols_vardist_solaccess_VarSolDistSasaCalculator_t method) (pyrosetta.rosetta.std.weak_ptr_utility_tag_Tag_t method) (pyrosetta.rosetta.std.weak_ptr_utility_tag_XMLSchemaRepeatableCTNode_t method) locked_res() (pyrosetta.rosetta.protocols.splice.Splice method) locked_res_id() (pyrosetta.rosetta.protocols.splice.Splice method) log() (in module pyrosetta.rosetta.numeric) (pyrosetta.rosetta.protocols.frag_picker.QuotaDebug method) log_angles() (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.LogFilePerturber static method) log_error() (pyrosetta.rosetta.numeric.expression_parser.TokenSet method) log_lengths() (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.LogFilePerturber static method) log_odds (pyrosetta.rosetta.protocols.indexed_structure_store.SegmentSequenceProfileResult property) log_pdb_number() (pyrosetta.rosetta.protocols.protein_interface_design.filters.FilterScanFilter method) log_separator() (pyrosetta.rosetta.protocols.protein_interface_design.filters.FilterScanFilter method) log_torsions() (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.LogFilePerturber static method) logarithm() (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator method) logdgaussian() (in module pyrosetta.rosetta.core.scoring.constraints) logdgaussian_deriv() (in module pyrosetta.rosetta.core.scoring.constraints) LogFilePerturber (class in pyrosetta.rosetta.protocols.kinematic_closure.perturbers) LoggedFragmentMover (class in pyrosetta.rosetta.protocols.simple_moves) LoggedFragmentMover.Item (class in pyrosetta.rosetta.protocols.simple_moves) LogicalSelector (class in pyrosetta.rosetta.protocols.pose_selectors) LogicResidueSelector (class in pyrosetta.rosetta.core.select.residue_selector) LogicResidueSelectorCreator (class in pyrosetta.rosetta.core.select.residue_selector) logit() (in module pyrosetta.rosetta.core.scoring.epr_deer) LonePairElectronAffinity (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.Properties attribute) LonePairElectronegativityMulliken (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.Properties attribute) LonePairIonizationPotential (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.Properties attribute) long_mutate_strategy() (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) long_of() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) long_range_container() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) long_range_damping_length() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) long_range_interactions_exist() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge method) long_range_type() (pyrosetta.rosetta.core.energy_methods.AspartimidePenaltyEnergy method) (pyrosetta.rosetta.core.energy_methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.CentroidDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.DEEREnergy method) (pyrosetta.rosetta.core.energy_methods.dfire.DFIRE_Energy method) (pyrosetta.rosetta.core.energy_methods.DisulfideMatchingEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_DihedralEnergy 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.FastDensEnergy method) (pyrosetta.rosetta.core.energy_methods.FullatomDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.GenBornEnergy method) (pyrosetta.rosetta.core.energy_methods.GenericBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.MultipoleElecEnergy method) (pyrosetta.rosetta.core.energy_methods.PoissonBoltzmannEnergy method) (pyrosetta.rosetta.core.energy_methods.RamaPreProEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_StubCoordinateEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.SASAEnergy method) (pyrosetta.rosetta.core.energy_methods.TNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.VdWTinkerEnergy method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintsEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.sym_e.symEnergy method) long_string_rep() (pyrosetta.rosetta.protocols.contact_map.Contact method) LongAxisRotationFreePeptideMover (class in pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers) longdouble_of() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) longer() (pyrosetta.rosetta.core.scoring.sc.Atom method) (pyrosetta.rosetta.numeric.xyzTriple_unsigned_long_t method) (pyrosetta.rosetta.numeric.xyzVector_double_t method) (pyrosetta.rosetta.numeric.xyzVector_float_t method) (pyrosetta.rosetta.numeric.xyzVector_int_t method) (pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t method) longer_or_equal() (pyrosetta.rosetta.core.scoring.sc.Atom method) (pyrosetta.rosetta.numeric.xyzTriple_unsigned_long_t method) (pyrosetta.rosetta.numeric.xyzVector_double_t method) (pyrosetta.rosetta.numeric.xyzVector_float_t method) (pyrosetta.rosetta.numeric.xyzVector_int_t method) (pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t method) LongestContinuousApolarSegmentFilter (class in pyrosetta.rosetta.protocols.simple_filters) LongestContinuousApolarSegmentFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) LongestContinuousPolarSegmentFilter (class in pyrosetta.rosetta.protocols.simple_filters) LongestContinuousPolarSegmentFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) longestSide() (pyrosetta.rosetta.core.grid.CartGrid_double_t method) (pyrosetta.rosetta.core.grid.CartGrid_int_t method) longMessage (pyrosetta.tests.bindings.core.test_pose.TestPoseIO attribute) (pyrosetta.tests.bindings.core.test_pose.TestPoseResidueAccessor attribute) (pyrosetta.tests.bindings.core.test_pose.TestPoseResidueLabelAccessor attribute) (pyrosetta.tests.bindings.core.test_pose.TestPoseScoresAccessor attribute) (pyrosetta.tests.bindings.core.test_pose.TestPosesToSilent attribute) (pyrosetta.tests.distributed.test_dask_worker.TestDaskArgs attribute) LongRangeEnergyType (class in pyrosetta.rosetta.core.scoring.methods) LongRangeTwoBodyEnergy (class in pyrosetta.rosetta.core.scoring.methods) look_for_dna() (in module pyrosetta.rosetta.core.import_pose) look_for_jumps() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar) look_for_jumps_to_next() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar) look_for_jumps_to_previous() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar) look_for_non_jump_reference_to_next() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar) look_for_non_jump_reference_to_previous() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar) look_for_unique_jump_to_moving_res() (in module pyrosetta.rosetta.protocols.stepwise.modeler) lookback() (pyrosetta.rosetta.protocols.indexed_structure_store.SSHashedFragmentStore method) lookback_account_for_dssp_inaccuracy() (pyrosetta.rosetta.protocols.indexed_structure_store.SSHashedFragmentStore method) lookback_stub() (pyrosetta.rosetta.protocols.indexed_structure_store.SSHashedFragmentStore method) lookup() (pyrosetta.rosetta.core.scoring.mm.MMBondAngleLibrary method) (pyrosetta.rosetta.core.scoring.mm.MMBondAngleResidueTypeParamSet method) (pyrosetta.rosetta.core.scoring.mm.MMBondLengthLibrary method) (pyrosetta.rosetta.core.scoring.mm.MMLJLibrary method) (pyrosetta.rosetta.core.scoring.mm.MMTorsionLibrary method) (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) lookup_angle() (pyrosetta.rosetta.core.energy_methods.IdealParametersDatabase method) lookup_angle_legacy() (pyrosetta.rosetta.core.energy_methods.IdealParametersDatabase method) lookup_closest_fragment() (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentLookup method) lookup_config() (pyrosetta.rosetta.protocols.indexed_structure_store.movers.DirectSegmentLookupMover method) lookup_counts() (pyrosetta.rosetta.numeric.histograms.TwoDHistogram_unsigned_long_long_t method) lookup_cp_map() (in module pyrosetta.rosetta.core.scoring.trie) lookup_fragment() (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentLookup method) lookup_idx() (in module pyrosetta.rosetta.core.scoring.rna.data) lookup_improper() (pyrosetta.rosetta.core.energy_methods.IdealParametersDatabase method) lookup_length() (pyrosetta.rosetta.core.energy_methods.IdealParametersDatabase method) lookup_length_legacy() (pyrosetta.rosetta.core.energy_methods.IdealParametersDatabase method) lookup_pseudoprotons() (in module pyrosetta.rosetta.core.scoring.nmr) lookup_result() (pyrosetta.rosetta.protocols.indexed_structure_store.filters.FragmentLookupFilter method) lookup_stored_constraints() (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator static method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG static method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG static method) (pyrosetta.rosetta.protocols.forge.constraints.NtoCConstraintGenerator static method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator static method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator static method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG static method) lookup_three_bond() (pyrosetta.rosetta.core.scoring.mm.MMLJLibrary method) lookup_tors_distr_params() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.TorsionSampler method) lookup_torsion_legacy() (pyrosetta.rosetta.core.energy_methods.IdealParametersDatabase method) lookup_withkey() (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) LookupMode (class in pyrosetta.rosetta.protocols.indexed_structure_store.filters) Loop (class in pyrosetta.rosetta.core.scoring.loop_graph) (class in pyrosetta.rosetta.protocols.fldsgn.topology) (class in pyrosetta.rosetta.protocols.loops) LOOP (pyrosetta.rosetta.protocols.denovo_design.components.SegmentCounts attribute) (pyrosetta.rosetta.protocols.denovo_design.components.SegmentCounts.SegmentType attribute) loop() (pyrosetta.rosetta.core.scoring.loop_graph.LoopCycle method) (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) loop_ang() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CstResInteractions method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions method) loop_begin() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) loop_bump_check (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.filter_type attribute) loop_centroid_relax() (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) loop_close (pyrosetta.rosetta.core.scoring.ScoreType attribute) loop_close_use_6D_potential() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) LOOP_CLOSURE (pyrosetta.rosetta.protocols.abinitio.StageID attribute) loop_closure_energy() (pyrosetta.rosetta.core.scoring.loop_graph.evaluator.GaussianChainFuncPotentialEvaluator method) (pyrosetta.rosetta.core.scoring.loop_graph.evaluator.LoopClosePotentialEvaluator method) (pyrosetta.rosetta.core.scoring.loop_graph.evaluator.SixDTransRotPotentialEvaluator method) loop_cut() (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) loop_cycles() (pyrosetta.rosetta.core.scoring.loop_graph.LoopGraph method) loop_dbase_file_name() (pyrosetta.rosetta.protocols.splice.Splice method) loop_def_loader_ct_namer() (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerLoader static method) loop_definer_xml_schema_group_name() (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerFactory static method) loop_dih() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CstResInteractions method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions method) LOOP_E_SUBMOTIF (pyrosetta.rosetta.core.scoring.rna.RNA_MotifType attribute) loop_end() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) loop_fa_relax() (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) loop_file_name() (pyrosetta.rosetta.protocols.loops.Loops method) loop_fixed_cost() (pyrosetta.rosetta.core.scoring.loop_graph.evaluator.GaussianChainFuncPotentialEvaluator method) (pyrosetta.rosetta.core.scoring.loop_graph.evaluator.LoopClosePotentialEvaluator method) (pyrosetta.rosetta.core.scoring.loop_graph.evaluator.SixDTransRotPotentialEvaluator method) loop_fraction() (pyrosetta.rosetta.core.fragment.SecondaryStructure method) loop_frags() (pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer method) (pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer method) (pyrosetta.rosetta.protocols.topology_broker.CoordConstraintClaimer method) (pyrosetta.rosetta.protocols.topology_broker.CutBiasClaimer method) (pyrosetta.rosetta.protocols.topology_broker.DensityScoringClaimer method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FibrilModelingClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FoldandDockClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.LoopFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer method) (pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts2 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts3 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts4 method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.SequenceClaimer method) (pyrosetta.rosetta.protocols.topology_broker.StartStructClaimer method) (pyrosetta.rosetta.protocols.topology_broker.SymmetryClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TMHTopologySamplerClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TopologyBroker method) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer method) loop_id() (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) loop_incident() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintNode method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.TenANeighborNode method) (pyrosetta.rosetta.core.scoring.TwelveANeighborNode method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) (pyrosetta.rosetta.utility.graph.Node method) loop_index_of_residue() (pyrosetta.rosetta.protocols.loops.Loops method) loop_info() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile method) loop_length() (pyrosetta.rosetta.protocols.indel.IndelOptimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoop method) loop_local_rmsd() (in module pyrosetta.rosetta.protocols.loops) Loop_lt (class in pyrosetta.rosetta.protocols.loops) loop_model() (pyrosetta.rosetta.protocols.LoopRebuild method) loop_modeling() (pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo method) loop_mover() (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial method) loop_mover_fold_tree_constant() (pyrosetta.rosetta.protocols.denovo_design.components.VLBProtected method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) loop_mover_from_tag() (in module pyrosetta.rosetta.protocols.loop_modeling.utilities) loop_mover_str() (pyrosetta.rosetta.protocols.denovo_design.components.VLBProtected method) (pyrosetta.rosetta.protocols.fldsgn.BluePrintBDR method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) loop_of_residue() (pyrosetta.rosetta.protocols.loops.Loops method) loop_pdb_source() (pyrosetta.rosetta.protocols.splice.Splice method) loop_protocol_attlist() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol static method) loop_residues() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) loop_rmsd (pyrosetta.rosetta.protocols.stepwise.modeler.rna.output_data_struct property) loop_rmsd() (in module pyrosetta.rosetta.protocols.loops) loop_rmsd_with_superimpose() (in module pyrosetta.rosetta.protocols.loops) loop_rmsd_with_superimpose_core() (in module pyrosetta.rosetta.protocols.loops) loop_rmsd_wrt_correct_minimized (pyrosetta.rosetta.protocols.stepwise.modeler.rna.output_data_struct property) loop_rmsd_wrt_minimized (pyrosetta.rosetta.protocols.stepwise.modeler.rna.output_data_struct property) loop_score_evaluator() (pyrosetta.rosetta.core.scoring.loop_graph.LoopGraph method) loop_seqid_threshold() (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) loop_seqid_thresholds() (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) loop_size() (pyrosetta.rosetta.protocols.loops.Loops method) loop_sizes() (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) loop_start() (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) loop_start_without_overlap() (in module pyrosetta.rosetta.protocols.denovo_design) loop_stop_without_overlap() (in module pyrosetta.rosetta.protocols.denovo_design) loop_suites() (pyrosetta.rosetta.core.scoring.loop_graph.LoopGraph method) LoopAnalyzerFilter (class in pyrosetta.rosetta.protocols.loops.filters) LoopAnalyzerFilterCreator (class in pyrosetta.rosetta.protocols.loops.filters) LoopAnalyzerMover (class in pyrosetta.rosetta.protocols.analysis) LoopAnalyzerMoverCreator (class in pyrosetta.rosetta.protocols.analysis) LoopAnchorFeatures (class in pyrosetta.rosetta.protocols.features) LoopAnchorFeaturesCreator (class in pyrosetta.rosetta.protocols.features) LoopBuild_main() (in module pyrosetta.rosetta.protocols.loop_build) LoopBuilder (class in pyrosetta.rosetta.protocols.loop_modeling) LoopBuilderCreator (class in pyrosetta.rosetta.protocols.loop_modeling) LoopBuildMover (class in pyrosetta.rosetta.protocols.loop_build) LoopCloseEnergy (class in pyrosetta.rosetta.core.energy_methods) LoopCloseEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) LoopClosePotentialEvaluator (class in pyrosetta.rosetta.core.scoring.loop_graph.evaluator) LoopClosure (class in pyrosetta.rosetta.protocols.loops.loop_closure.ccd) LoopCM (class in pyrosetta.rosetta.protocols.loops.loop_mover) LoopCMCreator (class in pyrosetta.rosetta.protocols.loops.loop_mover) LoopComparator (class in pyrosetta.rosetta.protocols.loop_grower) LoopConfiguration (class in pyrosetta.rosetta.protocols.loops) LoopCycle (class in pyrosetta.rosetta.core.scoring.loop_graph) loopdb_range() (pyrosetta.rosetta.protocols.loophash.LoopHashLibrary method) LoopFilter (class in pyrosetta.rosetta.protocols.loop_modeling.utilities) LoopFinder (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) loopfinder() (in module pyrosetta.rosetta.protocols.loops) LoopFinderCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) LoopFragmentClaimer (class in pyrosetta.rosetta.protocols.topology_broker) LoopFromFileData (class in pyrosetta.rosetta.protocols.loops) LoopGraph (class in pyrosetta.rosetta.core.scoring.loop_graph) LoopGrower (class in pyrosetta.rosetta.protocols.loop_grower) loophash_cycles() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) loophash_main() (in module pyrosetta.rosetta.protocols.loophash) LoopHashDiversifier (class in pyrosetta.rosetta.protocols.loophash) LoopHashDiversifierCreator (class in pyrosetta.rosetta.protocols.loophash) LoopHashLibrary (class in pyrosetta.rosetta.protocols.loophash) LoopHashLibraryLoader (class in pyrosetta.rosetta.protocols.loophash) LoopHashLibraryLoaderCreator (class in pyrosetta.rosetta.protocols.loophash) LoopHashMap (class in pyrosetta.rosetta.protocols.loophash) LoopHashMoverWrapper (class in pyrosetta.rosetta.protocols.loophash) LoopHashMoverWrapperCreator (class in pyrosetta.rosetta.protocols.loophash) LoopHashPerturber (class in pyrosetta.rosetta.protocols.loop_modeler.perturbers) LoopHashRelaxProtocol (class in pyrosetta.rosetta.protocols.loophash) LoopHashSampler (class in pyrosetta.rosetta.protocols.loophash) LoopInfo (class in pyrosetta.rosetta.protocols.denovo_design.task_operations) LoopJumpFoldCst (class in pyrosetta.rosetta.protocols.abinitio) LoopLengthChange (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) LoopLengthChangeCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) LoopModeler (class in pyrosetta.rosetta.protocols.loop_modeler) LoopModelerCreator (class in pyrosetta.rosetta.protocols.loop_modeler) LoopmodelWrapper (class in pyrosetta.rosetta.protocols.loop_build) LoopmodelWrapperCreator (class in pyrosetta.rosetta.protocols.loop_build) LoopMover (class in pyrosetta.rosetta.protocols.loop_modeling) (class in pyrosetta.rosetta.protocols.loops.loop_mover) LoopMover_Perturb_CCD (class in pyrosetta.rosetta.protocols.loops.loop_mover.perturb) LoopMover_Perturb_CCDCreator (class in pyrosetta.rosetta.protocols.loops.loop_mover.perturb) LoopMover_Perturb_KIC (class in pyrosetta.rosetta.protocols.loops.loop_mover.perturb) LoopMover_Perturb_KICCreator (class in pyrosetta.rosetta.protocols.loops.loop_mover.perturb) LoopMover_Perturb_QuickCCD (class in pyrosetta.rosetta.protocols.loops.loop_mover.perturb) LoopMover_Perturb_QuickCCD_Moves (class in pyrosetta.rosetta.protocols.loops.loop_mover.perturb) LoopMover_Perturb_QuickCCD_MovesCreator (class in pyrosetta.rosetta.protocols.loops.loop_mover.perturb) LoopMover_Perturb_QuickCCDCreator (class in pyrosetta.rosetta.protocols.loops.loop_mover.perturb) LoopMover_Refine_Backrub (class in pyrosetta.rosetta.protocols.loops.loop_mover.refine) LoopMover_Refine_BackrubCreator (class in pyrosetta.rosetta.protocols.loops.loop_mover.refine) LoopMover_Refine_CCD (class in pyrosetta.rosetta.protocols.loops.loop_mover.refine) LoopMover_Refine_CCDCreator (class in pyrosetta.rosetta.protocols.loops.loop_mover.refine) LoopMover_Refine_KIC (class in pyrosetta.rosetta.protocols.loops.loop_mover.refine) LoopMover_Refine_KICCreator (class in pyrosetta.rosetta.protocols.loops.loop_mover.refine) LoopMover_SlidingWindow (class in pyrosetta.rosetta.protocols.loop_build) LoopMover_SlidingWindowCreator (class in pyrosetta.rosetta.protocols.loop_build) LoopMoverFactory (class in pyrosetta.rosetta.protocols.loops) LoopMoverFromCommandLine (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) LoopMoverFromCommandLineCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) LoopMoverGroup (class in pyrosetta.rosetta.protocols.loop_modeling.utilities) LoopOver (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) LoopOverCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) LoopPartialSolution (class in pyrosetta.rosetta.protocols.loop_grower) LoopPartialSolutionStore (class in pyrosetta.rosetta.protocols.loop_grower) LoopPivots (class in pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers) LoopProtocol (class in pyrosetta.rosetta.protocols.loop_modeling) LoopProtocolCreator (class in pyrosetta.rosetta.protocols.loop_modeling) LoopRebuild (class in pyrosetta.rosetta.protocols) LoopRefine (class in pyrosetta.rosetta.protocols) LoopRefineInnerCycle (class in pyrosetta.rosetta.protocols.loops.loop_mover.refine) LoopRefineInnerCycleContainer (class in pyrosetta.rosetta.protocols.loops.loop_mover.refine) LoopRefineInnerCycleContainerCreator (class in pyrosetta.rosetta.protocols.loops.loop_mover.refine) LoopRefineInnerCycleFactory (class in pyrosetta.rosetta.protocols.loops.loop_mover.refine) LoopRefineInnerCycleName (class in pyrosetta.rosetta.protocols.loops.loop_mover.refine) LoopRelaxMover (class in pyrosetta.rosetta.protocols.relax.loop) LoopRelaxMoverCreator (class in pyrosetta.rosetta.protocols.relax.loop) LoopRelaxThreadingMover (class in pyrosetta.rosetta.protocols.comparative_modeling) LoopRemodel (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) LoopRemodelCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) loopres_atom_names() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CstResInteractions method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions method) loopres_atoms() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) loopres_base2_atom_names() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CstResInteractions method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions method) loopres_base2_atoms() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) loopres_base_atom_names() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CstResInteractions method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions method) loopres_base_atoms() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) LoopResult (class in pyrosetta.rosetta.protocols.loops.loop_mover) LoopRlxMover (class in pyrosetta.rosetta.protocols.antibody_legacy) LoopRmsdEvaluator (class in pyrosetta.rosetta.protocols.simple_filters) Loops (class in pyrosetta.rosetta.protocols.loops) loops (pyrosetta.rosetta.protocols.forge.remodel.RemodelWorkingSet property) loops() (pyrosetta.rosetta.core.scoring.loop_graph.LoopCycle method) (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.FoldTreeFromLoops method) (pyrosetta.rosetta.protocols.loops.GuardedLoopsFromFile method) (pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC method) (pyrosetta.rosetta.protocols.loops.Loops method) (pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoops method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighbors method) loops_are_closed() (in module pyrosetta.rosetta.protocols.comparative_modeling) loops_around_residues() (in module pyrosetta.rosetta.protocols.loops) loops_buns_polar_calc_name() (pyrosetta.rosetta.protocols.forge.components.BDR static method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelMover static method) loops_definer() (pyrosetta.rosetta.protocols.loops.GuardedLoopsFromFile method) loops_file_data() (pyrosetta.rosetta.protocols.loops.GuardedLoopsFromFile method) (pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover method) loops_from_alignment() (in module pyrosetta.rosetta.protocols.comparative_modeling) loops_from_string() (in module pyrosetta.rosetta.protocols.loops) loops_from_transitive_alignments() (in module pyrosetta.rosetta.protocols.comparative_modeling) loops_set_chainbreak_weight() (in module pyrosetta.rosetta.protocols.loops.loop_mover) loops_set_move_map() (in module pyrosetta.rosetta.protocols.loops) loops_to_build (pyrosetta.rosetta.protocols.forge.remodel.RemodelData property) LoopsDatabaseDefiner (class in pyrosetta.rosetta.protocols.loops.loops_definers) LoopsDatabaseDefinerCreator (class in pyrosetta.rosetta.protocols.loops.loops_definers) LoopsDefiner (class in pyrosetta.rosetta.protocols.loops.loops_definers) LoopsDefinerCreator (class in pyrosetta.rosetta.protocols.loops.loops_definers) LoopsDefinerFactory (class in pyrosetta.rosetta.protocols.loops.loops_definers) LoopsDefinerLoader (class in pyrosetta.rosetta.protocols.loops.loops_definers) LoopsDefinerLoaderCreator (class in pyrosetta.rosetta.protocols.loops.loops_definers) LoopsExplicitDefiner (class in pyrosetta.rosetta.protocols.loops.loops_definers) LoopsExplicitDefinerCreator (class in pyrosetta.rosetta.protocols.loops.loops_definers) LoopsFileData (class in pyrosetta.rosetta.protocols.loops) LoopsFileDefiner (class in pyrosetta.rosetta.protocols.loops.loops_definers) LoopsFileDefinerCreator (class in pyrosetta.rosetta.protocols.loops.loops_definers) LoopsFileIO (class in pyrosetta.rosetta.protocols.loops) LoopsFileLoader (class in pyrosetta.rosetta.protocols.loops) LoopsFileLoaderCreator (class in pyrosetta.rosetta.protocols.loops) LoopsStringDefiner (class in pyrosetta.rosetta.protocols.loops.loops_definers) LoopsStringDefinerCreator (class in pyrosetta.rosetta.protocols.loops.loops_definers) loopstring_to_loopregions() (in module pyrosetta.rosetta.protocols.mpi_refinement) loopstring_to_loopvector() (in module pyrosetta.rosetta.protocols.mpi_refinement) lores() (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) lores_pose() (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryJobResult method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo method) lores_score_early() (pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo method) lores_score_final() (pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo method) lores_scorefxn() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) low (pyrosetta.rosetta.protocols.cryst.CheshireCell property) (pyrosetta.rosetta.protocols.make_rot_lib.TorsionRange property) low_energy_conformers_are_known() (pyrosetta.rosetta.core.chemical.rings.RingConformerSet method) low_memory_mode() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) low_res() (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) low_res_inner_cycles() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) low_res_kink_constraint() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol method) low_res_outer_cycles() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) low_res_refinement() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) low_ring_conformers() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) low_temp() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) lower (pyrosetta.rosetta.core.chemical.sdf.BondData property) lower() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.numeric.geometry.BoundingBox_numeric_xyzVector_double_t method) (pyrosetta.rosetta.numeric.kdtree.HyperRectangle method) (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.Torsion method) (pyrosetta.rosetta.protocols.simple_filters.DeltaFilter method) (pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperation method) (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) lower_anchor() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) lower_bound (pyrosetta.rosetta.protocols.qsar.ColorGradient property) lower_bound() (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapMathConstraint method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERChiSqMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERDistanceDistribution method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERJaccardMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERJSMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERMiscMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEEROverlapMethod method) (pyrosetta.rosetta.core.scoring.PoissonBoltzmannPotential method) (pyrosetta.rosetta.protocols.simple_filters.DisulfideEntropyFilter method) lower_chain() (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation method) lower_connect() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) lower_connect_angle_params() (pyrosetta.rosetta.core.energy_methods.ResidueCartBondedParameters method) lower_connect_atom() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) lower_connect_id() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) lower_dihedrals() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) lower_edge_list_begin() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintNode method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.TenANeighborNode method) (pyrosetta.rosetta.core.scoring.TwelveANeighborNode method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) (pyrosetta.rosetta.utility.graph.Node method) lower_edge_list_end() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintNode method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.TenANeighborNode method) (pyrosetta.rosetta.core.scoring.TwelveANeighborNode method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) (pyrosetta.rosetta.utility.graph.Node method) lower_local() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) lower_neighbor_id() (pyrosetta.rosetta.core.scoring.constraints.CstResNeighbConstIterator method) (pyrosetta.rosetta.core.scoring.constraints.CstResNeighbIterator method) (pyrosetta.rosetta.core.scoring.DenseNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.DenseNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfResNeighbConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfResNeighbIterator method) (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideEnergyContainer method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator method) (pyrosetta.rosetta.core.scoring.ResidueNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.ResidueNeighborIterator method) lower_no_under() (pyrosetta.rosetta.utility.options.OptionCollection static method) lower_numbered_node_symmetry_copy_index() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbond method) lower_padding() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) lower_phi() (pyrosetta.rosetta.protocols.denovo_design.components.ResidueDihedrals method) lower_residue() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) lower_segment() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) LOWER_TERMINUS (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) LOWER_TERMINUS_VARIANT (pyrosetta.rosetta.core.chemical.VariantType attribute) lower_threshold() (pyrosetta.rosetta.protocols.matdes.InterfacePackingFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DesignableResiduesFilter method) lower_upper_connected_across_cutpoint() (in module pyrosetta.rosetta.core.scoring.methods) lowercase() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) lowercased() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) LOWERTERM_CAP (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) LOWERTERM_TRUNC (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) LOWERTERM_TRUNC_VARIANT (pyrosetta.rosetta.core.chemical.VariantType attribute) lowest_delta_torsion_selector (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.selector_type attribute) lowest_energy_selector (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.selector_type attribute) lowest_ring_conformer() (pyrosetta.rosetta.core.chemical.MutableResidueType method) lowest_ring_conformers() (pyrosetta.rosetta.core.chemical.ResidueType method) lowest_rmsd_selector (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.selector_type attribute) lowest_score() (pyrosetta.rosetta.protocols.canonical_sampling.BiasedMonteCarlo method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.DualMonteCarlo method) (pyrosetta.rosetta.protocols.moves.MixedMonteCarlo method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) (pyrosetta.rosetta.protocols.moves.ReplicaExchangeMC method) lowest_score_pose() (pyrosetta.rosetta.protocols.canonical_sampling.BiasedMonteCarlo method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.DualMonteCarlo method) (pyrosetta.rosetta.protocols.moves.MixedMonteCarlo method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) (pyrosetta.rosetta.protocols.moves.ReplicaExchangeMC method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) lowest_scores() (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) LowMemEdge (class in pyrosetta.rosetta.utility.graph) LowMemEdgeListConstIter (class in pyrosetta.rosetta.utility.graph) LowMemEdgeListIter (class in pyrosetta.rosetta.utility.graph) LowMemGraph_core_scoring_hbonds_graph_HBondNode_core_scoring_hbonds_graph_HBondEdge_t (class in pyrosetta.rosetta.utility.graph) LowMemGraphBase (class in pyrosetta.rosetta.utility.graph) LowMemNode (class in pyrosetta.rosetta.utility.graph) lowres_abinitio (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags property) lowres_inner_cycle() (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) lowres_preoptimize (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags property) lowres_reference_energy() (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) lowres_score_function() (pyrosetta.rosetta.protocols.moves.MixedMonteCarlo method) lowval() (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) lpad() (in module pyrosetta.rosetta.ObjexxFCL) lpadded() (in module pyrosetta.rosetta.ObjexxFCL) Lr (pyrosetta.rosetta.core.chemical.element.Elements attribute) lr() (pyrosetta.rosetta.core.conformation.PseudoBond method) LR_AtomData (class in pyrosetta.rosetta.core.scoring.packstat) lr_conn_id() (pyrosetta.rosetta.core.conformation.PseudoBond method) LR_MP_AtomData (class in pyrosetta.rosetta.core.scoring.packstat) lr_resconnid() (pyrosetta.rosetta.core.conformation.PseudoBond method) LREnergyContainer (class in pyrosetta.rosetta.core.scoring) LRmsdFilter (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) LRmsdFilterCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) LSMSearchPattern (class in pyrosetta.rosetta.protocols.hotspot_hashing) lstart() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) lstop() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) lstrip() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) lstrip_whitespace() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) lstripped() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) lstripped_whitespace() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) lt (pyrosetta.rosetta.protocols.simple_filters.comparison_type attribute) lt_dih() (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityInfo method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.CstResInteractions method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ResInteractions method) LT_Expression (class in pyrosetta.rosetta.numeric.expression_parser) lt_or_eq (pyrosetta.rosetta.protocols.simple_filters.comparison_type attribute) LTE_Expression (class in pyrosetta.rosetta.numeric.expression_parser) ltrim() (in module pyrosetta.rosetta.utility) Lu (pyrosetta.rosetta.core.chemical.element.Elements attribute) LU3_COORDINATION (pyrosetta.rosetta.core.chemical.VariantType attribute) Lv (pyrosetta.rosetta.core.chemical.element.Elements attribute) LW_BaseDoubletOrientation (class in pyrosetta.rosetta.core.chemical.rna) LW_orientation() (pyrosetta.rosetta.core.pose.rna.BasePair method) LYS_METHYLATION (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric.PTMPredictionMetricModes attribute) lys_ok_with_1 (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.UnsatCorrectionOptions property) lz() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method)