- d -

• d : protocols::simple_moves::MinimalRotamer
• d0 : protocols::hybridization::TMalign
• D0_MIN : protocols::hybridization::TMalign
• d0_out_ : protocols::hybridization::TMalign
• d0_search : protocols::hybridization::TMalign
• d0A : protocols::hybridization::TMalign
• d0B : protocols::hybridization::TMalign
• d12_ : protocols::toolbox::match_enzdes_util::LigandConformer
• d2 : protocols::normalmode::ContactStruct
• d23_ : protocols::toolbox::match_enzdes_util::LigandConformer
• d2target_ : core::scoring::constraints::ChainbreakDistFunc
• d77_48_lys_ : protocols::ub_e2c::ubi_e2c_modeler
• d77_75g_mtsl_ : protocols::ub_e2c::ubi_e2c_modeler
• d77_ctr_of_mass_ : protocols::ub_e2c::ubi_e2c_modeler
• d77_docking_map_ : protocols::ub_e2c::ubi_e2c_modeler
• d77_end_ : protocols::ub_e2c::ubi_e2c_modeler
• d77_trim_ctr_mass_ : protocols::ub_e2c::ubi_e2c_modeler
• d77_trim_end_ : protocols::ub_e2c::ubi_e2c_modeler
• d_ : protocols::scoring::methods::saxs::PDDFEnergy
• daemon_poses_ : protocols::pack_daemon::DaemonSet
• daemon_set_ : protocols::pack_daemon::MultistateFitnessFunction
• daemon_tasks_ : protocols::pack_daemon::DaemonSet
• daemons_ : protocols::pack_daemon::DaemonSet
• dampen_ : protocols::normalmode::NormalModeMinimizer
• dangle_seq1_3prime_ : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• dangle_seq1_5prime_ : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• dangle_seq2_3prime_ : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• dangle_seq2_5prime_ : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• DATA : protocols::sparta::GDB
• data_ : protocols::analysis::InterfaceAnalyzerMover , protocols::canonical_sampling::BiasEnergy::Histogram< T > , protocols::frag_picker::JCouplingIO , protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering > , protocols::frag_picker::scores::AdaptiveScoreHistogram , protocols::frag_picker::scores::AtomPairConstraintsScore , protocols::frag_picker::scores::DihedralConstraintsScore , protocols::frag_picker::scores::InterbondAngleScore , protocols::frag_picker::scores::JCoupling , protocols::loophash::BackboneDB , protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch , protocols::optimize_weights::OptEData , protocols::optimize_weights::PNatAAOptEPositionData , protocols::optimize_weights::PNatAAOptERotamerData , protocols::optimize_weights::PNatRotOptEPositionData
• data_filename_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• data_format_ : protocols::frag_picker::CSTalosIO , protocols::frag_picker::PhiPsiTalosIO
• data_map_ : protocols::qsar::qsarOptFunc
• data_ndx_ : protocols::toolbox::KClusterElement
• database_filter_ : protocols::features::ProteinSilentReport
• database_fname_ : protocols::toolbox::task_operations::DatabaseThread
• database_name_ : protocols::features::DatabaseJobInputter , protocols::features::DatabaseJobOutputter , protocols::rotamer_recovery::RRReporterSQLite
• database_pq_schema_ : protocols::features::DatabaseJobInputter , protocols::features::DatabaseJobOutputter , protocols::rotamer_recovery::RRReporterSQLite
• database_table_ : protocols::loops::loops_definers::LoopsDatabaseDefiner , protocols::toolbox::task_operations::ReadResfileFromDB
• dataloader_creator_map_ : protocols::jd2::parser::DataLoaderFactory
• dataset_ : protocols::toolbox::KClusterData
• db_ : protocols::features::ProteinBondGeometryFeatures
• db_ang_ : protocols::stepwise::sampler::rna::RNA_KinematicCloser
• DB_FNAME_LEVEL1_1 : protocols::sparta::ANN
• DB_FNAME_LEVEL1_2 : protocols::sparta::ANN
• DB_FNAME_LEVEL1_3 : protocols::sparta::ANN
• DB_FNAME_LEVEL2_1 : protocols::sparta::ANN
• DB_FNAME_LEVEL2_2 : protocols::sparta::ANN
• DB_FNAME_LEVEL2_3 : protocols::sparta::ANN
• db_len_ : protocols::stepwise::sampler::rna::RNA_KinematicCloser
• DB_NAME_PREFIX : protocols::sparta::ANN
• DB_PATH : protocols::sparta::ANN
• db_path_ : protocols::antibody::AntibodyDatabaseManager , protocols::loophash::LoopHashLibrary
• db_session_ : protocols::antibody::AntibodyDatabaseManager , protocols::canonical_sampling::DbTrajectoryReader , protocols::features::ReportToDB , protocols::loops::loops_definers::LoopsDatabaseDefiner , protocols::rotamer_recovery::RRReporterSQLite , protocols::toolbox::task_operations::ReadResfileFromDB , protocols::trajectory::DbTrajectoryReader , protocols::wum::DatabaseEntryWorkUnit
• dbg_output_ : protocols::ddg::ddGMover
• dcalibrate_ : protocols::noesy_assign::PeakAssignmentParameters , protocols::noesy_assign::StructureDependentPeakCalibrator
• dCOM_ : protocols::constraints_additional::COMCoordinateConstraint
• dcu0 : protocols::hybridization::TMalign
• dcut_ : protocols::noesy_assign::DistanceScoreMover , protocols::noesy_assign::PeakAssignmentParameters
• ddg_ : protocols::pb_potential::SetupPoissonBoltzmannPotential , protocols::seeded_abinitio::GrowPeptides
• ddg_based_ : protocols::seeded_abinitio::SeedFoldTree
• ddG_bind_files_ : protocols::optimize_weights::IterativeOptEDriver
• ddG_bind_optE_data_ : protocols::optimize_weights::IterativeOptEDriver
• DDG_cutoff_ : protocols::pmut_scan::PointMutScanDriver
• ddG_cutoff_ : protocols::toolbox::task_operations::RestrictConservedLowDdgOperation
• ddg_cycles_ : protocols::protein_interface_design::Revert
• ddG_filter_ : protocols::simple_filters::InterfaceBindingEnergyDensityFilter
• ddG_mover_ : protocols::simple_filters::DdGScan
• ddg_mut_wt_pairs_ : protocols::optimize_weights::IterativeOptEDriver
• ddG_mutation_data_ : protocols::optimize_weights::IterativeOptEDriver
• ddG_predictions_filename_ : protocols::toolbox::task_operations::RestrictConservedLowDdgOperation
• ddG_scan_mover_ : protocols::features::DdGFeatures
• ddG_threshold_ : protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover
• ddg_threshold_ : protocols::simple_filters::DdgFilter
• ddG_threshold_ : protocols::simple_filters::RotamerBoltzmannWeight
• ddg_tolerance_ : protocols::protein_interface_design::Revert
• ddGs_ : protocols::optimize_weights::IterativeOptEDriver , protocols::simple_filters::RotamerBoltzmannWeight
• ddGs_binding_ : protocols::optimize_weights::IterativeOptEDriver
• dDist_dv1 : protocols::pockets::ray_distance_derivs
• dDist_dv2 : protocols::pockets::ray_distance_derivs
• dDist_dv3 : protocols::pockets::ray_distance_derivs
• dDist_dv4 : protocols::pockets::ray_distance_derivs
• dDist_dv5 : protocols::pockets::ray_distance_derivs
• dDist_dv6 : protocols::pockets::ray_distance_derivs
• debug_ : protocols::anchored_design::AnchoredPerturbMover , protocols::anchored_design::AnchoredRefineMover , protocols::antibody::SnugDock , protocols::hybridization::CartesianSampler , protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::simple_moves::MSDMover , protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers , protocols::toolbox::task_operations::InteractingRotamerExplosion , protocols::toolbox::task_operations::SeqprofConsensusOperation
• decdisc_crystal_natives_ : protocols::optimize_weights::IterativeOptEDriver
• decdisc_decoy_poses_ : protocols::optimize_weights::IterativeOptEDriver
• decdisc_native_decoy_pairs_ : protocols::optimize_weights::IterativeOptEDriver
• decdisc_native_poses_ : protocols::optimize_weights::IterativeOptEDriver
• decdisc_xtal_natives_ : protocols::optimize_weights::IterativeOptEDriver
• decoy_compatibility_ : protocols::noesy_assign::PeakAssignment
• decoy_count_ : protocols::boinc::Boinc
• decoy_discrim_data_ : protocols::optimize_weights::IterativeOptEDriver
• decoy_loop_cutpoint_ : protocols::antibody_legacy::CDRH3Modeler
• decoys_ : protocols::jd2::archive::ArchiveBase , protocols::optimize_weights::PNatStructureOptEData , protocols::wum::WorkUnit_SilentStructStore
• decoys_returned_to_archive_ : protocols::jd2::archive::Batch
• deep_optimization_ : protocols::antibody::GraftedStemOptimizer
• def_parameters : protocols::relax::CentroidRelax
• default_allow_bondangles_ : protocols::helical_bundle::MakeBundle
• default_allow_bondangles_set_ : protocols::helical_bundle::MakeBundle
• default_allow_bondlengths_ : protocols::helical_bundle::MakeBundle
• default_allow_bondlengths_set_ : protocols::helical_bundle::MakeBundle
• default_allow_dihedrals_ : protocols::helical_bundle::MakeBundle
• default_allow_dihedrals_set_ : protocols::helical_bundle::MakeBundle
• default_and_user_ : protocols::antibody::CDRSetOptionsParser , protocols::antibody::design::CDRGraftDesignOptionsParser , protocols::antibody::design::CDRSeqDesignOptionsParser
• DEFAULT_APBS_PATH : protocols::pb_potential::SetupPoissonBoltzmannPotential
• default_bias_ : protocols::canonical_sampling::BiasEnergy
• default_crick_params_file_ : protocols::helical_bundle::MakeBundle
• default_crick_params_file_set_ : protocols::helical_bundle::MakeBundle
• default_delta_omega0_ : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::PerturbBundle
• default_delta_omega0_set_ : protocols::helical_bundle::MakeBundle
• default_delta_omega1_ : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::PerturbBundle
• default_delta_omega1_all_ : protocols::helical_bundle::MakeBundle
• default_delta_omega1_all_set_ : protocols::helical_bundle::MakeBundle
• default_delta_t_ : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::PerturbBundle
• default_delta_t_set_ : protocols::helical_bundle::MakeBundle
• default_displacement : protocols::hotspot_hashing::SICPatternAtTransform
• default_fold_tree_ : protocols::protein_interface_design::movers::PlaceStubMover
• default_helix_length_ : protocols::helical_bundle::MakeBundle
• default_helix_length_set_ : protocols::helical_bundle::MakeBundle
• default_instruction_path_ : protocols::antibody::design::AntibodySeqDesignMover
• default_invert_ : protocols::helical_bundle::MakeBundle
• default_invert_set_ : protocols::helical_bundle::MakeBundle
• default_omega0_ : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::PerturbBundle
• default_omega0_set_ : protocols::helical_bundle::MakeBundle
• default_omega1_ : protocols::helical_bundle::MakeBundle
• default_omega1_set_ : protocols::helical_bundle::MakeBundle
• default_precision_ : protocols::frag_picker::scores::FragmentScoreManager
• default_r0_ : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::PerturbBundle
• default_r0_set_ : protocols::helical_bundle::MakeBundle
• default_repeats_ : protocols::relax::FastRelax
• default_residue_name_ : protocols::helical_bundle::MakeBundle
• default_residue_name_set_ : protocols::helical_bundle::MakeBundle
• default_sample_range_ : protocols::stepwise::monte_carlo::rna::RNA_TorsionMover
• DEFAULT_STATE : protocols::pb_potential::SetupPoissonBoltzmannPotential
• default_value_ : protocols::helical_bundle::PerturbBundleOptions
• default_width_ : protocols::frag_picker::scores::FragmentScoreManager
• default_z1_ : protocols::helical_bundle::MakeBundle
• default_z1_set_ : protocols::helical_bundle::MakeBundle
• define_match_by_single_downstream_positioning_ : protocols::match::MatcherTask
• definition_threshold_ : protocols::features::HBondFeatures
• definition_type_ : protocols::features::HBondFeatures
• degree_vicinity_ : protocols::loops::loop_closure::kinematic_closure::VicinitySamplingKinematicPerturber
• degrees : protocols::ligand_docking::Rotate_info
• degrees_ : protocols::ligand_docking::MinimizeLigand , protocols::nonlocal::HelixRotate
• delay_noesy_reassign_ : protocols::abinitio::IterativeBase
• delete_checkpoints_ : protocols::checkpoint::CheckPointer
• delete_content_only_ : protocols::simple_filters::FileRemoveFilter
• delete_interface_native_sidechains_ : protocols::anchored_design::AnchoredDesignMover
• delete_mover_ : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• delete_res_range_list_ : protocols::stepwise::legacy::modeler::rna::SlicedPoseWorkingParameters
• delete_virtual_residues_after_FastRelax_ : protocols::relax::FastRelax
• delta : protocols::moves::TrialMover
• delta_ : protocols::dna::DNABase , protocols::moves::IteratedConvergenceMover , protocols::protein_interface_design::filters::FilterScanFilter , protocols::protein_interface_design::movers::LoopLengthChange , protocols::scoring::methods::pcs2::GridSearchIterator , protocols::scoring::methods::pcs::GridSearchIterator , protocols::scoring::methods::pcsTs1::GridSearchIterator_Ts1 , protocols::scoring::methods::pcsTs2::GridSearchIterator_Ts2 , protocols::scoring::methods::pcsTs3::GridSearchIterator_Ts3 , protocols::scoring::methods::pcsTs4::GridSearchIterator_Ts4 , protocols::simple_moves::ContingentAcceptMover
• delta_atr_score_ : protocols::stepwise::modeler::protein::checker::ProteinAtrRepChecker , protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker
• delta_coms : protocols::simple_filters::SymmetricMotifFilter
• delta_filters_ : protocols::protein_interface_design::filters::FilterScanFilter
• delta_grid_ : protocols::canonical_sampling::BiasEnergy::Histogram< T >
• delta_length_ : protocols::protein_interface_design::movers::PlaceOnLoop
• delta_omega0_ : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::parameters::BundleParameters , protocols::helical_bundle::PerturbBundle
• delta_omega1_ : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::parameters::BundleParameters , protocols::helical_bundle::PerturbBundle
• delta_omega1_all_ : protocols::helical_bundle::parameters::BundleParameters
• delta_omega1_vals_output_ : protocols::helical_bundle::FitSimpleHelix
• delta_rep_score_ : protocols::stepwise::modeler::protein::checker::ProteinAtrRepChecker , protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker
• delta_t_ : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::parameters::BundleParameters , protocols::helical_bundle::PerturbBundle
• delta_unsat_hbonds : protocols::analysis::InterfaceData
• delta_z1_ : protocols::helical_bundle::parameters::BundleParameters
• delta_z1_vals_output_ : protocols::helical_bundle::FitSimpleHelix
• deltaG_bind_ : protocols::optimize_weights::DGBindOptEData
• deltaT_ : protocols::canonical_sampling::BiasEnergy
• denovo_scorefxn_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::RNA_DeNovoProtocol
• density_redraw : protocols::viewer::GraphicsState
• density_sigma : protocols::viewer::GraphicsState
• densityPtr : protocols::viewer::triangleIterator
• dependencies_ : protocols::forge::build::BuildInstruction
• dependent_dof_names_ : protocols::optimize_weights::WrapperOptEMultifunc
• depth_ : protocols::viewer::triangle
• deque_ : protocols::wum2::WUQueue
• deriv_check_ : protocols::electron_density::BfactorFittingMover , protocols::electron_density::BfactorMultifunc , protocols::farna::RNA_Minimizer , protocols::normalmode::NormalModeMultifunc
• deriv_check_result_ : protocols::normalmode::NormalModeMinimizer , protocols::normalmode::NormalModeMultifunc
• deriv_check_verbose_ : protocols::normalmode::NormalModeMultifunc
• derivs_of_ray_distances_ : protocols::pockets::PlaidFingerprint
• descriptors_ : protocols::features::ScreeningFeatures
• design_ : protocols::antibody::design::CDRGraftDesignOptions , protocols::antibody::design::CDRSeqDesignOptions , protocols::docking::DockingHighResLegacy , protocols::docking::DockingProtocol , protocols::enzdes::DetectProteinLigandInterface , protocols::enzdes::EnzRepackMinimize , protocols::seeded_abinitio::SeedSetupMover , protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockProtocol , protocols::toolbox::task_operations::DatabaseThread , protocols::toolbox::task_operations::RestrictToMoveMapChiOperation
• design_all_aas_ : protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• design_antigen_ : protocols::antibody::design::AntibodySeqDesignTFCreator
• design_chain1_ : protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• design_chain2_ : protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• design_chains_ : protocols::docking::DockTaskFactory
• design_foldpose_ : protocols::seeded_abinitio::SeedSetupMover
• design_framework_ : protocols::antibody::design::AntibodySeqDesignTFCreator
• design_framework_conservative_ : protocols::antibody::design::AntibodySeqDesignTFCreator
• design_framework_conserved_res_ : protocols::antibody::design::AntibodySeqDesignTFCreator
• design_info_ : protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover
• design_layer_ : protocols::flxbb::LayerDesignOperation
• design_loops_ : protocols::toolbox::task_operations::RestrictToLoops
• design_matrix : protocols::forge::remodel::RemodelWorkingSet
• design_method_ : protocols::antibody::design::AntibodySeqDesignMover
• design_mode : protocols::forge::remodel::RemodelData
• design_mover2_ : protocols::protein_interface_design::movers::InterfaceRecapitulationMover
• design_mover_ : protocols::protein_interface_design::movers::InterfaceRecapitulationMover , protocols::simple_moves::MSDMover
• design_movers_ : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover , protocols::protein_interface_design::movers::PlaceStubMover
• design_neighbor : protocols::forge::remodel::RemodelData
• design_neighbors_ : protocols::toolbox::task_operations::RestrictToLoopsAndNeighbors
• design_only_target_residues_ : protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation
• design_partner1_ : protocols::simple_moves::DesignRepackMover
• design_partner2_ : protocols::simple_moves::DesignRepackMover
• design_peptide : protocols::flexpep_docking::FlexPepDockingFlags
• design_post_graft_ : protocols::antibody::design::AntibodyGraftDesignMover
• design_proline_ : protocols::antibody::design::AntibodySeqDesignTFCreator
• design_res_ : protocols::seeded_abinitio::SeedSetupMover
• design_scorefxn_ : protocols::antibody::design::AntibodyDesignMover
• design_shell_ : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator , protocols::toolbox::task_operations::DesignAroundOperation
• design_strategy_ : protocols::antibody::design::CDRSeqDesignOptions
• design_target_ : protocols::seeded_abinitio::SeedSetupMover
• design_target_res_ : protocols::enzdes::DetectProteinLigandInterface
• design_targets_ : protocols::enzdes::EnzdesBaseProtocol , protocols::enzdes::EnzdesFlexibleRegion
• design_taskset_ : protocols::flxbb::FlxbbDesign
• design_type : protocols::forge::remodel::LineObject
• designable : protocols::dna::PositionType
• designable_ : protocols::protein_interface_design::filters::DesignableResiduesFilter , protocols::toolbox::task_operations::DatabaseThread
• designable_only_ : protocols::outputter::ResFileOutputter , protocols::simple_filters::SaveResfileToDiskFilter , protocols::simple_filters::TaskAwareSASAFilter , protocols::simple_moves::symmetry::TaskAwareSymMinMover
• designable_residues_ : protocols::toolbox::match_enzdes_util::EnzdesSeqRecoveryCache
• designable_second_shell_ : protocols::dna::DesignProteinBackboneAroundDNA
• designed_residues_ : protocols::dna::PDBOutput
• desired_conformer_ : protocols::enzdes::ResidueConformerFilter
• desired_entity_history_size_ : protocols::pack_daemon::TopEntitySet
• desired_remodel_ss_strings_ : protocols::enzdes::EnzdesFlexibleRegion
• desired_remodelres_in_vicinity_ : protocols::forge::remodel::ResidueVicinityInfo
• desired_sequence_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• desired_ss_chars_ : protocols::match::SecondaryStructureMPM
• desymmeterize_ : protocols::match::upstream::DunbrackSCSampler
• detach_after_modify_ : protocols::forge::build::BuildInstruction
• detailed_balance_ : protocols::canonical_sampling::CanonicalSamplingMover
• detect_design_interface_ : protocols::enzdes::DetectProteinLigandInterface
• deviation_ : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• dG : protocols::analysis::InterfaceData , protocols::analysis::PerResidueInterfaceData
• dG_binding_ : protocols::optimize_weights::IterativeOptEDriver
• dG_binding_data_ : protocols::optimize_weights::IterativeOptEDriver
• dG_bound_unbound_pairs_ : protocols::optimize_weights::IterativeOptEDriver
• dG_dSASA_ratio : protocols::analysis::InterfaceData
• dhSASA : protocols::analysis::InterfaceData , protocols::analysis::PerResidueInterfaceData
• dhSASA_rel_by_charge : protocols::analysis::InterfaceData , protocols::analysis::PerResidueInterfaceData
• dhSASA_sc : protocols::analysis::InterfaceData , protocols::analysis::PerResidueInterfaceData
• diff_torsions : protocols::stepwise::modeler::rna::output_data_struct
• dihedral_constraints_ : protocols::metal_interface::AddZincSiteConstraints
• dihedrallist : protocols::cartesian::MolecularDynamics
• dim_ : protocols::pockets::PocketGrid , protocols::toolbox::ClusterBase
• dim_prods_ : protocols::match::OccupiedSpaceHash
• dimer_seqsep_cutoff_ : protocols::fldsgn::potentials::sspot::SSPairPotential
• dimprods_ : protocols::match::Bool3DGrid
• dimsizes_ : protocols::match::Bool3DGrid
• dip_score_ : protocols::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments
• dir_ : protocols::rigid::RigidBodyMover
• direction : protocols::hotspot_hashing::VectorPair
• direction_ : protocols::normalmode::NormalModeRelaxMover
• directory_ : protocols::ligand_docking::WriteLigandMolFile
• dis_ : protocols::forge::remodel::ResidueVicinityInfo , protocols::toolbox::match_enzdes_util::ResInteractions
• dis_D1D2_ : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• dis_D2D3_ : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• dis_U1D1_ : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• dis_U1D1_samples_ : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• disAB_ : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• disable_sampling_of_loop_takeoff_ : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• disabled_ : protocols::checkpoint::CheckPointer , protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers
• disallow_deletion_of_last_residue_ : protocols::stepwise::monte_carlo::mover::AddOrDeleteMover
• disallow_quench_ : protocols::toolbox::task_operations::ModifyAnnealer
• disallow_realign_ : protocols::stepwise::modeler::options::StepWiseBasicModelerOptions
• disallowed_host_pos_ : protocols::protein_interface_design::movers::PlaceStubMover
• disallowed_value_ : protocols::flxbb::FilterStructs_TotalCharge
• discard_jumps_ : protocols::topology_broker::FragmentJumpClaimer
• dist : protocols::pockets::UnionEdge
• dist2_cut_ : protocols::normalmode::NormalMode
• dist_ : protocols::fldsgn::SheetConstraintsRCG , protocols::fldsgn::topology::DimerPairing , protocols::fldsgn::topology::HelixPairing , protocols::forge::constraints::NtoC_RCG
• dist_cutoff_ : protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::potentials::sspot::HSPairPotential , protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculator , protocols::toolbox::pose_metric_calculators::NeighborhoodByDistanceCalculator , protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator
• dist_list_ : protocols::toolbox::KClusterElement
• dist_sigma2_ : protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential
• dist_squared_ : protocols::frag_picker::Contact , protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker
• dist_track_ : protocols::noesy_assign::FragsToAtomDist::DistanceRecord
• dist_wts_ : protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential
• distal_partition_res_ : protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSampler
• distance : protocols::antibody::CDRPose
• distance_ : protocols::antibody::clusters::CDRCluster , protocols::contact_map::Contact , protocols::nonlocal::SheetTranslate , protocols::scoring::InterfaceInfo , protocols::simple_filters::AtomicContactFilter , protocols::simple_filters::AtomicDistanceFilter , protocols::simple_filters::TerminusDistanceFilter , protocols::symmetric_docking::SymRestrictTaskForDocking , protocols::toolbox::ClusterBase , protocols::toolbox::task_operations::RestrictToInterface
• distance_bin_width_ : protocols::qsar::scoring_grid::ShapeGrid
• distance_bound_ : protocols::noesy_assign::CrossPeak
• distance_constraints_ : protocols::metal_interface::AddZincSiteConstraints
• distance_cutoff_ : protocols::contact_map::ContactMap , protocols::features::ChargeChargeFeatures , protocols::features::SaltBridgeFeatures , protocols::matdes::InterfacePackingFilter , protocols::protein_interface_design::filters::AtomicContactCountFilter , protocols::seeded_abinitio::CAcstGenerator , protocols::toolbox::pose_metric_calculators::CatPiCalculator , protocols::toolbox::pose_metric_calculators::PiPiCalculator , protocols::toolbox::pose_metric_calculators::SaltBridgeCalculator
• distance_cutoff_for_electrostatic_interactions_ : protocols::features::strand_assembly::SandwichFeatures
• distance_matrix : protocols::cluster::ClusterBase
• distance_matrix_ : protocols::contact_map::ContactMap
• distance_pair_ : protocols::simple_moves::symmetry::SetupNCSMover
• distance_sampling_ : protocols::hotspot_hashing::LSMSearchPattern
• distance_squared_ : protocols::scoring::Interface
• distance_threshold_ : protocols::enzdes::LigBurialFilter , protocols::matdes::OligomericAverageDegreeFilter , protocols::protein_interface_design::filters::AverageDegreeFilter , protocols::simple_filters::AlaScan , protocols::simple_filters::NeighborTypeFilter , protocols::simple_filters::NonSequentialNeighborsFilter , protocols::simple_filters::ResidueBurialFilter , protocols::simple_filters::ResidueDistanceFilter , protocols::toolbox::task_operations::ProteinCore
• distance_weights_ : protocols::frag_picker::scores::ProfileScoreDistWeight
• distanceFromStart : protocols::toolbox::Node
• disth : protocols::kinmatch::KRSQuery
• distinguish_pucker_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection , protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• distribute_over_mpi_ : protocols::optimize_weights::OptEMultifunc
• distribution : protocols::ligand_docking::Rotate_info , protocols::ligand_docking::Translate_info
• distribution_map_ : protocols::ligand_docking::DistributionMap
• distThresh_ : protocols::simple_filters::InterRepeatContactFilter , protocols::simple_filters::IntraRepeatContactFilter
• disulf_fa_max_ : protocols::forge::remodel::RemodelMover
• disulf_file_ : protocols::hybridization::HybridizeProtocol , protocols::hybridization::HybridizeSetup
• disulfide_cutpoint : protocols::forge::remodel::RemodelWorkingSet
• disulfide_data_ : protocols::frag_picker::scores::DisulfideDistance
• disulfide_file_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• disulfide_jump_points : protocols::forge::remodel::RemodelWorkingSet
• disulfide_ss : protocols::forge::remodel::RemodelWorkingSet
• disulfides_ : protocols::simple_moves::ForceDisulfidesMover
• disulfLandingRange : protocols::forge::remodel::RemodelData
• disulfMobileRange : protocols::forge::remodel::RemodelData
• disulfs_ : protocols::hybridization::MRMover
• diversify_ : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• diversify_loop_only_ : protocols::loophash::LoopHashDiversifier
• dle_flag_ : protocols::antibody::ModelCDRH3 , protocols::antibody_legacy::CDRH3Modeler
• dlig_nmeg_limit_ : protocols::pack_daemon::DaemonSet
• dmatrix_ : protocols::scoring::methods::saxs::PDDFEnergy
• dme_threshold_ : protocols::simple_moves::DME_FilterMover
• dmp_pdb_ : protocols::ddg::ddGMover
• dna_base_positions_ : protocols::dna::DNAParameters
• dna_chains_ : protocols::dna::DnaInterfaceMultiStateDesign , protocols::dna::DnaInterfacePacker , protocols::dna::RestrictDesignToProteinDNAInterface
• dna_design_ : protocols::motifs::MotifDnaPacker
• dna_move_ : protocols::relax::FastRelax
• dna_neighbors_ : protocols::dna::DnaInterfaceFinder
• dna_packer_ : protocols::motifs::MotifDnaPacker
• dna_positions_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• dna_sequences_ : protocols::dna::DnaInterfacePacker
• do_add_delete_ : protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo
• do_align_ : protocols::protein_interface_design::filters::RmsdSimpleFilter
• do_chain_closure_ : protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSampler
• do_checks_ : protocols::stepwise::modeler::align::StepWiseClusterer
• do_close_loops_ : protocols::farna::RNA_DeNovoProtocol
• do_cter_insert_ : protocols::antibody::ModelCDRH3
• do_dump_pdb_ : protocols::farna::RNA_Minimizer
• do_h3_modeling_ : protocols::antibody_legacy::CDRH3Modeler
• do_hardsphere_bump_check_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• do_minimize_ : protocols::simple_moves::CombinePoseMover , protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSampler
• do_not_connect_sheets_by_loops_ : protocols::features::strand_assembly::SandwichFeatures
• do_not_sample_multiple_virtual_sugar_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• do_not_write_resfile_of_sandwich_that_has_non_canonical_LR_ : protocols::features::strand_assembly::SandwichFeatures
• do_preminimize_move_ : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• do_rama_check_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• do_sanity_check_ : protocols::loophash::LoopHashLibrary
• do_screen_ : protocols::stepwise::screener::NativeRMSD_Screener
• do_screening_ : protocols::stepwise::modeler::rna::phosphate::PhosphateMover
• do_sfxn_eval_every_iteration_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• dock_chains_ : protocols::analysis::InterfaceAnalyzerMover
• dock_design_filter_map_ : protocols::protein_interface_design::DockDesignFilterFactory
• dock_design_loop_num_ : protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• dock_into_dens_strategy_ : protocols::electron_density::SetupForDensityScoringMover
• dock_lowres_cst_scorefxn_ : protocols::ub_e2c::ubi_e2c_modeler
• dock_lowres_scorefxn_ : protocols::ub_e2c::ubi_e2c_modeler
• dock_mcm_ : protocols::docking::DockMCMProtocol , protocols::surface_docking::FullatomRelaxMover
• dock_mcm_cycle_ : protocols::docking::DockMCMCycle
• dock_mcm_protocol_ : protocols::antibody::RefineBetaBarrel
• dock_min_ : protocols::docking::DockingProtocol
• dock_pert_ : protocols::docking::DockingInitialPerturbation
• dock_post_graft_ : protocols::antibody::design::AntibodyGraftDesignMover
• dock_ppk_ : protocols::docking::DockingPrepackProtocol , protocols::symmetric_docking::SymDockProtocol
• dock_rounds_ : protocols::antibody::design::AntibodyGraftDesignMover
• dock_scorefxn_ : protocols::antibody::LHRepulsiveRamp , protocols::antibody::LHRepulsiveRampLegacy , protocols::antibody::RefineBetaBarrel
• dock_scorefxn_highres_ : protocols::antibody::AntibodyModelerProtocol
• dock_trials_ : protocols::enzdes::PredesignPerturbMover
• dockfa_cst_min_scorefxn_ : protocols::ub_e2c::ubi_e2c_modeler
• dockfa_cst_scorefxn_ : protocols::ub_e2c::ubi_e2c_modeler
• dockfa_min_scorefxn_ : protocols::ub_e2c::ubi_e2c_modeler
• dockfa_scorefxn_ : protocols::ub_e2c::ubi_e2c_modeler
• docking_ : protocols::antibody::SnugDockProtocol
• docking_constraint_ : protocols::docking::DockingProtocol , protocols::docking::TemperedDocking
• docking_frequency_ : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions , protocols::stepwise::monte_carlo::SWA_MoveSelector
• docking_ft_ : protocols::protein_interface_design::movers::SetAtomTree
• docking_high_ : protocols::symmetric_docking::SymDockProtocol
• docking_highres_mover_ : protocols::docking::DockingProtocol
• docking_highres_protocol_mover_ : protocols::docking::DockingHighResLegacy , protocols::symmetric_docking::SymDockingHiRes
• docking_jump_ : protocols::topology_broker::AsymFoldandDockClaimer
• docking_local_refine_ : protocols::antibody_legacy::CDRH3Modeler , protocols::docking::DockingProtocol , protocols::topology_broker::AsymFoldandDockClaimer
• docking_low_ : protocols::symmetric_docking::SymDockProtocol
• docking_lowres_mover_ : protocols::docking::DockingProtocol
• docking_lowres_protocol_ : protocols::docking::DockingLowRes , protocols::symmetric_docking::SymDockingLowRes
• docking_map_ : protocols::ub_e2c::ubi_e2c_modeler
• docking_mover_ : protocols::protein_interface_design::movers::DockAndRetrieveSidechains
• docking_protocol_ : protocols::docking::membrane::MPDockingMover
• docking_score_high_ : protocols::symmetric_docking::SymDockProtocol
• docking_score_high_min_ : protocols::symmetric_docking::SymDockProtocol
• docking_score_low_ : protocols::symmetric_docking::SymDockProtocol
• docking_score_pack_ : protocols::symmetric_docking::SymDockProtocol
• docking_scorefxn_high_ : protocols::antibody::design::AntibodyDesignModeler , protocols::antibody::design::AntibodyDesignMoverGenerator , protocols::docking::DockingProtocol , protocols::docking::TemperedDocking
• docking_scorefxn_low_ : protocols::antibody::design::AntibodyDesignModeler , protocols::antibody::design::AntibodyDesignMoverGenerator , protocols::docking::DockingProtocol , protocols::docking::TemperedDocking
• docking_scorefxn_output_ : protocols::docking::DockingProtocol , protocols::docking::TemperedDocking
• docking_scorefxn_pack_ : protocols::docking::DockingProtocol , protocols::docking::TemperedDocking
• dof : protocols::sic_dock::CorrectionVisitor
• dof_ : protocols::rigid::RigidBodyDofPerturbMover , protocols::rigid::RigidBodyDofRandomizeMover , protocols::rigid::RigidBodyDofTransMover
• dof_conformers_ : protocols::jumping::ResiduePairJump
• dof_ids1_ : protocols::coarse_rna::CoarseRNA_LoopCloser
• dof_ids2_ : protocols::coarse_rna::CoarseRNA_LoopCloser
• dof_ids_ : protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser , protocols::stepwise::sampler::rna::RNA_KinematicCloser
• dof_lower_vals_ : protocols::helical_bundle::BundleGridSamplerHelper
• dof_sample_vals_ : protocols::helical_bundle::BundleGridSamplerHelper
• dof_samples_ : protocols::helical_bundle::BundleGridSamplerHelper
• dof_tasks_ : protocols::simple_moves::MinMover
• dof_upper_vals_ : protocols::helical_bundle::BundleGridSamplerHelper
• dof_values_ : protocols::simple_moves::DOFHistogramRecorder
• dof_variables_ : protocols::optimize_weights::WrapperOptEMultifunc
• dofs_ : protocols::rigid::RigidBodyDofRandomTransMover , protocols::rigid::RigidBodyDofSeqPerturbMover , protocols::rigid::RigidBodyDofSeqRandomizeMover , protocols::rigid::RigidBodyDofSeqTransMover , protocols::simple_moves::DOFHistogramRecorder , protocols::simple_moves::symmetry::FaSymDockingSlideTogether , protocols::simple_moves::symmetry::SymDockingSlideIntoContact , protocols::simple_moves::symmetry::SymmetrySlider
• dofs_for_pose0_ : protocols::normalmode::NormalModeMultifunc
• domain_assembly_ : protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol , protocols::hybridization::HybridizeSetup
• domain_assembly_weights_ : protocols::hybridization::HybridizeProtocol , protocols::hybridization::HybridizeSetup
• domain_map : protocols::cartesian::MolecularDynamics
• domain_move_frequency_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• domains_ : protocols::hybridization::HybridizeProtocol , protocols::hybridization::HybridizeSetup
• dominant_ : protocols::match::output::ResidueKinemageWriter , protocols::match::output::WriteUpstreamHitKinemage
• don_dist_cutoff_ : protocols::features::WaterFeatures
• donor_atom_xyz_list_ : protocols::stepwise::modeler::rna::phosphate::PhosphateMover
• donor_base_atom_xyz_list_ : protocols::stepwise::modeler::rna::phosphate::PhosphateMover
• donorList : protocols::sparta::PDB
• donors : protocols::sic_dock::EdgeStandScore
• donors_ : protocols::protein_interface_design::movers::DesignMinimizeHbonds
• dotscore_ : protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential
• double_lazy_ : protocols::toolbox::task_operations::SetIGTypeOperation
• double_mutant_scan_ : protocols::pmut_scan::PointMutScanDriver
• down_jump_atom_ : protocols::simple_filters::JumpEvaluator
• down_stub_ : protocols::simple_filters::JumpEvaluator
• downhill_accepts_ : protocols::moves::MoverStatistics
• downstream_algorithms_ : protocols::match::Matcher
• downstream_atom_coordinates_needed_ : protocols::match::downstream::SecondaryMatcherToDownstreamResidue
• downstream_atom_inds_used_in_matching_ : protocols::match::MatcherTask
• downstream_atoms_ : protocols::match::output::UpstreamDownstreamCollisionFilter
• downstream_atoms_required_inside_active_site_ : protocols::match::Matcher , protocols::match::MatcherTask
• downstream_builders_ : protocols::match::Matcher
• downstream_chains_ : protocols::analysis::InterfaceAnalyzerMover
• downstream_conf_id : protocols::match::match_dspos1
• downstream_conf_id_ : protocols::match::downstream_hit
• downstream_orientation_atoms_ : protocols::match::Matcher , protocols::match::MatcherTask
• downstream_pose_ : protocols::match::Matcher , protocols::match::MatcherTask , protocols::match::output::UpstreamDownstreamCollisionFilter
• downstream_pose_from_task_ : protocols::match::output::PDBWriter
• downstream_restype_ : protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder , protocols::match::downstream::SecondaryMatcherToDownstreamResidue
• dp_ : protocols::fldsgn::topology::DimerPairing
• dphi : protocols::simple_moves::BBConRotMover , protocols::simple_moves::BBGaussianMover
• dr_cycles_ : protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover
• drift_ : protocols::protein_interface_design::movers::LoopOver , protocols::simple_moves::GenericMonteCarloMover
• drop_random_rate_ : protocols::topology_broker::ConstraintClaimer
• drop_rots_above_cutoff_ : protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers
• dry_run_ : protocols::match::upstream::FullChiSampleSet , protocols::relax::RelaxProtocolBase
• ds_atom_ids_needed_ : protocols::match::downstream::TargetRotamerCoords
• ds_builders_ : protocols::match::output::DownstreamRMSEvaluator
• ds_hitset_end_its_ : protocols::match::output::CloudPDBWriter
• ds_hitset_its_ : protocols::match::output::CloudPDBWriter
• dSASA : protocols::analysis::InterfaceData , protocols::analysis::PerResidueInterfaceData
• dSASA_cutoff_ : protocols::features::InterfaceFeatures
• dSASA_fraction : protocols::analysis::PerResidueInterfaceData
• dSASA_sc : protocols::analysis::InterfaceData , protocols::analysis::PerResidueInterfaceData
• dsbuilder_ : protocols::match::downstream::DownstreamAlgorithm , protocols::match::output::SingleDownstreamResidueWriter
• dsbuilders_ : protocols::match::downstream::ClassicMatchAlgorithm , protocols::match::output::PDBWriter , protocols::match::output::SameSequenceAndDSPositionGrouper , protocols::match::output::UpstreamDownstreamCollisionFilter
• dscore_binding : protocols::dna::Reversion
• dscore_bound : protocols::dna::Reversion
• dsgn_boundary_ : protocols::flxbb::DesignTask_Layer
• dsgn_core_ : protocols::flxbb::DesignTask_Layer
• dsgn_surface_ : protocols::flxbb::DesignTask_Layer
• dspec_binding : protocols::dna::Reversion
• dspec_bound : protocols::dna::Reversion
• dspos : protocols::match::match_dspos1
• dspos1_mode_ : protocols::match::output::BestMatchesCollection
• dspose_ : protocols::match::output::DownstreamRMSEvaluator
• dssp : protocols::features::SecondaryStructureSegment
• dssp_phi_ : protocols::frag_picker::VallResidue
• dssp_psi_ : protocols::frag_picker::VallResidue
• dssp_updated_ss : protocols::forge::remodel::RemodelData
• dsspSS_ : protocols::forge::remodel::RemodelMover::instruction_flags
• dswriter_ : protocols::match::output::WriteUpstreamCoordinateKinemage , protocols::match::output::WriteUpstreamHitKinemage
• dswriters_ : protocols::match::output::WriteKinemageOutputter
• dt_ : protocols::md::MDBase
• dt_ang_ : protocols::stepwise::sampler::rna::RNA_KinematicCloser
• dtest_cutoff_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• dtor_ : protocols::normalmode::TorsionNormalModeMover
• dualspace_ : protocols::antibody::design::AntibodyDesignMoverGenerator , protocols::relax::FastRelax
• dummy_pose_ : protocols::sic_dock::NoPoseXYX_Func
• dummy_score_variations_ : protocols::jd2::archive::EvaluatedArchive
• dump_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::modeler::options::StepWiseBasicModelerOptions , protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• dump_loops_only_ : protocols::canonical_sampling::CanonicalSamplingMover
• dump_motifs_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• dump_pdb_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::farna::RNA_DeNovoProtocol , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator , protocols::protein_interface_design::filters::FilterScanFilter
• dump_pdb_when_fail_ : protocols::fldsgn::BluePrintBDR
• dump_pdbs_ : protocols::helical_bundle::BundleGridSampler
• dump_pose_ : protocols::cryst::TagPoseWithRefinementStatsMover
• dump_pose_fname_ : protocols::simple_filters::RelativePoseFilter
• dump_rounds_ : protocols::mpi_refinement::MPI_Refine_Emperor
• dump_snapshots_ : protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionSampler
• dump_table_ : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover , protocols::simple_filters::NMerSVMEnergyFilter
• dump_weights_file_ : protocols::abinitio::LoopJumpFoldCst
• dumpall_ : protocols::relax::FastRelax
• dumpExemplars_ : protocols::pockets::PocketGrid
• dumpfile_ : protocols::matdes::SchemePlaceMotifsMover
• dumppdb_ : protocols::pockets::PocketConstraint
• dumpPDB_abinitio : protocols::flexpep_docking::FlexPepDockingFlags
• dumpPDB_hires : protocols::flexpep_docking::FlexPepDockingFlags
• dumpPDB_lowres : protocols::flexpep_docking::FlexPepDockingFlags
• dynamic_grid_refinement_ : protocols::match::Matcher , protocols::match::MatcherTask
• dz1_initial_ : protocols::helical_bundle::FitSimpleHelix