Here is a list of all class members with links to the classes they belong to:

- a -

• A() : core::io::CrystInfo
• a() : core::scoring::electron_density::OneGaussianScattering , core::scoring::fiber_diffraction::OneGaussianScattering , core::scoring::packstat::PointPair
• A() : protocols::cryst::Spacegroup , protocols::cryst::WallpaperGroup , protocols::ligand_docking::ga_ligand_dock::hbAcc
• a : protocols::md::Constraint , protocols::pockets::UnionEdge , protocols::sic_dock::Vec3
• a0() : core::scoring::FACTSRsdTypeInfo
• a0_ : core::scoring::FACTSRsdTypeInfo
• a1() : core::scoring::FACTSRsdTypeInfo
• a1_ : core::scoring::FACTSRsdTypeInfo
• a2() : core::scoring::FACTSRsdTypeInfo
• a2_ : core::scoring::FACTSRsdTypeInfo
• a3() : core::scoring::FACTSRsdTypeInfo
• a3_ : core::scoring::FACTSRsdTypeInfo
• A3BHbsPatcher() : protocols::simple_moves::a3b_hbs::A3BHbsPatcher
• A_ : core::io::CrystInfo
• a_ : core::scoring::carbohydrates::CHIEnergyFunction , core::scoring::electron_density::KromerMann , core::scoring::fiber_diffraction::FiberDiffractionEnergy , core::scoring::fiber_diffraction::FiberDiffractionEnergyDens , core::scoring::fiber_diffraction::KromerMann
• A_ : core::scoring::func::KarplusFunc
• a_ : protocols::cryst::Spacegroup , protocols::cryst::WallpaperGroup
• A_ : protocols::frag_picker::JCouplingIO , protocols::frag_picker::scores::JCoupling
• a_ : protocols::scoring::methods::pcs2::PcsTensor , protocols::scoring::methods::pcs::PCS_tensor , protocols::scoring::methods::pcsTs1::PCS_tensor_Ts1 , protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2 , protocols::scoring::methods::pcsTs3::PCS_tensor_Ts3 , protocols::scoring::methods::pcsTs4::PCS_tensor_Ts4
• A_all_ : protocols::scoring::methods::pcs2::PcsDataCenter , protocols::scoring::methods::pcs::PCS_data , protocols::scoring::methods::pcsTs1::PCS_data_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_Ts4
• a_axis_ : protocols::docking::EllipsoidalRandomizationMover
• A_bins : core::scoring::dna::DirectReadoutPotential
• a_form_range() : protocols::recces::options::RECCES_Options
• a_form_range_ : protocols::recces::options::RECCES_Options , protocols::recces::sampler::rna::MC_RNA_Suite
• a_form_torsions_ : protocols::recces::sampler::rna::MC_RNA_Suite
• a_ids_ : core::scoring::saxs::SAXSEnergy , protocols::scoring::methods::saxs::PDDFEnergy
• a_ik : protocols::cluster::Exemplar
• a_ind() : core::scoring::hbonds::HBDerivAssigner
• a_ind_ : core::scoring::hbonds::HBDerivAssigner
• A_index_ : protocols::scoring::methods::pcs2::PcsDataLanthanide , protocols::scoring::methods::pcs::PCS_data_per_lanthanides , protocols::scoring::methods::pcsTs1::PCS_data_per_lanthanides_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_per_lanthanides_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_per_lanthanides_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_per_lanthanides_Ts4
• a_kappa : core::scoring::disulfides::FullatomDisulfideParams13
• a_kk : protocols::cluster::DataPoint
• a_little_verbose_ : protocols::rna::denovo::coarse::CoarseRNA_LoopCloser
• a_logA : core::scoring::disulfides::FullatomDisulfideParams13
• a_mu : core::scoring::disulfides::FullatomDisulfideParams13
• a_to_i() : protocols::normalmode::NormalMode
• a_to_i_ : protocols::normalmode::NormalMode
• aa() : core::chemical::ResidueTypeBase , core::chemical::ResidueTypeFinder , core::chemical::rotamers::CenrotRotamerLibrarySpecification , core::chemical::rotamers::DunbrackRotamerLibrarySpecification , core::conformation::Conformation , core::conformation::Residue , core::fragment::picking_old::vall::VallResidue , core::fragment::torsions
• AA : core::pack::annealer::Key , core::pack::dunbrack::cenrot::CenrotLibrary , core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary
• aa() : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary
• AA : core::pack::dunbrack::RotamerLibrary , core::pack::dunbrack::SingleResidueDunbrackLibrary
• aa() : core::pack::dunbrack::SingleResidueDunbrackLibrary
• AA : core::pack::rotamer_set::WaterAnchorInfo
• aa() : core::pack::rotamer_set::WaterAnchorInfo
• AA : core::pack::task::PackerTask
• aa() : core::pose::Pose
• AA : core::scoring::dna::DNA_EnvPairPotential
• aa() : core::scoring::motif::Xfres
• AA : core::scoring::OmegaTether , core::scoring::PointWaterPotential , core::scoring::Ramachandran2B , core::scoring::Ramachandran , core::scoring::RamaPrePro
• aa() : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters , core::scoring::tableID
• AA : core::select::util::SelectResiduesByLayer
• aa() : core::sequence::AnnotatedSequence
• AA : protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter , protocols::fldsgn::potentials::AACompositionEnergy , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::flxbb::DesignTask
• aa() : protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::remodel::RemodelWorkingSet , protocols::frag_picker::VallResidue , protocols::hbnet::HBondResStruct , protocols::indexed_structure_store::ResidueSidechainEntry
• AA : protocols::minimization_packing::MinimalRotamer
• aa() : protocols::minimization_packing::MinimalRotamer , protocols::noesy_assign::MethylNames , protocols::noesy_assign::Resonance
• AA : protocols::optimize_weights::DDGBindOptEData , protocols::optimize_weights::DDGMutationOptEData , protocols::optimize_weights::PNatAAOptEPositionData , protocols::optimize_weights::PNatAAOptERotamerData
• aa() : protocols::optimize_weights::PNatRotOptEPositionData , protocols::protein_interface_design::movers::VLBInstruction , protocols::simple_filters::ResidueDepthData , protocols::simple_filters::ResidueDepthFrag , protocols::simple_filters::SecretionPredictionFilter::mutt , protocols::simple_moves::Hit
• AA : protocols::splice::ROT
• aa1 : core::import_pose::libraries::BasePairType , core::scoring::motif::ResPairMotif
• aa1_ : core::scoring::motif::ResPairMotif
• aa2 : core::import_pose::libraries::BasePairType , core::scoring::motif::ResPairMotif
• aa2_ : core::scoring::motif::ResPairMotif
• aa_ : core::chemical::ResidueTypeBase , core::chemical::ResidueTypeFinder , core::chemical::rotamers::CenrotRotamerLibrarySpecification , core::chemical::rotamers::DunbrackRotamerLibrarySpecification , core::chemical::Set_AA , core::fragment::picking_old::vall::eval::IdentityEval , core::fragment::picking_old::vall::VallResidue , core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary , core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::rotamer_set::WaterAnchorInfo , core::scoring::motif::Xfres , protocols::denovo_design::task_operations::AAFrequency , protocols::forge::build::Bridge , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::frag_picker::VallResidue , protocols::noesy_assign::MethylNames , protocols::noesy_assign::Resonance , protocols::optimize_weights::PNatRotOptEPositionData , protocols::parser::FragmentReader , protocols::pose_creation::MakePolyXMover
• AA_ : protocols::protein_interface_design::movers::BuildAlaPose
• aa_ : protocols::simple_moves::WaterRot
• aa_background_distribution : protocols::indexed_structure_store::SegmentSequenceProfile
• aa_block_for_baserotamer_ : core::pack::rotamer_set::ContinuousRotamerSet
• aa_block_for_samplingrotamer_ : core::pack::rotamer_set::ContinuousRotamerSet
• aa_comp_setup_ : core::scoring::aa_composition_energy::AACompositionConstraint
• aa_composition_energy_setup() : core::scoring::aa_composition_energy::AACompositionConstraint
• aa_composition_setup_file() : core::scoring::methods::EnergyMethodOptions
• aa_composition_setup_file_count() : core::scoring::methods::EnergyMethodOptions
• aa_composition_setup_files_ : core::scoring::methods::EnergyMethodOptions
• aa_composition_setup_helpers_ : core::scoring::ScoringManager
• aa_encoder_ : core::scoring::methods::NMerSVMEnergy
• aa_exists() : protocols::task_operations::ResidueProbDesignOperation
• aa_exp_ : protocols::optimize_weights::IterativeOptEDriver
• aa_for_rotblock_ : core::pack::rotamer_set::ContinuousRotamerSet
• aa_freq_ : protocols::denovo_design::task_operations::AAFrequencies
• aa_freq_exp_ : protocols::optimize_weights::IterativeOptEDriver
• aa_freq_obs_ : protocols::optimize_weights::IterativeOptEDriver
• aa_frequencies() : protocols::denovo_design::task_operations::ConsensusLoopDesignOperation
• aa_from_resid() : protocols::noesy_assign::ResonanceList
• aa_ind() : protocols::mean_field::AAProb , protocols::mean_field::RotProb
• aa_ind_ : protocols::mean_field::AAProb
• aa_indices_from_submatrix_index() : core::pack::interaction_graph::DoubleLazyEdge
• aa_libraries_ : core::pack::dunbrack::RotamerLibrary
• aa_map_ : protocols::frag_picker::SidechainContactDistCutoff
• aa_matrices() : protocols::mean_field::FlexBBDesignMeanField
• aa_matrices_ : protocols::mean_field::FlexBBDesignMeanField
• aa_matrix() : protocols::mean_field::DesignMeanField , protocols::mean_field::FlexBBDesignMeanField
• aa_matrix_ : protocols::mean_field::DesignMeanField , protocols::mean_field::GenMeanFieldMover
• aa_name() : protocols::noesy_assign::MethylNames
• AA_name3s_ : protocols::constraint_movers::ResidueTypeConstraintMover
• aa_neighbors_for_edges_ : core::pack::interaction_graph::LinearMemNode
• aa_no_extension : protocols::denovo_design::components::IdealAbegoGenerator
• aa_obs_ : protocols::optimize_weights::IterativeOptEDriver
• aa_offsets_ : core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >
• aa_offsets_for_edges_ : core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::PDNode
• AA_OMG_INDEX : core::pack::dunbrack::RotamerLibraryScratchSpace
• aa_order_ : protocols::simple_moves::StructProfileMover
• aa_order_map_ : protocols::frag_picker::scores::ProfileScoreDistWeight
• aa_penalty() : core::fragment::picking_old::vall::eval::IdentityEval
• aa_penalty_ : core::fragment::picking_old::vall::eval::IdentityEval
• AA_PHI_INDEX : core::pack::dunbrack::RotamerLibraryScratchSpace
• aa_potentials_ : core::scoring::PointWaterPotential
• AA_PSI_INDEX : core::pack::dunbrack::RotamerLibraryScratchSpace
• aa_sasa_atoms : protocols::constel::FilterBySASA
• aa_seq_weights_ : core::scoring::methods::SequenceDependentRefEnergy
• aa_sequence() : protocols::splice::ResidueBBDofs
• aa_sequence_ : protocols::splice::ResidueBBDofs
• aa_sets_dec_line_ : protocols::pack_daemon::EntityFunc
• aa_sets_name_map_ : protocols::pack_daemon::EntityFunc
• aa_str() : core::fragment::picking_old::vall::eval::IdentityEval
• aa_submatrix_energies_retrievable() : core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::FixedBBInteractionGraph , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::PDInteractionGraph
• aa_submatrix_history_list_ : core::pack::interaction_graph::DoubleLazyInteractionGraph
• aa_to_index_map_ : protocols::frag_picker::SidechainContactDistCutoff
• aa_type_ : core::pack::interaction_graph::SparseMatrixIndex
• aa_types_for_states_on_file_nodes_ : core::pack::interaction_graph::PDInteractionGraph
• AA_vec : protocols::splice::RotLibOut
• aa_weights_ : core::scoring::methods::ReferenceEnergy
• AACompositionConstraint() : core::scoring::aa_composition_energy::AACompositionConstraint
• AACompositionEnergy() : core::scoring::aa_composition_energy::AACompositionEnergy , protocols::fldsgn::potentials::AACompositionEnergy
• AACompositionEnergySetup() : core::scoring::aa_composition_energy::AACompositionEnergySetup
• AACompositionPropertiesSet() : core::scoring::aa_composition_energy::AACompositionPropertiesSet
• AAFrequencies() : protocols::denovo_design::task_operations::AAFrequencies
• AAFrequency() : protocols::denovo_design::task_operations::AAFrequency
• AAFrequencyMap : protocols::denovo_design::task_operations::AAFrequencies
• AAlist : protocols::sparta::Sparta::SpartaLib
• aalist_ : core::scoring::methods::CenPairMotifDegreeEnergy , core::scoring::methods::CenPairMotifEnergy
• AAMatrix() : protocols::mean_field::AAMatrix
• AAname : core::scoring::constraints::NonResidueTypeConstraint , core::scoring::constraints::ResidueTypeConstraint
• AAProb() : protocols::mean_field::AAProb
• AAProbabilities : protocols::task_operations::ResidueProbDesignOperation
• AARepeatEnergy() : core::scoring::aa_repeat_energy::AARepeatEnergy
• AAs : protocols::denovo_design::task_operations::ConsensusLoopDesignOperation
• aas_ : core::chemical::Selector_AA
• aas_at_grid : core::scoring::dna::DirectReadoutPotential
• aas_to_keep() : core::pack::task::operation::RestrictAbsentCanonicalAASExceptNativeRLT , core::pack::task::operation::RestrictAbsentCanonicalAASRLT
• AASynthesisFitnessCost() : protocols::evolution::AASynthesisFitnessCost
• aatm_ : protocols::simple_moves::WaterRot
• aatype_for_node_state() : core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::FixedBBInteractionGraph , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::PDInteractionGraph
• aatype_for_state() : core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::PDNode
• ab : protocols::denovo_design::components::IdealAbegoGenerator
• ab_db_path_ : protocols::tcr::TCRmodel
• ab_dock_chains() : protocols::antibody::design::GeneralAntibodyModeler
• ab_dock_chains_ : protocols::antibody::design::GeneralAntibodyModeler
• ab_fold_tree() : protocols::protein_interface_design::movers::SetAtomTree
• ab_fold_tree_ : protocols::protein_interface_design::movers::SetAtomTree
• ab_has_light_chain_ : protocols::antibody::snugdock::SnugDock , protocols::antibody::snugdock::SnugDockProtocol
• ab_info_ : protocols::antibody::AntibodyCDRGrafter , protocols::antibody::AntibodyDatabaseManager , protocols::antibody::AntibodyFeatures , protocols::antibody::AntibodyModelerProtocol , protocols::antibody::CDRsMinPackMin , protocols::antibody::clusters::CDRClusterSet , protocols::antibody::constraints::CDRDihedralConstraintMover , protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover , protocols::antibody::constraints::ParatopeSiteConstraintMover , protocols::antibody::design::AntibodyDesignMover , protocols::antibody::design::AntibodySeqDesignTFCreator , protocols::antibody::design::GeneralAntibodyModeler , protocols::antibody::design::MutateFrameworkForCluster , protocols::antibody::GraftCDRLoopsProtocol , protocols::antibody::GraftedStemOptimizer , protocols::antibody::GraftOneCDRLoop , protocols::antibody::H3CterInsert , protocols::antibody::H3PerturbCCD , protocols::antibody::H3RefineCCD , protocols::antibody::LHRepulsiveRampLegacy , protocols::antibody::LHSnugFitLegacy , protocols::antibody::RefineBetaBarrel , protocols::antibody::residue_selector::AntibodyRegionSelector , protocols::antibody::residue_selector::CDRResidueSelector , protocols::antibody::task_operations::AddCDRProfileSetsOperation , protocols::antibody::task_operations::AddCDRProfilesOperation , protocols::antibody::task_operations::DisableAntibodyRegionOperation , protocols::antibody::task_operations::DisableCDRsOperation , protocols::antibody::task_operations::RestrictToCDRsAndNeighbors
• ab_manager_ : protocols::antibody::CDRSetOptionsParser , protocols::antibody::design::CDRGraftDesignOptionsParser , protocols::antibody::design::CDRSeqDesignOptionsParser
• ab_movemap : protocols::antibody_legacy::Antibody
• ab_no_extension : protocols::denovo_design::components::IdealAbegoGenerator
• ab_residues_ : protocols::antibody::snugdock::SnugDockProtocol
• ab_sequence_ : protocols::antibody::AntibodyInfo
• ab_t_info_ : protocols::antibody::GraftCDRLoopsProtocol , protocols::antibody::GraftOneCDRLoop
• Ab_TemplateInfo() : protocols::antibody::Ab_TemplateInfo
• abase1_ : protocols::simple_moves::WaterRot
• abase2() : core::chemical::ResidueType , core::conformation::Residue
• abase2_ : protocols::simple_moves::WaterRot
• abase2_deriv : core::scoring::hbonds::HBondDerivs
• abase2_ind() : core::scoring::hbonds::HBDerivAssigner
• abase2_ind_ : core::scoring::hbonds::HBDerivAssigner
• abase2_indices_ : core::chemical::ResidueType
• abase_deriv : core::scoring::hbonds::HBondDerivs
• abase_ind() : core::scoring::hbonds::HBDerivAssigner
• abase_ind_ : core::scoring::hbonds::HBDerivAssigner
• abase_prime_ind() : core::scoring::hbonds::HBDerivAssigner
• abase_prime_ind_ : core::scoring::hbonds::HBDerivAssigner
• abba_bins_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• Abego() : core::scoring::methods::Abego
• ABEGO() : core::sequence::ABEGO
• abego : protocols::denovo_design::architects::SecStructInfo
• Abego : protocols::denovo_design::components::IdealAbegoGenerator
• abego() : protocols::denovo_design::components::Segment , protocols::denovo_design::components::StructureData
• Abego : protocols::denovo_design::task_operations::ConsensusLoopDatabase
• abego : protocols::denovo_design::task_operations::LoopInfo , protocols::forge::remodel::RemodelData , protocols::forge::remodel::RemodelWorkingSet , protocols::parser::BluePrint
• abego_ : core::fragment::picking_old::vall::eval::ABEGOEval , protocols::denovo_design::components::Segment , protocols::denovo_design::components::StructureData , protocols::denovo_design::movers::AddSegmentDataMover , protocols::forge::components::VarLengthBuild , protocols::parser::BluePrint
• abego_char() : protocols::frag_picker::quota::ABEGO_SS_Map
• ABEGO_SS_Config() : protocols::frag_picker::quota::ABEGO_SS_Config
• ABEGO_SS_Map() : protocols::frag_picker::quota::ABEGO_SS_Map
• ABEGO_SS_Pool() : protocols::frag_picker::quota::ABEGO_SS_Pool
• ABEGO_SS_Score() : protocols::frag_picker::scores::ABEGO_SS_Score
• abego_str() : core::fragment::picking_old::vall::eval::ABEGOEval
• ABEGOEval() : core::fragment::picking_old::vall::eval::ABEGOEval
• ABEGOManager : core::fragment::picking_old::vall::eval::ABEGOEval , core::sequence::ABEGOManager
• abegoManager_ : core::scoring::methods::Abego
• ABEGOManagerOP : core::fragment::picking_old::vall::eval::ABEGOEval
• Abegos : protocols::denovo_design::components::IdealAbegoGenerator
• AbegoToLoopAAsMap : protocols::denovo_design::task_operations::ConsensusLoopDatabase
• abinitio_ : protocols::surface_docking::SurfaceDockingProtocol
• abinitio_mover_weight_ : protocols::topology_broker::TopologyClaimer
• abinitio_score_ : protocols::fold_from_loops::NubInitioMover
• abinitio_stage() : protocols::forge::remodel::RemodelLoopMover
• AbinitioBaseFilter() : protocols::simple_filters::AbinitioBaseFilter
• abort_bad_call() : core::kinematics::tree::Atom_
• abort_min() : core::optimization::Multifunc , core::pack::scmin::CartSCMinMultifunc , core::pack::scmin::SCMinMultifunc , protocols::scoring::methods::pcs2::TensorsOptimizer , protocols::scoring::methods::pcs2::TensorsOptimizerSvd
• abort_on_failed_loop_ : protocols::LoopRebuild
• abrelax_checkpoints_ : protocols::abinitio::AbrelaxApplication
• AbrelaxApplication() : protocols::abinitio::AbrelaxApplication
• AbrelaxMover() : protocols::abinitio::AbrelaxMover
• abs_deriv_dev() : core::optimization::SimpleDerivCheckResult , core::optimization::symmetry::MinDebug
• abs_deriv_dev_ : core::optimization::SimpleDerivCheckResult
• abs_score_convergence_threshold() : protocols::minimization_packing::MinMover
• abs_score_convergence_threshold_ : protocols::minimization_packing::MinMover
• abs_score_diff_after_minimization() : protocols::minimization_packing::MinMover
• abs_stereochem_ : core::chemical::Atom
• AbscriptLoopCloserCM() : protocols::abinitio::abscript::AbscriptLoopCloserCM
• AbscriptMover() : protocols::abinitio::abscript::AbscriptMover
• AbscriptStageMover() : protocols::abinitio::abscript::AbscriptStageMover
• absolute_ccd_tolerance_ : protocols::rna::movers::RNA_LoopCloser
• absolute_stereochemistry() : core::chemical::Atom
• absolute_threshold_ : protocols::rotamer_recovery::RRComparerAutomorphicRMSD , protocols::rotamer_recovery::RRComparerChiDiff , protocols::rotamer_recovery::RRComparerElecDensDiff , protocols::rotamer_recovery::RRComparerRotBins
• abstract_parse_tag() : protocols::splice::SpliceOut , protocols::splice::SpliceOutTail
• AbstractArchiveBase() : protocols::jd2::archive::AbstractArchiveBase
• absX : protocols::pockets::CCluster::Cxyz
• absY : protocols::pockets::CCluster::Cxyz
• absZ : protocols::pockets::CCluster::Cxyz
• acc() : protocols::md::MDBase
• acc_ : protocols::md::MDBase
• acc_atm() : core::scoring::hbonds::HBond
• acc_atm_ : core::pack::interaction_graph::NPDHBond , core::scoring::hbonds::HBond
• acc_atm_is_backbone() : core::scoring::hbonds::HBond
• acc_atm_is_backbone_ : core::scoring::hbonds::HBond
• acc_atm_is_protein_backbone() : core::scoring::hbonds::HBond
• acc_atm_is_protein_backbone_ : core::scoring::hbonds::HBond
• acc_bbg_in_bb_bb_hbond() : core::scoring::hbonds::HBondSet
• acc_chem_type2name_ : core::scoring::hbonds::HBondTypeManager
• acc_chem_type_from_name() : core::scoring::hbonds::HBondTypeManager
• acc_deriv : core::scoring::hbonds::HBondDerivs
• acc_dist_cutoff() : protocols::features::WaterFeatures
• acc_dist_cutoff_ : protocols::features::WaterFeatures
• acc_hybrid_ : core::scoring::hbonds::HBDerivAssigner
• acc_index() : core::scoring::hbonds::HBond
• acc_index_ : core::scoring::hbonds::HBond
• acc_npd_weight() : core::scoring::hbonds::HBond
• acc_npd_weight_ : core::scoring::hbonds::HBond
• acc_occ_data_ : core::scoring::geometric_solvation::DatabaseOccSolEne
• acc_occ_type_has_data() : core::scoring::geometric_solvation::DatabaseOccSolEne
• acc_occ_type_has_data_ : core::scoring::geometric_solvation::DatabaseOccSolEne
• acc_occ_type_mapping() : core::scoring::geometric_solvation::DatabaseOccSolEne
• acc_occ_type_mapping_ : core::scoring::geometric_solvation::DatabaseOccSolEne
• acc_res() : core::scoring::hbonds::HBond
• acc_res_ : core::scoring::hbonds::HBond
• acc_res_is_dna() : core::scoring::hbonds::HBond
• acc_res_is_dna_ : core::scoring::hbonds::HBond
• acc_res_is_protein() : core::scoring::hbonds::HBond
• acc_res_is_protein_ : core::scoring::hbonds::HBond
• acc_rsd_ : core::pack::interaction_graph::NPDHBond
• acc_strength() : core::scoring::hbonds::HBondDatabase
• acc_strength_lookup_ : core::scoring::hbonds::HBondDatabase
• acc_type() : core::scoring::hbonds::HBEvalTuple
• acc_type_ : core::scoring::hbonds::HBEvalTuple
• acc_type_has_data() : core::scoring::geometric_solvation::DatabaseOccSolEne
• acc_type_has_data_ : core::scoring::geometric_solvation::DatabaseOccSolEne
• acc_type_mapping() : core::scoring::geometric_solvation::DatabaseOccSolEne
• acc_type_mapping_ : core::scoring::geometric_solvation::DatabaseOccSolEne
• acc_wt_ : core::pack::interaction_graph::NPDHBond
• acc_wt_alt_ : core::pack::interaction_graph::NPDHBond
• accept : core::pack::annealer::RotSub , core::scoring::BondOrderParser , protocols::monte_carlo::GenericMonteCarloMover
• accept_aborted_loops_ : protocols::loops::loop_mover::IndependentLoopMover
• accept_according_to_dunbrack_ : protocols::simple_moves::sidechain_moves::SidechainMover
• accept_blocks_missing_header_ : protocols::enzdes::AddOrRemoveMatchCsts
• accept_claims() : protocols::topology_broker::TopologyBroker
• accept_count : protocols::relax::SRelaxPose
• accept_counter() : protocols::monte_carlo::GenericMonteCarloMover
• accept_counter_ : protocols::monte_carlo::GenericMonteCarloMover , protocols::moves::TrialCounter
• accept_declined_claim() : protocols::topology_broker::DensityScoringClaimer , protocols::topology_broker::FragmentClaimer , protocols::topology_broker::RigidChunkClaimer , protocols::topology_broker::TopologyClaimer
• accept_hists_ : protocols::backrub::BackrubSidechainMover
• accept_log_ : protocols::antibody::design::AntibodyDesignMover , protocols::carbohydrates::GlycanSampler
• accept_new_conformation() : protocols::loops::loop_closure::ccd::RamaCheckBase
• accept_no_op_moves() : protocols::recces::options::RECCES_Options
• accept_no_op_moves_ : protocols::recces::options::RECCES_Options
• accept_rate_ : protocols::docking::DockingLowRes , protocols::symmetric_docking::SymDockingLowRes
• accept_rate_ens1_ : protocols::docking::DockingLowResEnsemble
• accept_rate_ens2_ : protocols::docking::DockingLowResEnsemble
• acceptable_rmsd_change() : protocols::LoopRebuild
• acceptance_history_ : protocols::jd2::archive::ArchiveBase
• acceptance_rate() : protocols::moves::MoverStatistics , protocols::moves::TrialMover
• ACCEPTANCE_REJECTION_HISTORY_LENGTH : core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::SymmLinearMemNode
• AcceptanceCheck() : protocols::loop_modeling::utilities::AcceptanceCheck
• ACCEPTED : core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::SymmLinearMemNode
• accepted() : protocols::moves::MoverStatistics , protocols::moves::TrialCounter
• accepted_ : protocols::moves::MoverStatistics
• accepted_hbond_count_ : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode
• accepted_history_head_ : core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::SymmLinearMemNode
• accepted_rejected_substitution_history_ : core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::SymmLinearMemNode
• accepted_scores() : protocols::monte_carlo::GenericSimulatedAnnealer
• accepted_scores_ : protocols::monte_carlo::GenericSimulatedAnnealer
• AcceptedScores() : protocols::monte_carlo::AcceptedScores
• AcceptHistoryQueue : protocols::jd2::archive::ArchiveBase
• acceptor() : protocols::ligand_docking::ga_ligand_dock::AtomProperties
• acceptor_group() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbond
• acceptor_group_index_ : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbond
• acceptor_selector() : protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter
• acceptor_selector_ : protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter
• acceptor_symmetry_copy_index() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbond
• AcceptorAtomFilter() : core::chemical::AcceptorAtomFilter
• acceptorList : protocols::sparta::PDB
• acceptorRes_occludingRes_geometric_sol_intra() : core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• acceptorRes_occludingRes_geometric_sol_one_way() : core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• acceptorRes_occludingRes_geometric_sol_one_way_bb_bb() : core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• acceptorRes_occludingRes_geometric_sol_one_way_sc() : core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• acceptors : protocols::sic_dock::EdgeStandScore
• acceptors_ : protocols::hbnet::UnsatSelector , protocols::protein_interface_design::movers::DesignMinimizeHbonds
• accepts() : protocols::frag_picker::quota::ABEGO_SS_Pool
• accepts_ : protocols::simple_moves::sidechain_moves::SidechainMCMover
• accepts_since_last_batch() : protocols::jd2::archive::ArchiveBase
• accepts_since_last_batch_ : protocols::jd2::archive::ArchiveBase
• AcceptToBestMover() : protocols::relax::AcceptToBestMover
• access : core::scoring::sc::Atom
• access_check() : core::environment::DofPassport
• accessible_dofs_ : core::environment::DofPassport
• accomodate_length_change() : protocols::rna::movers::RNAThreadAndMinimizeMover
• accpt_pos() : core::chemical::ResidueType , core::conformation::Residue
• accpt_pos_ : core::chemical::ResidueType
• accpt_pos_sc() : core::chemical::ResidueType , core::conformation::Residue
• accpt_pos_sc_ : core::chemical::ResidueType
• acctype : protocols::ligand_docking::ga_ligand_dock::hbAcc
• accum_ : core::scoring::packstat::Slice , core::scoring::packstat::trace
• accumulate() : core::scoring::EMapVector
• accumulate_area() : core::scoring::packstat::Accumulator , core::scoring::packstat::AreaAccumulator , core::scoring::packstat::MultiProbePerSphereAccumulator , core::scoring::packstat::MultiProbePoseAccumulator , core::scoring::packstat::PerSphereAccumulator
• accumulate_dxdy() : core::scoring::packstat::Accumulator , core::scoring::packstat::AreaAccumulator , core::scoring::packstat::MultiProbePerSphereAccumulator , core::scoring::packstat::MultiProbePoseAccumulator , core::scoring::packstat::PerSphereAccumulator
• accumulate_energy() : core::scoring::constraints::CstResNeighbConstIterator , core::scoring::constraints::CstResNeighbIterator , core::scoring::DenseNeighborConstIterator , core::scoring::DenseNeighborIterator , core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::CentroidDisulfideNeighborConstIterator , core::scoring::disulfides::CentroidDisulfideNeighborIterator , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::DisulfideMatchingNeighborConstIterator , core::scoring::disulfides::DisulfideMatchingNeighborIterator , core::scoring::disulfides::DisulfResNeighbConstIterator , core::scoring::disulfides::DisulfResNeighbIterator , core::scoring::disulfides::FullatomDisulfideEnergyContainer , core::scoring::OneToAllNeighborConstIterator , core::scoring::OneToAllNeighborIterator , core::scoring::PolymerBondedNeighborConstIterator , core::scoring::PolymerBondedNeighborIterator , core::scoring::ResidueNeighborConstIterator , core::scoring::ResidueNeighborIterator
• accumulate_residue_energies() : core::scoring::Energies
• accumulate_residue_total_energies() : core::scoring::Energies
• accumulate_residue_total_energy() : core::scoring::Energies
• accumulate_single_atom_contributions() : core::scoring::lkball::LK_BallEnergy
• accumulate_stack_energy() : core::scoring::methods::FreeDOF_Energy
• accumulated_count_ : protocols::noesy_assign::PeakCalibrator
• accumulated_target_ : protocols::noesy_assign::PeakCalibrator
• accumulator_ : protocols::forge::remodel::RemodelMover
• accuracy_weight : core::scoring::rna::chemical_shift::ChemicalShiftData
• accuracy_weights_ : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• achiral_set() : core::io::NomenclatureManager
• achiral_set_ : core::io::NomenclatureManager
• acid_base_ : protocols::simple_moves::IonizableResidue
• acid_base_coefficient() : protocols::simple_moves::IonizableResidue
• acknowledge_last_substititon_not_committed() : core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode
• acknowledge_neighbors_partial_state_assignment() : core::pack::interaction_graph::FASTERNode
• acknowledge_neighbors_partial_state_substitution() : core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode
• acknowledge_neighbors_perturbed_state() : core::pack::interaction_graph::FASTERNode
• acknowledge_neighbors_state_substitution() : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode
• acknowledge_neighbors_state_zeroed() : core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G > , core::pack::interaction_graph::NPDHBondNode< V, E, G >
• acknowledge_neighbors_substitution() : core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::NPDHBondNode< V, E, G > , core::pack::interaction_graph::NPDHBSimpleNode , protocols::flexpack::interaction_graph::MinimalistFlexbbNode
• acknowledge_neighbors_substitution_surface() : core::pack::interaction_graph::SurfaceNode< V, E, G >
• acknowledge_partial_state_assignment() : core::pack::interaction_graph::FASTEREdge , protocols::flexpack::interaction_graph::FlexbbEdge
• acknowledge_partial_state_change() : core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmMinimalistEdge
• acknowledge_participation_in_perturbation() : core::pack::interaction_graph::FASTEREdge
• acknowledge_perturbed_state() : core::pack::interaction_graph::FASTEREdge
• acknowledge_state_change() : core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G > , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G > , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmMinimalistEdge
• acknowledge_state_zeroed() : core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::HPatchEdge< V, E, G > , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::NPDHBondBackgroundEdge< V, E, G > , core::pack::interaction_graph::NPDHBondEdge< V, E, G > , core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmMinimalistEdge , protocols::flexpack::interaction_graph::MinimalistFlexbbEdge
• acknowledge_state_zeroed_surface() : core::pack::interaction_graph::SurfaceEdge< V, E, G >
• acknowledge_substitution() : core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G > , core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchEdge< V, E, G > , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::NPDHBondBackgroundEdge< V, E, G > , core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G > , core::pack::interaction_graph::NPDHBondEdge< V, E, G > , core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmMinimalistEdge , protocols::flexpack::interaction_graph::MinimalistFlexbbEdge
• acknowledge_substitution_surface() : core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G > , core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceEdge< V, E, G >
• ACO_AOH_orb_Hpol_splines_ : core::scoring::orbitals::OrbitalsLookup
• actcoord() : core::conformation::Residue
• actcoord_ : core::conformation::Residue
• actcoord_atoms() : core::chemical::MutableResidueType , core::chemical::ResidueType , core::conformation::Residue
• actcoord_atoms_indices_ : core::chemical::ResidueType
• action : core::select::movemap::MoveMapFactory::MMJumpAction , core::select::movemap::MoveMapFactory::MMResAction , core::select::movemap::MoveMapFactory::MMResIndexAction
• action_ : core::simple_metrics::metrics::ResidueSummaryMetric , protocols::loophash::EXCN_DB_IO_Failed
• action_pair : core::pack::task::operation::DesignRestrictions
• actions_ : core::pack::task::operation::DesignRestrictions
• activate_daemon_mode() : protocols::pack_daemon::DaemonSet
• activate_residue_dofs() : core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::SCMinMinimizerMap
• activated_ : protocols::jd2::archive::NormalizedEvaluatedArchive
• active : protocols::relax::SRelaxPose
• active_ : protocols::optimize_weights::WeightRangeConstraint
• active_1benmeths_ : core::scoring::MinimizationNode
• active_1benmeths_begin() : core::scoring::MinimizationNode
• active_1benmeths_end() : core::scoring::MinimizationNode
• active_1benmeths_ext_ : core::scoring::MinimizationNode
• active_1benmeths_ext_begin() : core::scoring::MinimizationNode
• active_1benmeths_ext_end() : core::scoring::MinimizationNode
• active_1benmeths_std_ : core::scoring::MinimizationNode
• active_1benmeths_std_begin() : core::scoring::MinimizationNode
• active_1benmeths_std_end() : core::scoring::MinimizationNode
• active_2b_score_types() : core::scoring::EnergyGraph
• active_2b_score_types_ : core::scoring::EnergyGraph
• active_2benmeths_ : core::scoring::MinimizationEdge
• active_2benmeths_begin() : core::scoring::MinimizationEdge
• active_2benmeths_end() : core::scoring::MinimizationEdge
• active_2benmeths_ext_ : core::scoring::MinimizationEdge
• active_2benmeths_ext_begin() : core::scoring::MinimizationEdge
• active_2benmeths_ext_end() : core::scoring::MinimizationEdge
• active_2benmeths_std_ : core::scoring::MinimizationEdge
• active_2benmeths_std_begin() : core::scoring::MinimizationEdge
• active_2benmeths_std_end() : core::scoring::MinimizationEdge
• active_angle() : protocols::recces::sampler::MC_OneTorsion
• active_angle_ : protocols::recces::sampler::MC_OneTorsion
• active_atom_tree() : core::pack::scmin::ResidueAtomTreeCollection
• active_atom_tree_ : core::pack::scmin::ResidueAtomTreeCollection
• active_constraint() : core::scoring::constraints::AmbiguousConstraint
• active_constraint_ : core::scoring::constraints::AmbiguousConstraint
• active_constraints() : core::scoring::constraints::KofNConstraint
• active_constraints_ : core::scoring::constraints::KofNConstraint , protocols::constraints_additional::AmbiguousMultiConstraint
• active_dofs() : core::environment::DofPassport
• active_environment() : protocols::environment::ClientMover
• active_intrares2benmeths_ : core::scoring::MinimizationNode
• active_intrares2benmeths_begin() : core::scoring::MinimizationNode
• active_intrares2benmeths_end() : core::scoring::MinimizationNode
• active_intrares2benmeths_ext_ : core::scoring::MinimizationNode
• active_intrares2benmeths_ext_begin() : core::scoring::MinimizationNode
• active_intrares2benmeths_ext_end() : core::scoring::MinimizationNode
• active_intrares2benmeths_std_ : core::scoring::MinimizationNode
• active_intrares2benmeths_std_begin() : core::scoring::MinimizationNode
• active_intrares2benmeths_std_end() : core::scoring::MinimizationNode
• active_jump() : protocols::recces::sampler::rna::MC_RNA_OneJump
• active_jump_ : protocols::recces::sampler::rna::MC_RNA_OneJump
• active_jumps() : core::environment::DofPassport
• active_ligand_contact_ : protocols::sewing::requirements::LigandClashRequirement
• active_ligand_residue_ : protocols::sewing::requirements::LigandClashRequirement
• active_movable_residues() : protocols::fold_from_loops::movers::NubInitioLoopClosureMover
• active_packable_residues() : protocols::fold_from_loops::movers::NubInitioLoopClosureMover
• active_peaks_ : protocols::noesy_assign::DistanceScoreMover
• active_pose_constraints() : protocols::toolbox::match_enzdes_util::EnzdesCstParamCache
• active_pose_constraints_ : protocols::toolbox::match_enzdes_util::EnzdesCstParamCache
• active_pucker_state_ : protocols::recces::sampler::rna::MC_RNA_Sugar
• active_residue() : core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::ResidueAtomTreeCollection , core::pack::scmin::SCMinMinimizerMap
• active_residue_ : core::pack::scmin::ResidueAtomTreeCollection , protocols::sewing::requirements::ClashRequirement , protocols::sewing::requirements::LigandClashRequirement
• active_residue_atom_to_dofnode_index_ : core::pack::scmin::AtomTreeSCMinMinimizerMap
• active_residue_cop() : core::pack::scmin::ResidueAtomTreeCollection
• active_residue_data() : core::pack::scmin::ResidueAtomTreeCollection
• active_residue_index_for_res_ : core::pack::scmin::SCMinMinimizerMap
• active_residues_ : core::pack::scmin::SCMinMinimizerMap
• active_resnum_ : protocols::sewing::requirements::ClashRequirement , protocols::sewing::requirements::LigandClashRequirement
• active_restype() : core::pack::scmin::ResidueAtomTreeCollection
• active_restype_ : core::pack::scmin::ResidueAtomTreeCollection
• active_restype_index() : core::pack::scmin::ResidueAtomTreeCollection
• active_score_types() : core::pack::interaction_graph::SymmOnTheFlyInteractionGraph , core::scoring::EnergyGraph
• active_score_types_ : core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• active_segment_ : protocols::sewing::requirements::ClashRequirement , protocols::sewing::requirements::LigandClashRequirement , protocols::sewing::requirements::NonTerminalStartingSegmentRequirement
• active_sequence_labels_ : protocols::topology_broker::FragmentClaimer
• active_site_grid() : protocols::match::downstream::DownstreamAlgorithm , protocols::match::downstream::DownstreamBuilder
• active_site_grid_ : protocols::match::downstream::DownstreamAlgorithm , protocols::match::downstream::DownstreamBuilder , protocols::match::Matcher
• active_site_grid_set() : protocols::match::downstream::DownstreamAlgorithm , protocols::match::downstream::DownstreamBuilder
• active_variables() : protocols::pack_daemon::IterativeVectorExpression , protocols::pack_daemon::Mean , protocols::pack_daemon::SurrogateVariableExpression , protocols::pack_daemon::VariableVectorExpression , protocols::pack_daemon::VMax , protocols::pack_daemon::VMaxBy , protocols::pack_daemon::VMin , protocols::pack_daemon::VMinBy
• active_variables_ : protocols::optimize_weights::WrapperOptEMultifunc
• active_variables_this_dependent_dof_ : protocols::optimize_weights::WrapperOptEMultifunc
• active_variables_vector() : protocols::pack_daemon::IterativeVectorExpression , protocols::pack_daemon::VariableVectorExpression , protocols::pack_daemon::VectorExpression
• ActiveSiteGrid() : protocols::match::downstream::ActiveSiteGrid
• ActiveVoxelSet : protocols::match::OccupiedSpaceHash
• activity : protocols::qsar::qsarOptData
• actual_bb() : protocols::match::Bool3DGrid
• actual_cycles() : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• actual_cycles_ : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• actual_phosphate_move_list_ : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• actual_rep_cutoff_ : protocols::stepwise::screener::PartitionContactScreener
• actual_residue_connection() : core::conformation::Residue
• actual_topology() : protocols::simple_filters::SpanTopologyMatchPoseFilter
• actual_twobody_memory_use() : core::pack::interaction_graph::DoubleLazyEdge
• actually_moving_res() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters , protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• adapt_graft_ : protocols::antibody::design::AntibodyDesignMover
• adapt_order_to_pair() : protocols::fold_from_loops::movers::SplitAndMixPoseMover
• adaptation_period() : protocols::monte_carlo::GenericMonteCarloMover
• adaptation_period_ : protocols::monte_carlo::GenericMonteCarloMover
• adaptive() : protocols::monte_carlo::GenericMonteCarloMover
• adaptive_ : protocols::monte_carlo::GenericMonteCarloMover
• adaptive_inner_cycle() : protocols::docking::DockingLowResEnsemble
• adaptive_movers() : protocols::monte_carlo::GenericMonteCarloMover
• adaptive_movers_ : protocols::monte_carlo::GenericMonteCarloMover
• AdaptiveScoreHistogram() : protocols::frag_picker::scores::AdaptiveScoreHistogram
• add() : core::fragment::FragSet , core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > , core::pack::palette::BaseTypeList , protocols::abinitio::StructureStore , protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD , protocols::cluster::calibur::AdjacentList , protocols::forge::build::BuildManager , protocols::frag_picker::BoundedCollector< StrictWeakOrdering > , protocols::frag_picker::CandidatesCollector , protocols::frag_picker::GrabAllCollector , protocols::frag_picker::quota::ABEGO_SS_Pool , protocols::frag_picker::quota::QuotaCollector , protocols::frag_picker::quota::SecondaryStructurePool , protocols::kinematic_closure::perturbers::PerturberSet , protocols::multistage_rosetta_scripts::NoFailDataMap , protocols::network::NetworkQueue , protocols::noesy_assign::PeakAssignmentResidueMap , protocols::pockets::CCluster , protocols::pockets::CClusterSet , protocols::pockets::PCluster , protocols::pockets::PClusterSet , protocols::recces::Histogram , protocols::topology_broker::TopologyBroker , protocols::wum::SilentStructStore , protocols::wum::WorkUnitQueue , protocols::wum::WorkUnitQueue_Swapped
• add_() : core::fragment::ConstantLengthFragSet , core::fragment::FragSet , core::fragment::FragSetCollection , core::fragment::MinimalFragSet , core::fragment::OrderedFragSet
• add_aa_virt_rsd_as_root() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• add_acceptance_check() : protocols::loop_modeling::LoopProtocol
• add_actcoord_atom() : core::chemical::MutableResidueType
• add_active_1benmeth_ext() : core::scoring::MinimizationNode
• add_active_1benmeth_std() : core::scoring::MinimizationNode
• add_active_2benmeth_ext() : core::scoring::MinimizationNode
• add_active_2benmeth_std() : core::scoring::MinimizationNode
• add_active_enmeth_ext() : core::scoring::MinimizationEdge
• add_active_enmeth_std() : core::scoring::MinimizationEdge
• add_additional_low_resolution_step() : protocols::docking::DockingProtocol
• add_additional_task_operaration() : protocols::docking::DockingHighRes , protocols::docking::DockingProtocol , protocols::docking::DockTaskFactory
• add_adduct() : core::chemical::ResidueTypeBase
• add_alanine_constraints() : protocols::aa_composition::AddHelixSequenceConstraintsMover
• add_alanine_constraints_ : protocols::aa_composition::AddHelixSequenceConstraintsMover
• add_all_atoms() : protocols::noesy_assign::PeakAssignmentResidueMap
• add_all_evaluators() : protocols::evaluation::EvaluatorFactory
• add_all_model_edges_from_binary() : protocols::legacy_sewing::SewGraph
• add_aln() : protocols::comparative_modeling::AlignmentCluster
• add_amide_bond_cyclic_constraints() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• add_and_average() : protocols::nmr::pre::PREDistanceRecord
• add_and_initialize_reference_pose() : core::pose::reference_pose::ReferencePoseSet
• add_angle_constraints() : protocols::cyclic_peptide::crosslinker::Metal_HelperBase , protocols::cyclic_peptide::crosslinker::OctahedralMetal_Helper , protocols::cyclic_peptide::crosslinker::SquarePlanarMetal_Helper , protocols::cyclic_peptide::crosslinker::TetrahedralMetal_Helper , protocols::cyclic_peptide::crosslinker::TrigonalPlanarMetal_Helper , protocols::cyclic_peptide::crosslinker::TrigonalPyramidalMetal_Helper
• add_angle_parameter() : core::scoring::methods::ResidueCartBondedParameters
• add_apply_mover() : protocols::environment::EnvMover
• add_arbitrary_score_data_from_pose() : core::io::raw_data::ScoreMap
• add_arbitrary_string_data_from_pose() : core::io::raw_data::ScoreMap
• add_architect() : protocols::denovo_design::architects::CompoundArchitect
• add_as_other_struct_if_relevant() : core::io::silent::SilentFileData
• add_assignment() : protocols::noesy_assign::CrossPeak::Spin
• add_at_ind() : protocols::match::downstream::AtomGeometrySecMatchRPE
• add_atmname_using() : core::scoring::methods::GoapRsdType
• add_atom() : core::chemical::MutableResidueType , core::chemical::sdf::MolFileIOMolecule , core::kinematics::MinimizerMapBase , core::optimization::CartesianMinimizerMap , core::optimization::DOF_Node , core::optimization::MinimizerMap , core::optimization::symmetry::SymMinimizerMap , core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::SCMinMinimizerMap , core::scoring::PDinter , core::scoring::power_diagram::PDinter , protocols::pockets::SmallMol
• add_atom_alias() : core::chemical::MutableResidueType
• add_atom_definitions() : protocols::constraint_generator::HydrogenBondConstraintGenerator
• add_atom_set() : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• add_atom_to_sfr() : core::io::pose_to_sfr::PoseToStructFileRepConverter
• add_atom_to_trie() : core::scoring::trie::RotamerTrie< AT, CPDATA >
• add_atomgeom_evaluator() : protocols::match::downstream::GeometrySecMatchRPE
• add_atoms_from_string() : protocols::constraint_generator::HydrogenBondInfo
• add_atomset_to_perturber_atomset_list() : protocols::generalized_kinematic_closure::GeneralizedKIC
• add_author() : core::io::HeaderInformation
• add_background_edge() : core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > , core::pack::interaction_graph::FirstClassNode< V, E, G >
• add_backrub_mover() : protocols::canonical_sampling::MetropolisHastingsMover
• add_base_name_to_exclude() : core::pack::task::NOTAA
• add_base_name_to_keep() : core::pack::task::PIKAA
• add_base_residue_type() : core::chemical::PoseResidueTypeSet , core::chemical::ResidueTypeSet , core::pack::palette::PackerPalette
• add_base_residue_types_by_properties() : core::pack::palette::PackerPalette
• add_batch() : protocols::jd2::JobDistributor
• add_bb_action() : core::select::movemap::MoveMapFactory
• add_bb_clone() : core::conformation::symmetry::SymmetryInfo
• add_bb_csts_to_loop() : protocols::protein_interface_design::movers::PlaceOnLoop
• add_bb_index_action() : core::select::movemap::MoveMapFactory
• add_bbdep_angle_parameter() : core::scoring::methods::ResidueCartBondedParameters
• add_bbdep_length_parameter() : core::scoring::methods::ResidueCartBondedParameters
• add_behavior() : core::pack::task::PackerTask , core::pack::task::PackerTask_ , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• add_big_fragments() : protocols::hybridization::HybridizeProtocol
• add_bin_transition_data() : core::scoring::bin_transitions::BinTransitionCalculator
• add_binders() : protocols::fold_from_loops::utils::Nub
• add_blacklist() : protocols::wum::WorkUnitBase
• add_bond() : core::chemical::MutableResidueType , core::chemical::sdf::MolFileIOMolecule
• add_bond_angle_constraint() : protocols::rna::movers::RNAIdealizeMover , protocols::simple_moves::ConstrainToIdealMover
• add_bond_constraint() : protocols::rna::movers::RNAIdealizeMover
• add_bond_dihedral_constraint() : protocols::simple_moves::ConstrainToIdealMover
• add_bond_length() : core::chemical::IdealBondLengthSet
• add_bond_length_constraint() : protocols::simple_moves::ConstrainToIdealMover
• add_bondangle_perturbation() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• add_bondangles_action() : core::select::movemap::MoveMapFactory
• add_bonded_orbital() : core::chemical::Atom
• add_bondlength_perturbation() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• add_bondlengths_action() : core::select::movemap::MoveMapFactory
• add_bonus_map_entry() : core::scoring::constraints::ResidueTypeLinkingConstraint
• add_boolean_parameter() : core::conformation::parametric::ParametrizationCalculator
• add_branches_action() : core::select::movemap::MoveMapFactory
• add_build_set() : protocols::match::upstream::ProteinUpstreamBuilder
• add_c_terminal_constraints() : protocols::aa_composition::AddHelixSequenceConstraintsMover
• add_c_terminal_constraints_ : protocols::aa_composition::AddHelixSequenceConstraintsMover
• add_calculator() : core::pose::metrics::PoseMetricContainer
• add_canonical_atom_alias() : core::chemical::MutableResidueType
• add_cap_seq() : protocols::simple_moves::RepeatPropagationMover
• add_cap_seq_and_structure() : protocols::simple_moves::RepeatPropagationMover
• add_capping_base_pairs_to_full_sequence() : core::import_pose::RNA_HelixAssembler
• add_case() : core::chemical::Patch
• add_CDR_to_MoveMap() : protocols::antibody::AntibodyInfo
• add_cenrot_residue_library() : core::pack::dunbrack::cenrot::CenrotLibrary
• add_chain_ending() : core::io::silent::BinarySilentStruct , core::io::silent::ProteinSilentStruct_Template< T >
• add_chain_id() : protocols::features::InterfaceDdGMover
• add_chain_name() : protocols::features::InterfaceDdGMover
• add_chainbreak_variants() : protocols::abinitio::KinematicControl , protocols::environment::EnvClaimBroker , protocols::topology_broker::TopologyBroker
• add_chainbreaks() : protocols::jumping::JumpSample
• add_chainbreaks_as_distance_constraint() : protocols::jumping::JumpSample
• add_chainbreakweights() : protocols::seeded_abinitio::CloseFold , protocols::seeded_abinitio::DefineMovableLoops
• add_chem_shift_info() : protocols::rna::denovo::movers::RNA_DeNovoProtocolMover , protocols::rna::denovo::RNA_DeNovoProtocol
• add_chi() : core::chemical::MutableResidueType
• add_chi_action() : core::select::movemap::MoveMapFactory
• add_chi_clone() : core::conformation::symmetry::SymmetryInfo
• add_chi_rotamer() : core::chemical::MutableChiRecord , core::chemical::MutableResidueType
• add_chi_rotamer_to_last_chi() : core::chemical::MutableResidueType
• add_child() : protocols::jd3::JGResultNode , protocols::loop_modeling::LoopMover
• add_choice() : protocols::genetic_algorithm::DiscreteRandomizer
• add_chunk() : protocols::abinitio::abscript::ResidueChunkSelection
• add_chunk_filter() : protocols::frag_picker::FragmentPicker
• add_chunk_set() : core::import_pose::libraries::RNA_ChunkLibrary
• add_circle() : core::scoring::packstat::Slice
• add_claim() : protocols::environment::ScriptCM
• add_closebond_logic() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• add_closebond_logic_isopeptide() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• add_closebond_logic_n_to_c_amide_bond() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• add_closebond_logic_terminal_disulfide() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• add_combined_solutions() : protocols::denovo_design::components::FoldGraph
• add_comment() : core::io::silent::SilentStruct
• add_common_denovo_architect_attributes() : protocols::denovo_design::architects::DeNovoArchitect
• add_common_xml_elements() : protocols::denovo_design::components::SegmentPairing
• add_complementary_sequence() : protocols::dna::DnaInterfacePacker
• add_components_to_pose_if_necessary() : protocols::matdes::SymDofMover
• add_compositeSegmentMover() : protocols::rbsegment_relax::RBSegmentRelax
• add_condition() : protocols::filters::IfThenFilter
• add_connected_resonance() : protocols::noesy_assign::Resonance
• add_connection() : protocols::denovo_design::architects::CompoundArchitect , protocols::legacy_sewing::SegmentGraph
• add_constant() : core::simple_metrics::metrics::CalculatorMetric , protocols::filters::CalculatorFilter
• add_constrained_atoms_from_atom_pair_constraint() : protocols::enzdes::EnzdesConstraintReporter
• add_constrained_atoms_from_multiconstraint() : protocols::enzdes::EnzdesConstraintReporter
• add_constrained_lig_atom() : protocols::enzdes::EnzdesConstraintReporter
• add_constrained_nonligand_atom() : protocols::enzdes::EnzdesConstraintReporter
• add_constraint() : core::pose::Pose , core::scoring::constraints::Constraints , core::scoring::constraints::ConstraintSet , protocols::forge::remodel::RemodelConstraintGenerator
• add_constraints() : core::pose::Pose , core::scoring::constraints::ConstraintSet , protocols::abinitio::AbrelaxApplication , protocols::constraint_generator::AtomPairConstraintGenerator , protocols::constraint_movers::ConstraintSetMover , protocols::forge::remodel::RemodelConstraintGenerator , protocols::metal_interface::AddZincSiteConstraints , protocols::topology_broker::ConstraintClaimer , protocols::topology_broker::CoordConstraintClaimer , protocols::topology_broker::DensityScoringClaimer , protocols::topology_broker::MetalloClaimer , protocols::topology_broker::TopologyBroker , protocols::topology_broker::TopologyClaimer
• add_constraints_ : protocols::constraint_movers::ConstraintSetMover , protocols::protein_interface_design::movers::PlaceStubMover , protocols::simple_moves::CyclizationMover , protocols::simple_moves::SetupMetalsMover
• add_constraints_to_pose() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• add_constraints_to_pose_for_block_without_clearing_and_header_processing() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• add_constraints_to_scorefunction() : protocols::docking::DockingProtocol
• add_contact() : protocols::sewing::data_storage::LigandResidue
• add_coord_cst() : protocols::abinitio::LoopJumpFoldCst
• add_coordinate_constraints() : protocols::splice::Splice , protocols::splice::SpliceManager
• add_coordinate_constraints_for_res_stub() : protocols::protein_interface_design::movers::PlaceStubMover
• add_coordinate_constraints_from_map() : protocols::stepwise::modeler::align::StepWisePoseAligner
• add_coordinate_csts_from_lookback() : protocols::pose_length_moves::PossibleLoop
• add_coordinate_from_string() : core::conformation::symmetry::VirtualCoordinate
• add_coordinatecst_for_hotspot_packing() : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• add_coords() : protocols::ligand_docking::StartFrom
• add_coords_hash() : protocols::ligand_docking::StartFrom
• add_core_evaluator() : protocols::abinitio::IterativeBase
• add_covalent_bond() : protocols::denovo_design::components::StructureData
• add_cp_variants_ : protocols::loops::FoldTreeFromLoops
• add_creator() : core::pack::palette::PackerPaletteFactory , core::pack::task::operation::ResFilterFactory , core::pack::task::operation::ResLvlTaskOperationFactory , core::pack::task::operation::TaskOperationFactory , protocols::denovo_design::architects::DeNovoArchitectFactory
• add_cst_files() : protocols::relax::RelaxProtocolBase
• add_cst_seed_ : protocols::seeded_abinitio::CAcstGenerator
• add_csts_to_pose_ : protocols::simple_moves::StructProfileMover
• add_ct_name() : protocols::canonical_sampling::MetropolisHastingsMover
• add_custom_parameter() : core::conformation::parametric::ParametrizationCalculator
• add_custom_type() : core::chemical::Patch
• add_cut_bond() : core::chemical::MutableResidueType
• add_cut_points() : protocols::ligand_docking::MinimizeBackbone
• add_cutpoint_open() : core::import_pose::RNA_DeNovoParameters
• add_cutpoint_variants() : protocols::grafting::simple_movers::DeleteRegionMover , protocols::loops::FoldTreeFromLoops , protocols::protein_interface_design::movers::SetAtomTree
• add_cutpoint_variants_at_termini() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• add_cutpoints() : protocols::denovo_design::components::IdealAbegoGenerator
• add_cyclic_constraints() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication , protocols::energy_based_clustering::EnergyBasedClusteringProtocol
• add_data_point() : protocols::cyclic_peptide_predict::PNearCalculator
• add_datum() : core::pose::rna::RNA_DataInfo
• add_decoy() : protocols::optimize_weights::PNatStructureOptEData
• add_delete_frequency() : protocols::magnesium::MgMonteCarlo , protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions
• add_delete_frequency_ : protocols::magnesium::MgMonteCarlo , protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions
• add_dependency_to() : protocols::forge::build::BuildInstruction
• add_deriv_data() : core::optimization::NumericalDerivCheckResult
• add_design_task() : protocols::flxbb::FlxbbDesign
• add_deviations() : protocols::mpi_refinement::StructAvrgMover
• add_dihedral_constraint_to_stream() : protocols::cyclic_peptide::crosslinker::SquarePlanarMetal_Helper
• add_dihedral_constraints() : protocols::cyclic_peptide::crosslinker::Metal_HelperBase , protocols::cyclic_peptide::crosslinker::SquarePlanarMetal_Helper , protocols::cyclic_peptide::crosslinker::SquarePyramidalMetal_Helper , protocols::cyclic_peptide::crosslinker::TrigonalPlanarMetal_Helper , protocols::splice::Splice , protocols::splice::SpliceManager
• add_dihedral_constraints_to_pose() : protocols::ncbb::SecStructMinimizeMover
• add_dihedral_csts_from_lookback() : protocols::pose_length_moves::PossibleLoop
• add_dist_viol_to_assignments() : protocols::noesy_assign::NoesyModule
• add_distance() : protocols::contact_map::Contact
• add_dna_base_distance_constraints() : core::scoring::dna::DNATorsionPotential
• add_dna_states() : protocols::dna::DnaInterfaceMultiStateDesign
• add_DNA_torsion_constraint() : core::scoring::dna::DNATorsionPotential
• add_dna_torsion_tethers() : core::scoring::dna::DNATorsionPotential
• add_DoF() : protocols::helical_bundle::BundleGridSamplerHelper
• add_dof_access() : core::environment::DofPassport
• add_dof_constraint() : core::scoring::constraints::ConstraintSet
• add_dof_deriv_1benmeth() : core::scoring::MinimizationNode
• add_dof_deriv_2benmeth() : core::scoring::MinimizationNode
• add_dof_from_string() : core::conformation::symmetry::SymDof
• add_edge() : core::kinematics::FoldTree , core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph , core::pack::interaction_graph::BackgroundNode< V, E, G > , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::NodeBase , core::pack::interaction_graph::PDInteractionGraph , protocols::denovo_design::components::FoldGraph , protocols::hbnet::NetworkState , protocols::legacy_sewing::LegacyMonteCarloAssemblyMover
• add_edge_to_new_node() : protocols::jd3::JobDigraphUpdater
• add_edges_from_binary() : protocols::legacy_sewing::SewGraph
• add_elem_to_cache() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• add_element() : protocols::electron_density::ResultDB< T, Tcomp >
• add_encoded_termini() : core::scoring::methods::NMerSVMEnergy
• add_energies_data_from_scored_pose() : core::io::raw_data::ScoreMap
• add_energy() : core::io::silent::SilentStruct
• add_energy_edge() : core::scoring::EnergyGraph
• add_entity() : protocols::genetic_algorithm::GeneticAlgorithmBase
• add_entry() : protocols::abinitio::PairingStatistics
• add_entry_to_octahedral_metal_positions() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• add_entry_to_square_planar_metal_positions() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• add_entry_to_square_pyramidal_metal_positions() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• add_entry_to_tetrahedral_metal_positions() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• add_entry_to_trigonal_planar_metal_positions() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• add_entry_to_trigonal_pyramidal_metal_positions() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• add_enz_cst_interaction_to_pose() : protocols::enzdes::SecondaryMatchProtocol
• add_enzyme_template() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• add_equiv_atoms() : protocols::comparative_modeling::ThreadingMover
• add_evaluated_structure() : protocols::abinitio::HedgeArchive , protocols::jd2::archive::EvaluatedArchive , protocols::jd2::archive::NormalizedEvaluatedArchive , protocols::jd2::archive::VarianceStatisticsArchive
• add_evaluation() : protocols::abinitio::AbrelaxApplication , protocols::abinitio::Protocol , protocols::evaluation::MetaPoseEvaluator , protocols::jd2::archive::EvaluatedArchive , protocols::jd2::JobOutputter
• add_evaluator() : protocols::match::downstream::SecondaryMatcherToDownstreamResidue
• add_evaluator_for_target_restype() : protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• add_evaluators() : protocols::comparative_modeling::AlignRmsdTargetEvaluatorCreator , protocols::constraints_additional::CombinedConstraintEvaluatorCreator , protocols::constraints_additional::ConstraintEvaluatorCreator , protocols::evaluation::EvaluatorCreator , protocols::evaluation::EvaluatorFactory , protocols::simple_filters::CamShiftEvaluatorCreator , protocols::simple_filters::ChiWellRmsdEvaluatorCreator , protocols::simple_filters::ContactMapEvaluatorCreator , protocols::simple_filters::ExtraScoreEvaluatorCreator , protocols::simple_filters::JScoreEvaluatorCreator , protocols::simple_filters::JumpNrEvaluatorCreator , protocols::simple_filters::NativeEvaluatorCreator , protocols::simple_filters::PalesEvaluatorCreator , protocols::simple_filters::PoolEvaluatorCreator , protocols::simple_filters::PredictedBurialFnEvaluatorCreator , protocols::simple_filters::RdcEvaluatorCreator , protocols::simple_filters::RdcSelectEvaluatorCreator , protocols::simple_filters::RdcTargetEvaluatorCreator , protocols::simple_filters::RmsdEvaluatorCreator , protocols::simple_filters::RmsdTargetEvaluatorCreator , protocols::simple_filters::StructureSimilarityEvaluatorCreator , protocols::sparta::ChemicalShiftEvaluatorCreator , protocols::topology_broker::ConstraintEvaluatorWrapperCreator
• add_excluded_chains() : protocols::ligand_docking::Translate
• add_excluded_property() : core::scoring::aa_composition_energy::AACompositionPropertiesSet
• add_excluded_type() : core::scoring::aa_composition_energy::AACompositionPropertiesSet
• add_extent_eval() : core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library >
• add_extent_gen() : core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library >
• add_external_geom_sampler() : protocols::match::downstream::ClassicMatchAlgorithm
• add_external_geometry_samples_for_constraint() : protocols::match::Matcher
• add_external_loop_rotamer() : protocols::stepwise::sampler::StepWiseSamplerComb , protocols::stepwise::sampler::StepWiseSamplerOneValueComb , protocols::stepwise::sampler::StepWiseSamplerSizedAny , protocols::stepwise::sampler::StepWiseSamplerSizedComb
• add_extra_data() : protocols::loophash::BackboneDB
• add_extra_method() : core::scoring::ScoreFunction
• add_extra_restrict_operations() : protocols::antibody::design::AntibodySeqDesignTFCreator
• add_features_reporter() : protocols::features::ReportToDB
• add_file_contents() : protocols::pack_daemon::DynamicAggregateFunction
• add_filename() : protocols::simple_filters::StemFinder
• add_filter() : protocols::calc_taskop_filters::Operator , protocols::design_opt::GreedyOptMutationMover , protocols::filters::CalculatorFilter , protocols::filters::CombinedFilter , protocols::filters::FilterCollection , protocols::generalized_kinematic_closure::GeneralizedKIC , protocols::loop_modeling::LoopProtocol , protocols::loop_modeling::utilities::LoopMoverGroup , protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::match::MatcherTask , protocols::match::output::MatchProcessor , protocols::matdes::MatDesGreedyOptMutationMover , protocols::monte_carlo::GenericMonteCarloMover , protocols::moves::FilterMover
• add_filter_param() : protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter
• add_filter_parameter() : protocols::generalized_kinematic_closure::GeneralizedKIC
• add_fixed_res_constraints() : protocols::rna::movers::ErraserMinimizerMover
• add_flexible_region() : protocols::enzdes::EnzdesFlexBBProtocol
• add_frag_type() : core::fragment::FragFactory
• add_fragment() : core::fragment::Frame
• add_fragment_csts() : protocols::hybridization::HybridizeProtocol , protocols::loop_grower::LoopGrower
• add_fragment_eval() : core::fragment::picking_old::vall::VallLibrarian
• add_fragment_gen() : core::fragment::picking_old::vall::VallLibrarian
• add_fragments() : protocols::forge::remodel::RemodelLoopMover , protocols::loops::loop_mover::LoopMover
• add_frags() : protocols::abinitio::abscript::AbscriptMover
• add_fragset() : core::fragment::FragSetCollection
• add_frame_type() : core::fragment::FragFactory
• add_free_peptide_mover() : protocols::backbone_moves::local_backbone_mover::LocalBackboneMover
• add_fresh_param() : protocols::mpi_refinement::Scheduler
• add_from_file() : protocols::motifs::MotifLibrary
• add_full_assignment() : protocols::noesy_assign::CrossPeak
• add_fullatom_flags() : protocols::abinitio::IterativeBase
• add_func() : core::scoring::func::SumFunc
• add_function_name() : protocols::ligand_docking::rdf::RDFBase
• add_fuzzy_ : protocols::abinitio::HedgeArchive
• add_gaussian() : core::scoring::SmoothScoreTermCoeffs
• add_generator() : protocols::constraint_generator::AddConstraints , protocols::constraint_generator::RemoveConstraints
• add_genericRBMover() : protocols::rbsegment_relax::RBSegmentRelax
• add_global_parameter_perturbations() : protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator
• add_GlyCorrection_values() : core::pack::interaction_graph::SymmOnTheFlyEdge
• add_GlyCorrection_values_for_edge() : core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• add_grid() : protocols::qsar::scoring_grid::GridSet
• add_group() : protocols::symmetry::SetupNCSMover , protocols::task_operations::LinkResidues
• add_groupD() : protocols::symmetry::SetupNCSMover
• add_groupE() : protocols::symmetry::SetupNCSMover
• add_harmonic_cluster_constraint() : protocols::antibody::constraints::CDRDihedralConstraintMover
• add_hbond() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyEdgeData , core::scoring::hbonds::HBondResPairMinData
• add_helix() : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::PerturbBundle , protocols::helical_bundle_predict::HBPHelixAssignments
• add_helix_capping_ : protocols::flxbb::LayerDesignOperation
• add_helix_elongation_moves() : protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator
• add_helix_nucleation_moves() : protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator
• add_helix_retraction_moves() : protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator
• add_helix_update_moves() : protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator
• add_helixMover() : protocols::rbsegment_relax::RBSegmentRelax
• add_hetatm_ : protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol
• add_histogram_file() : protocols::nmr::pre::PREMover
• add_hits() : protocols::match::HitNeighborFinder , protocols::match::MatchCounter
• add_hotspot_constraints_to_pose() : protocols::hotspot_hashing::HotspotStubSet
• add_hotspot_constraints_to_wholepose() : protocols::hotspot_hashing::HotspotStubSet
• add_hsstriplets() : protocols::fldsgn::filters::HSSTripletFilter , protocols::fldsgn::topology::HSSTripletSet
• add_hydrophobic_constraints() : protocols::aa_composition::AddHelixSequenceConstraintsMover
• add_hydrophobic_constraints_ : protocols::aa_composition::AddHelixSequenceConstraintsMover
• add_ideal_contact() : protocols::sewing::data_storage::LigandResidue
• add_improper_parameter() : core::scoring::methods::ResidueCartBondedParameters
• add_impropers_from_stream() : core::scoring::methods::IdealParametersDatabase
• add_included_property() : core::scoring::aa_composition_energy::AACompositionPropertiesSet
• add_included_type() : core::scoring::aa_composition_energy::AACompositionPropertiesSet
• add_incoming_edge() : protocols::jd3::JobDirectedNode
• add_individual_constraint() : core::scoring::constraints::AmbiguousNMRConstraint , core::scoring::constraints::MultiConstraint
• add_info() : protocols::dna::PDBOutput
• add_info_for_csts() : protocols::constraint_movers::CstInfoMover
• add_inner_cycle_step() : protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer
• add_input_job_result_index() : protocols::jd3::InnerLarvalJob
• add_inputvalue() : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• add_instruction() : protocols::fldsgn::BluePrintBDR , protocols::forge::components::BDR
• add_interaction() : core::scoring::custom_pair_distance::AtomPairFuncList
• add_internal_loop_rotamer() : protocols::stepwise::sampler::StepWiseSamplerSizedComb
• add_ionized_restype() : protocols::simple_moves::IonizableResidue
• add_jump() : core::io::silent::BinarySilentStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RigidBodySilentStruct , core::io::silent::RNA_SilentStruct , core::io::silent::ScoreJumpFileSilentStruct , protocols::docking::DockingProtocol , protocols::docking::RigidBodyInfo , protocols::docking::TemperedDocking , protocols::jumping::JumpSelector , protocols::jumping::JumpSetup , protocols::jumping::ResiduePairJumpSetup , protocols::rigid::RigidBodyPerturbNoCenterMover , protocols::scoring::InterfaceInfo , protocols::simple_filters::InterfaceSasaFilter , protocols::simple_task_operations::RestrictToInterface
• add_jump_action() : core::select::movemap::MoveMapFactory
• add_jump_clone() : core::conformation::symmetry::SymmetryInfo
• add_jump_id() : protocols::features::InterfaceDdGMover
• add_jump_label() : core::environment::SequenceAnnotation
• add_jump_neighbor() : core::environment::FoldTreeSketch::Node
• add_jump_on_rechain_ : protocols::grafting::simple_movers::DeleteRegionMover
• add_jump_selector() : core::select::jump_selector::AndJumpSelector , core::select::jump_selector::OrJumpSelector
• add_kic_mover() : protocols::canonical_sampling::MetropolisHastingsMover
• add_labels() : protocols::fold_from_loops::utils::Nub
• add_labels_as_remark() : protocols::fold_from_loops::movers::DisplayPoseLabelsMover
• add_layer() : protocols::flxbb::LayerDesignOperation
• add_lead_zero_to_tag_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• add_leap() : protocols::loophash::LoopHashMap
• add_legacyleap() : protocols::loophash::LoopHashMap
• add_length_parameter() : core::scoring::methods::ResidueCartBondedParameters
• add_ligand_contact() : protocols::sewing::data_storage::LigandSegment
• add_ligand_from_file() : protocols::motifs::MotifLibrary
• add_ligand_to_pose_ : protocols::forge::constraints::InvrotTreeRCG
• add_line() : core::chemical::ResidueTypeSelector , core::sequence::ABEGO , protocols::frags::RMSVallData , protocols::frags::VallData
• add_linker() : protocols::cyclic_peptide::CrosslinkerMover
• add_linker_ : protocols::cyclic_peptide::CrosslinkerMover
• add_linker_asymmetric() : protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper , protocols::cyclic_peptide::crosslinker::Metal_HelperBase , protocols::cyclic_peptide::crosslinker::TBMB_Helper , protocols::cyclic_peptide::crosslinker::TMA_Helper , protocols::cyclic_peptide::CrosslinkerMover
• add_linker_bonds_asymmetric() : protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper , protocols::cyclic_peptide::crosslinker::Metal_HelperBase , protocols::cyclic_peptide::crosslinker::TBMB_Helper , protocols::cyclic_peptide::crosslinker::TMA_Helper
• add_linker_bonds_symmetric() : protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper , protocols::cyclic_peptide::crosslinker::Metal_HelperBase , protocols::cyclic_peptide::crosslinker::TBMB_Helper , protocols::cyclic_peptide::crosslinker::TMA_Helper
• add_linker_constraints_asymmetric() : protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper , protocols::cyclic_peptide::crosslinker::Metal_HelperBase , protocols::cyclic_peptide::crosslinker::TBMB_Helper , protocols::cyclic_peptide::crosslinker::TMA_Helper , protocols::cyclic_peptide::CrosslinkerMover
• add_linker_constraints_symmetric() : protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper , protocols::cyclic_peptide::crosslinker::Metal_HelperBase , protocols::cyclic_peptide::crosslinker::TBMB_Helper , protocols::cyclic_peptide::crosslinker::TMA_Helper , protocols::cyclic_peptide::CrosslinkerMover
• add_linker_symmetric() : protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper , protocols::cyclic_peptide::crosslinker::Metal_HelperBase , protocols::cyclic_peptide::crosslinker::TBMB_Helper , protocols::cyclic_peptide::crosslinker::TMA_Helper , protocols::cyclic_peptide::CrosslinkerMover
• add_list_filenames() : core::import_pose::pose_stream::PDBPoseInputStream
• add_local_parameter_perturbations() : protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator
• add_log_to_pose_ : protocols::antibody::design::AntibodyDesignMover
• add_long_range_damping() : core::scoring::etable::Etable
• add_long_range_damping_ : core::scoring::etable::Etable
• add_longrange_twobody_energies_multithreaded() : core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph
• add_loop() : protocols::forge::remodel::RemodelLoopMover , protocols::loops::Loops
• add_loop_residue() : protocols::generalized_kinematic_closure::GeneralizedKIC
• add_loop_segment() : protocols::legacy_sewing::Assembly
• add_loop_size() : protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashMoverWrapper
• add_lower_connect_angle_params() : core::scoring::methods::ResidueCartBondedParameters
• add_lower_padding() : protocols::denovo_design::components::Segment
• add_lr_gaussian() : core::scoring::CenHBPotential
• add_mainchain_segments() : protocols::backrub::BackrubMover
• add_mainchain_segments_from_options() : protocols::backrub::BackrubMover
• add_match() : protocols::match::output::BestMatchesCollection , protocols::match::output::MatchScoreWriter
• add_match_dspos1() : protocols::match::output::BestMatchesCollection
• add_mcfi() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList
• add_memb_etable() : core::scoring::ScoringManager
• add_member() : protocols::cluster::Cluster
• add_member_front() : protocols::cluster::Cluster
• add_membrane_again() : protocols::membrane::MPQuickRelaxMover , protocols::relax::RangeRelaxMover
• add_membrane_mover_ : protocols::docking::membrane::MPDockingMover
• add_membrane_virtual() : protocols::membrane::AddMembraneMover , protocols::membrane::symmetry::SymmetricAddMembraneMover
• add_metadata() : protocols::denovo_design::movers::AlignResiduesMover
• add_metalbinding_atom() : core::chemical::MutableResidueType
• add_metapatch() : core::chemical::PoseResidueTypeSet , core::chemical::ResidueTypeSet
• add_metapatch_connect() : core::chemical::MutableResidueType
• add_method() : core::scoring::ScoreFunction
• add_methyl() : protocols::noesy_assign::MethylNames
• add_metric() : protocols::jd3::jobs::MoverJob
• add_metric_value_getter() : protocols::multistate_design::MultiStateFitnessFunction
• add_metrics() : protocols::jd3::jobs::MoverJob
• add_model() : protocols::legacy_sewing::Assembly
• add_monomers_to_lattice() : protocols::cryst::MakeLatticeMover
• add_monomers_to_layer() : protocols::cryst::MakeLayerMover
• add_motif() : core::scoring::motif::MotifHash , protocols::simple_filters::SymmetricMotifFilter
• add_motif_scorers_to_score_file() : protocols::sewing::movers::AssemblyMover , protocols::sewing::movers::LigandBindingAssemblyMover
• add_motif_set_name() : core::scoring::motif::MotifHashManager
• add_movable_chain() : protocols::simple_task_operations::InterfaceTaskOperation
• add_movable_jump() : protocols::simple_task_operations::InterfaceTaskOperation
• add_mover() : protocols::canonical_sampling::CanonicalSamplingMover , protocols::canonical_sampling::MetropolisHastingsMover , protocols::jd3::jobs::MoverJob , protocols::loop_modeling::LoopProtocol , protocols::loop_modeling::utilities::LoopMoverGroup , protocols::moves::CompositionMover , protocols::moves::MoverContainer , protocols::stepwise::screener::AnchorSugarScreener , protocols::stepwise::screener::BulgeApplier , protocols::stepwise::screener::O2PrimeScreener , protocols::stepwise::screener::PackScreener , protocols::stepwise::screener::PhosphateScreener , protocols::stepwise::screener::ProteinCCD_ClosureScreener , protocols::stepwise::screener::RNA_ChainClosureScreener , protocols::stepwise::screener::StepWiseScreener , protocols::stepwise::screener::SugarInstantiator , protocols::topology_broker::AsymFoldandDockClaimer , protocols::topology_broker::FibrilModelingClaimer , protocols::topology_broker::FoldandDockClaimer , protocols::topology_broker::MembraneTopologyClaimer , protocols::topology_broker::PcsEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4 , protocols::topology_broker::TMHTopologySamplerClaimer , protocols::topology_broker::TopologyClaimer
• add_mover_ : protocols::stepwise::monte_carlo::mover::StepWiseMasterMover
• add_mover_filter_pair() : protocols::rosetta_scripts::ParsedProtocol
• add_mover_group() : protocols::loop_modeling::utilities::LoopMoverGroup
• add_MPI_rank_handling_message() : protocols::cyclic_peptide_predict::HierarchicalHybridJD_ResultsSummaryBase
• add_MSAcst_to_pose() : protocols::simple_moves::StructProfileMover
• add_mutant() : protocols::optimize_weights::DDGMutationOptEData
• add_mutant_complex() : protocols::optimize_weights::DDGBindOptEData
• add_mutant_unbounds() : protocols::optimize_weights::DDGBindOptEData
• add_mutation() : protocols::optimize_weights::DDGBindOptEData , protocols::pmut_scan::Mutant
• add_mutation_ddG() : core::io::PositionDdGInfo::PositionDdGInfo
• add_mutation_set() : protocols::task_operations::MutationSetDesignOperation
• add_n_methylation() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• add_n_terminal_constraints() : protocols::aa_composition::AddHelixSequenceConstraintsMover
• add_n_terminal_constraints_ : protocols::aa_composition::AddHelixSequenceConstraintsMover
• add_named_selector() : core::select::residue_selector::SelectorLogicParser
• add_native() : protocols::optimize_weights::PNatStructureOptEData
• add_native_fasta() : protocols::task_operations::JointSequenceOperation
• add_native_pdb() : protocols::task_operations::JointSequenceOperation
• add_native_pose() : protocols::task_operations::JointSequenceOperation
• add_nbr_radius_ : protocols::ligand_docking::LigandArea
• add_negative_filter() : protocols::protein_interface_design::filters::BoltzmannFilter
• add_neighbors_mass() : core::scoring::TenANeighborNode
• add_neutral_restype() : protocols::simple_moves::IonizableResidue
• add_new() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• add_new_chain() : protocols::simple_moves::AddChainMover
• add_new_cluster() : protocols::toolbox::KClusterElement
• add_new_data() : protocols::toolbox::KClusterElement
• add_new_dof_node() : core::optimization::symmetry::SymMinimizerMap
• add_new_RNA_jump() : core::import_pose::RNA_JumpMover
• add_newick_tree_for_node() : protocols::jd3::JobGenealogist
• add_node() : protocols::hbnet::NetworkState , protocols::jd3::JobDigraphUpdater
• add_non_init_chunks_ : protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol
• add_non_polymeric_connections() : protocols::denovo_design::components::FoldGraph
• add_nonhelix_small_moves() : protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator
• add_npd_property_calculator_for_state() : protocols::pack_daemon::DaemonSet
• add_npdpro_calculator_creator() : protocols::pack_daemon::DaemonSet
• add_nt_seq_to_pose() : protocols::evolution::NucleotideMutation
• add_nu() : core::chemical::MutableResidueType
• add_nu_action() : core::select::movemap::MoveMapFactory
• add_null_template() : protocols::hybridization::HybridizeProtocol
• add_numeric_property() : core::chemical::ResidueProperties , core::chemical::ResidueTypeBase
• add_objective_function_info() : protocols::mpi_refinement::MultiObjective
• add_obligate_pairing_set() : core::import_pose::RNA_DeNovoParameters
• add_observer() : protocols::canonical_sampling::MetropolisHastingsMover
• add_observer_cache_segments_to_set() : protocols::enzdes::DetectProteinLigandInterface
• add_observer_cache_segs_to_interface_ : protocols::enzdes::DetectProteinLigandInterface
• add_onebody_enmeth() : core::scoring::MinimizationNode
• add_operation() : core::chemical::PatchCase
• add_option() : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::standard::StandardJobQueen
• add_options() : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::standard::StandardJobQueen
• add_or_delete_mover_ : protocols::stepwise::monte_carlo::mover::StepWiseMasterMover
• add_or_property() : core::scoring::aa_composition_energy::AACompositionPropertiesSet
• add_orbital() : core::chemical::MutableResidueType
• add_orbital_bond() : core::chemical::MutableResidueType
• add_orbitals_to_restype() : core::chemical::orbitals::AssignOrbitals
• add_orientations() : protocols::denovo_design::architects::BetaSheetArchitect
• add_original_ : core::optimization::GA_Minimizer
• add_other_pose() : core::pose::full_model_info::FullModelInfo
• add_other_struct() : core::io::silent::SilentStruct
• add_output_observer() : protocols::jd2::Job
• add_overall_constraints() : protocols::aa_composition::AddHelixSequenceConstraintsMover
• add_overall_constraints_ : protocols::aa_composition::AddHelixSequenceConstraintsMover
• add_overlap() : core::select::residue_selector::SecondaryStructureSelector
• add_overlap_loop() : protocols::loops::Loops
• add_overlapping_pair_chunks() : protocols::hybridization::HybridizeFoldtreeDynamic
• add_pack_daemon() : protocols::pack_daemon::DaemonSet
• add_packer_screeners() : protocols::stepwise::modeler::packer::StepWiseMasterPacker
• add_padding_ : protocols::denovo_design::architects::PoseArchitect
• add_pair() : protocols::fldsgn::topology::StrandPairing
• add_pairing() : core::scoring::dssp::StrandPairingSet , protocols::abinitio::AlternativePairings , protocols::abinitio::PairingStatEntry , protocols::abinitio::StrandConstraints , protocols::denovo_design::components::StructureData
• add_pairings() : protocols::denovo_design::architects::BetaSheetArchitect
• add_parameter() : core::conformation::parametric::Parameters , core::conformation::parametric::ParametrizationCalculator
• add_parameter_info_to_pose() : protocols::helical_bundle::MakeBundleHelix
• add_parameters() : core::conformation::parametric::ParametersSet
• add_parameters_from_file() : core::chemical::AtomTypeSet
• add_parameters_set() : core::conformation::Conformation
• add_parent() : protocols::jd3::JGJobNode
• add_parent_entity() : protocols::genetic_algorithm::GeneticAlgorithmBase
• add_parent_name() : protocols::denovo_design::architects::CompoundArchitect
• add_parent_remark() : core::io::silent::SilentStruct
• add_parents_from_current_generation() : protocols::genetic_algorithm::GeneticAlgorithmBase
• add_pass_through() : core::chemical::ResidueTypeSetCache
• add_patch() : core::chemical::PoseResidueTypeSet , core::chemical::ResidueTypeSet
• add_patches() : core::chemical::PoseResidueTypeSet , core::chemical::ResidueTypeSet
• add_pcs_scores_to_scorefile() : protocols::nmr::ParaNMRScoreMover
• add_pdb() : protocols::task_operations::JointSequenceOperation
• add_pdb_id() : protocols::frag_picker::PdbIdChunkFilter
• add_pdb_ids() : protocols::frag_picker::PdbIdChunkFilter
• add_pdb_profile_pair() : protocols::splice::SpliceSegment
• add_peak() : protocols::noesy_assign::PeakCalibrator
• add_peptide_edge() : protocols::denovo_design::components::FoldGraph
• add_peptide_neighbor() : core::environment::FoldTreeSketch::Node
• add_peptide_plane_variants_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• add_perm_remark() : protocols::denovo_design::components::StructureDataFactory
• add_perturbation_magnitude() : protocols::simple_moves::SetTorsion
• add_perturbation_type() : protocols::simple_moves::SetTorsion
• add_perturber() : protocols::generalized_kinematic_closure::GeneralizedKIC , protocols::kinematic_closure::BalancedKicMover , protocols::kinematic_closure::KicMover
• add_point() : protocols::ligand_docking::ga_ligand_dock::GridHash3D< T > , protocols::qsar::qsarMap , protocols::simple_moves::AtomHash
• add_point_water() : protocols::simple_moves::ExplicitWaterMover
• add_polar_atom() : core::scoring::hbonds::graph::HBondNode
• add_polar_atom_if_doesnt_exist() : core::scoring::hbonds::graph::HBondNode
• add_polar_atoms() : protocols::hbnet::NetworkState
• add_pool() : protocols::frag_picker::quota::QuotaCollector
• add_pose() : core::pack::rotamer_set::UnboundRotamersOperation , core::pose::xyzStripeHashPose , protocols::loophash::BackboneDB , protocols::splice::SampleRotamersFromPDB_RotamerSetOperation , protocols::task_operations::JointSequenceOperation
• add_pose_input_stream() : core::import_pose::pose_stream::MetaPoseInputStream
• add_pose_segments_to_segment_vector() : protocols::sewing::hashing::AlignmentFileGeneratorMover
• add_position() : protocols::environment::claims::EnvLabelSelector
• add_position_data() : protocols::optimize_weights::OptEData
• add_position_in_pose() : protocols::toolbox::match_enzdes_util::EnzCstTemplateResCache
• add_positive_filter() : protocols::protein_interface_design::filters::BoltzmannFilter
• add_postfold_mover() : protocols::denovo_design::movers::BuildDeNovoBackboneMover
• add_pre_scores_to_scorefile() : protocols::nmr::ParaNMRScoreMover
• add_precomputed_energies() : protocols::minimization_packing::GreenPacker
• add_prefix_to_segments() : protocols::denovo_design::components::StructureData
• add_prefold_mover() : protocols::denovo_design::movers::BuildDeNovoBackboneMover
• add_pregenerated_constraints_to_pose() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• add_pregenerated_enzdes_constraints() : protocols::enzdes::EnzdesBaseProtocol
• add_preparer() : protocols::abinitio::abscript::AbscriptStageMover
• add_probability_ : protocols::legacy_sewing::LegacyMonteCarloAssemblyMover , protocols::sewing::movers::AssemblyMover
• add_probe_to_pose() : core::scoring::rna::data::RNA_DMS_Potential
• add_ProCorrection_values() : core::pack::interaction_graph::SymmOnTheFlyEdge
• add_ProCorrection_values_for_edge() : core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• add_profile() : protocols::splice::SpliceSegment
• add_prohibited() : core::chemical::ResidueTypeSetCache
• add_property() : core::chemical::AtomType , core::chemical::ResidueTypeBase , core::select::residue_selector::ResiduePropertySelector
• add_property_i() : core::scoring::bin_transitions::BinTransitionData
• add_property_iplus1() : core::scoring::bin_transitions::BinTransitionData
• add_proposal_density_factor() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• add_proposal_density_factor_ : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• add_protein() : protocols::loophash::BackboneDB
• add_proton() : protocols::noesy_assign::MethylNames
• add_proton_index() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup
• add_protonated_H1_adenosine_variants() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• add_pseudobond() : core::conformation::Conformation
• add_pssm_features() : core::scoring::methods::NMerSVMEnergy
• add_query_ss() : protocols::frag_picker::FragmentPicker
• add_range() : core::select::residue_selector::GlycanPositionSelector
• add_rcg() : protocols::forge::components::VarLengthBuild
• add_rdc_scores_to_scorefile() : protocols::nmr::ParaNMRScoreMover
• add_reactivity() : core::pose::rna::RNA_DataInfo
• add_real_parameter() : core::conformation::parametric::ParametrizationCalculator
• add_realvector_parameter() : core::conformation::parametric::ParametrizationCalculator
• add_refiner() : protocols::loop_modeling::LoopProtocol
• add_register_shifts() : protocols::denovo_design::architects::BetaSheetArchitect
• add_registered_mover() : protocols::environment::EnvMover
• add_relax_batch() : protocols::loophash::MPI_LoopHashRefine_Master
• add_relax_simple() : protocols::mpi_refinement::MPI_Refine_Master
• add_remodel_constraints_to_pose() : protocols::forge::remodel::RemodelConstraintGenerator
• add_repeats() : protocols::legacy_sewing::LegacyRepeatAssemblyMover
• add_reported_value() : core::simple_metrics::metrics::CalculatorMetric , protocols::filters::CalculatorFilter
• add_required_connection_for_residue() : protocols::simple_filters::PackerNeighborGraphFilter
• add_required_connections_between_regions() : protocols::simple_filters::PackerNeighborGraphFilter
• add_requirement() : protocols::legacy_sewing::sampling::requirements::LegacyRequirementSet , protocols::sewing::movers::AssemblyMover
• add_rerelaxed() : protocols::mpi_refinement::Scheduler
• add_res() : protocols::task_operations::SelectResiduesWithinChainOperation
• add_res_identity_i() : core::scoring::bin_transitions::BinTransitionData
• add_res_identity_iplus1() : core::scoring::bin_transitions::BinTransitionData
• add_resid_to_entity_list() : protocols::pack_daemon::EntityCorrespondence
• add_residue() : core::conformation::parametric::Parameters , core::fragment::FragData , core::pack::dunbrack::RotamerConstraint , protocols::cyclic_peptide::PeptideStubMover , protocols::enzdes::PoseFoundResiduesCombination , protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber , protocols::ligand_docking::ga_ligand_dock::RotamerPairEnergies
• add_residue_alternative_rotamer() : protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSamplerComb
• add_residue_alternative_set() : protocols::stepwise::modeler::StepWiseConnectionSampler
• add_residue_connection() : core::chemical::MutableResidueType
• add_residue_constraints() : protocols::protein_interface_design::FavorNativeResidue , protocols::protein_interface_design::FavorNonNativeResidue
• add_residue_dis() : core::scoring::TMscoreStore
• add_residue_exclude_torsions() : core::scoring::GenBondedExclInfo
• add_residue_labels_back() : protocols::relax::RepeatProteinRelax
• add_residue_library() : core::pack::dunbrack::RotamerLibrary
• add_residue_pair() : protocols::jumping::ResiduePairJump
• add_residue_pair_constraint() : core::scoring::constraints::ConstraintSet
• add_residue_pair_jump() : protocols::jumping::ResiduePairJumpSetup
• add_residue_property_by_name() : protocols::simple_filters::ResidueCountFilter
• add_residue_selector() : core::select::residue_selector::AndResidueSelector , core::select::residue_selector::OrResidueSelector , protocols::aa_composition::AddCompositionConstraintMover , protocols::aa_composition::AddMHCEpitopeConstraintMover , protocols::aa_composition::AddNetChargeConstraintMover , protocols::symmetry::SetupForSequenceSymmetryMover
• add_residue_single() : protocols::jumping::ResiduePairJump
• add_residue_to_empty_pose() : protocols::cyclic_peptide::PeptideStubMover
• add_residue_to_network_state() : protocols::hbnet::HBNet
• add_residue_to_perturber_residue_list() : protocols::generalized_kinematic_closure::GeneralizedKIC
• add_residue_type() : core::chemical::ResidueTypeSetCache
• add_residue_type_by_name() : protocols::simple_filters::ResidueCountFilter
• add_residue_types_to_list() : core::pack::palette::PackerPalette
• add_reslabel() : core::pose::PDBInfo
• add_resnum() : protocols::legacy_sewing::sampling::requirements::LegacyResidueRetentionRequirement
• add_reverse_motifs() : core::scoring::motif::ResPairMotifs
• add_reweighter() : core::pack::task::IGEdgeReweightContainer
• add_rigidity_jumps() : protocols::abinitio::LoopJumpFoldCst
• add_ring() : core::chemical::MutableResidueType
• add_rna_pairing() : core::import_pose::RNA_DeNovoParameters
• add_rotamer() : core::chemical::rotamers::StoredRotamerLibrarySpecification , core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset , protocols::recces::sampler::MC_Comb , protocols::recces::sampler::rna::MC_RNA_MultiSuite
• add_rotamer_ : protocols::splice::SampleRotamersFromPDB , protocols::splice::SampleRotamersFromPDB_RotamerSetOperation
• add_rotamer_bb_torsion_index() : core::chemical::rotamers::NCAARotamerLibrarySpecification
• add_rotamer_constraints() : protocols::splice::SampleRotamersFromPDB_RotamerSetOperation
• add_rotamer_into_existing_group() : core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• add_rotamer_line_data() : protocols::optimize_weights::PNatAAOptEPositionData , protocols::optimize_weights::PNatRotOptEPositionData
• add_rotamer_to_rotamer_set() : protocols::splice::SampleRotamersFromPDB_RotamerSetOperation
• add_rotamers() : core::chemical::rotamers::StoredRotamerLibrarySpecification
• add_rt() : core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RigidBodySilentStruct
• add_rv_info() : protocols::forge::remodel::ResidueVicinityRCG
• add_sampler() : protocols::simple_moves::BBDihedralSamplerMover
• add_schema() : core::simple_metrics::PerResidueRealMetric , core::simple_metrics::PerResidueStringMetric
• add_score() : core::scoring::motif::XformScore , protocols::moves::MoverStatistics , protocols::sic_dock::JointScore
• add_score_info_to_pose() : protocols::analysis::InterfaceAnalyzerMover
• add_score_type() : protocols::score_filters::ScoreCutoffFilter
• add_score_weights() : protocols::abinitio::CoordinateConstraintKC , protocols::abinitio::KinematicControl
• add_scored_pair() : core::sequence::PairScoringScheme
• add_scorer() : protocols::legacy_sewing::scoring::LegacyAssemblyScoreFunction , protocols::sewing::movers::AssemblyMover
• add_scores_to_job() : protocols::ligand_docking::GrowLigand , protocols::ligand_docking::LigandDesign
• add_scoring_method() : protocols::frag_picker::FragmentPicker , protocols::frag_picker::scores::FragmentScoreManager
• add_scoring_scheme() : core::sequence::CompositeScoringScheme
• add_secondary_downstream_match_geometry_for_constraint() : protocols::match::Matcher
• add_secondary_upstream_match_geometry_for_constraint() : protocols::match::Matcher
• add_section() : core::fragment::picking_old::vall::VallLibrary
• add_segment() : core::pose::datacache::SpecialSegmentsObserver , protocols::backrub::BackrubMover , protocols::denovo_design::components::StructureData , protocols::sewing::data_storage::HashedSmartAssembly , protocols::sewing::data_storage::SmartAssembly
• add_segment_and_neighbors_to_local_segments() : protocols::sewing::data_storage::SmartAssembly
• add_segment_fname() : protocols::splice::RotLibdb
• add_selector() : protocols::frag_picker::CompositeFragmentSelector , protocols::protein_interface_design::filters::RmsdFilter , protocols::protein_interface_design::movers::BackrubDDMover
• add_selector_rlto_pair() : core::pack::task::operation::DesignRestrictions
• add_seq_label() : core::environment::SequenceAnnotation
• add_sequence() : core::sequence::CompositeSequence , core::sequence::SequenceAlignment , protocols::switches::GraftSwitchMover
• add_sequence_constraint() : core::scoring::constraints::ConstraintSet
• add_sequence_constraints() : protocols::splice::Splice , protocols::splice::SpliceManager
• add_sequence_constraints_only() : protocols::splice::Splice , protocols::splice::SpliceManager
• add_sequence_constraints_only_ : protocols::splice::Splice , protocols::splice::SpliceManager
• add_setup_mover() : protocols::forge::components::VarLengthBuild
• add_sfd_1benmeth() : core::scoring::MinimizationNode
• add_sfd_2benmeth() : core::scoring::MinimizationNode
• add_sfd_enmeth() : core::scoring::MinimizationEdge
• add_sfs_dm_1benmeth() : core::scoring::MinimizationNode
• add_sfs_dm_2benmeth() : core::scoring::MinimizationNode
• add_sfs_drs_enmeth() : core::scoring::MinimizationNode
• add_sfs_enmeth() : core::scoring::MinimizationEdge
• add_shear_mover() : protocols::canonical_sampling::MetropolisHastingsMover
• add_sheet() : protocols::denovo_design::components::SheetDB
• add_sheets() : protocols::loop_grower::LoopPartialSolution
• add_sheets_from_pose() : protocols::denovo_design::components::SheetDB
• add_sheets_from_spairs() : protocols::denovo_design::components::SheetDB
• add_sidechain_conjugation() : protocols::cyclic_peptide::crosslinker::TMA_Helper
• add_sidechain_mc_mover() : protocols::canonical_sampling::MetropolisHastingsMover
• add_sidechain_mover() : protocols::canonical_sampling::MetropolisHastingsMover
• add_sigmoid() : core::scoring::SmoothScoreTermCoeffs
• add_silent_struct() : protocols::jd2::RNA_DeNovoJobOutputter , protocols::jd2::SilentFileJobOutputter
• add_similarity() : protocols::cluster::DataPoint
• add_simple_metric() : core::simple_metrics::metrics::CalculatorMetric , protocols::analysis::simple_metrics::RunSimpleMetricsMover , protocols::features::SimpleMetricFeatures
• add_single_atom_to_power_diagram() : core::scoring::power_diagram::PowerDiagram
• add_size_parameter() : core::conformation::parametric::ParametrizationCalculator
• add_sizevector_parameter() : core::conformation::parametric::ParametrizationCalculator
• add_small_fragments() : protocols::hybridization::HybridizeProtocol
• add_small_mover() : protocols::canonical_sampling::MetropolisHastingsMover
• add_solution() : protocols::generalized_kinematic_closure::GeneralizedKIC
• add_span() : core::conformation::membrane::SpanningTopology
• add_span_embedding() : protocols::membrane::geometry::Embedding
• add_spanning_region() : protocols::abinitio::MembraneAbinitio
• add_special_edges() : protocols::legacy_sewing::SewGraph
• add_sr_gaussian() : core::scoring::CenHBPotential
• add_start_from() : protocols::ligand_docking::LigandDockProtocol
• add_start_res() : protocols::hbnet::HBNet
• add_starting_model() : protocols::legacy_sewing::LegacyAppendAssemblyMover , protocols::legacy_sewing::LegacyAssemblyMover
• add_state() : protocols::multistate_design::MultiStateFitnessFunction
• add_states() : protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• add_str_str_data() : core::chemical::sdf::MolFileIOMolecule
• add_strand() : protocols::denovo_design::architects::BetaSheetArchitect
• add_strand_extension() : protocols::denovo_design::architects::BetaSheetArchitect
• add_strand_pairing() : protocols::hybridization::FoldTreeHybridize
• add_strand_pairings() : protocols::hybridization::FoldTreeHybridize
• add_strandMover() : protocols::rbsegment_relax::RBSegmentRelax
• add_string() : protocols::jd2::Job
• add_string_property() : core::chemical::ResidueProperties , core::chemical::ResidueTypeBase
• add_string_real_pair() : protocols::jd2::Job
• add_string_string_pair() : protocols::jd2::Job
• add_string_value() : core::io::silent::SilentStruct
• add_strings() : protocols::jd2::Job
• add_structure() : core::io::silent::SilentFileData , protocols::abinitio::IterativeBase , protocols::cluster::ClusterBase , protocols::jd2::archive::ArchiveBase , protocols::jd2::archive::EvaluatedArchive
• add_structure_at_position() : protocols::abinitio::IterativeCentroid , protocols::jd2::archive::ArchiveBase
• add_structure_based_on_rms() : protocols::optimize_weights::IterativeOptEDriver
• add_structure_replace_tag_if_necessary() : core::io::silent::SilentFileData
• add_structure_to_library() : protocols::loophash::MPI_LoopHashRefine , protocols::loophash::MPI_LoopHashRefine_Master , protocols::mpi_refinement::MPI_Refine_Master , protocols::mpi_refinement::MPI_Refinement
• add_structure_to_library_add_n_replace() : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• add_structure_to_library_direct() : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• add_structure_to_library_single_replace() : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• add_structures_to_library() : protocols::loophash::MPI_LoopHashRefine , protocols::loophash::MPI_LoopHashRefine_Emperor , protocols::mpi_refinement::MPI_Refine_Emperor , protocols::mpi_refinement::MPI_Refinement
• add_stub_() : protocols::hotspot_hashing::HotspotStubSet
• add_stub_set() : protocols::hotspot_hashing::HotspotStubSet
• add_sub_ct_name() : protocols::fold_from_loops::constraint_generator::AutomaticSheetConstraintGenerator , protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator
• add_submotif_info() : core::pose::full_model_info::FullModelInfo
• add_submotif_info_from_line() : core::io::silent::SilentStruct
• add_submover() : protocols::abinitio::abscript::AbscriptStageMover
• add_suckers() : protocols::simple_moves::AddCavitiesMover
• add_sugar_ring_closure_constraints() : core::scoring::dna::DNATorsionPotential , core::scoring::rna::RNA_SugarCloseEnergy
• add_sym_dof_name() : protocols::simple_filters::InterfaceSasaFilter
• add_symmetry_ : protocols::fldsgn::potentials::SetSecStructEnergies
• add_tail_residue() : protocols::generalized_kinematic_closure::GeneralizedKIC
• add_target_constraints() : protocols::abinitio::Templates
• add_target_restype() : protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• add_target_selector() : protocols::denovo_design::movers::AlignResiduesMover
• add_target_to_pose_ : protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover
• add_target_types_ : protocols::simple_moves::ModifyVariantTypeMover
• add_task_operation() : protocols::flxbb::DesignTask
• add_task_operations() : protocols::flxbb::DesignTask
• add_template() : protocols::hybridization::HybridizeProtocol
• add_template_selector() : protocols::denovo_design::movers::AlignResiduesMover
• add_terminal_res_repulsion() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• add_terminal_types_on_rechain_ : protocols::grafting::simple_movers::DeleteRegionMover
• add_termini_ : protocols::cyclic_peptide::DeclareBond , protocols::cyclic_peptide::PeptideCyclizeMover
• add_terminus_variants() : protocols::grafting::simple_movers::DeleteRegionMover
• add_thermodynamic_data_to_silent() : protocols::simple_moves::PeriodicBoxMover
• add_threshold_distance_allFrag() : protocols::indexed_structure_store::FragmentStore
• add_to_atom_id_map_after_checks() : protocols::stepwise::modeler::align::StepWisePoseAligner
• add_to_energy_map() : core::scoring::EnergyEdge
• add_to_library() : protocols::motifs::MotifLibrary
• add_to_list_of_partners_of_changed_nodes() : core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty
• add_to_nodes_one_body_energy() : core::pack::interaction_graph::InteractionGraphBase
• add_to_one_body_energies() : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::NodeBase , core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SymmOnTheFlyNode , protocols::flexpack::interaction_graph::FlexbbNode
• add_to_one_body_energy() : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::NodeBase , core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SymmOnTheFlyNode , protocols::flexpack::interaction_graph::FlexbbNode
• add_to_one_body_energy_for_node_state() : core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• add_to_swap() : protocols::wum::WorkUnitQueue_Swapped
• add_to_targets() : protocols::toolbox::match_enzdes_util::InvrotTree
• add_to_top_level() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• add_to_two_body_energies() : core::pack::hbonds::BareMinimumPDEdge , core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::PrecomputedPairEnergiesEdge
• add_to_two_body_energies_for_edge() : core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph
• add_to_two_body_energy() : core::pack::hbonds::BareMinimumPDEdge , core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::PrecomputedPairEnergiesEdge
• add_to_weight() : core::scoring::ScoreFunction
• add_topology() : protocols::abinitio::PairingStatistics
• add_torerelax() : protocols::mpi_refinement::Scheduler
• add_torsion() : core::fragment::rna::FragmentLibrary , core::kinematics::MinimizerMapBase , core::optimization::CartesianMinimizerMap , core::optimization::MinimizerMap , core::optimization::symmetry::SymMinimizerMap , core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::SCMinMinimizerMap , protocols::canonical_sampling::MetricRecorder
• add_torsion_parameter() : core::scoring::methods::ResidueCartBondedParameters
• add_torsion_to_fix() : protocols::helical_bundle::BackboneGridSampler
• add_torsion_to_sample() : protocols::helical_bundle::BackboneGridSampler
• add_trigger() : protocols::monte_carlo::GenericMonteCarloMover , protocols::simple_moves::rational_mc::RationalMonteCarlo
• add_trj() : protocols::md::MDBase
• add_trj_scratch() : protocols::md::MDBase
• add_twobody_enmeth() : core::scoring::MinimizationEdge , core::scoring::MinimizationNode
• add_type() : core::chemical::Patch , core::pack::palette::CustomBaseTypePackerPalette , core::scoring::func::FuncFactory , core::sequence::ScoringSchemeFactory , protocols::comparative_modeling::features::ResidueFeatureFactory , protocols::moves::PyMOLObserver , protocols::network::UIObserver , protocols::topology_broker::TopologyClaimerFactory
• add_unfolded_energy_data() : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorJobDistributor , protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor
• add_unpatchable_residue_type() : core::chemical::PoseResidueTypeSet , core::chemical::ResidueTypeSet
• add_unrecognized_atoms() : core::pose::PDBInfo
• add_upper_connect_angle_params() : core::scoring::methods::ResidueCartBondedParameters
• add_upper_padding() : protocols::denovo_design::components::Segment
• add_upstream_restype_for_constraint() : protocols::match::Matcher
• add_user_constraints() : protocols::energy_based_clustering::EnergyBasedClusteringProtocol
• add_user_csts() : protocols::loop_grower::LoopGrower
• add_user_provided_mover() : protocols::forge::components::VarLengthBuild
• add_value_to_perturber_value_list() : protocols::generalized_kinematic_closure::GeneralizedKIC
• add_values_to_job() : protocols::canonical_sampling::BiasEnergy , protocols::jd2::JobOutputterObserver , protocols::rosetta_scripts::ParsedProtocol
• add_variant_type() : core::chemical::ResidueTypeBase
• add_vec() : protocols::evaluation::PCA
• add_vertex() : core::kinematics::FoldTree
• add_virt_res_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• add_virt_res_as_root() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• add_virt_res_as_root_ : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• add_virtual_res() : protocols::rna::movers::ErraserMinimizerMover
• add_virtual_residues() : protocols::environment::EnvClaimBroker
• add_vital_residue() : protocols::sewing::data_storage::SmartSegment
• add_weight() : protocols::aa_composition::AddMHCEpitopeConstraintMover
• add_weights_from_file() : core::scoring::ScoreFunction
• add_whole_pose_context_enmeth() : core::scoring::MinimizationGraph
• add_wholeStructureMover() : protocols::rbsegment_relax::RBSegmentRelax
• add_wt() : protocols::optimize_weights::DDGMutationOptEData
• add_wt_complex() : protocols::optimize_weights::DDGBindOptEData
• add_wt_unbounds() : protocols::optimize_weights::DDGBindOptEData
• add_xsd_options() : core::pack::palette::CustomBaseTypePackerPalette
• AddAllPositionsMPM() : protocols::match::AddAllPositionsMPM
• AddAromaticAtomType() : core::chemical::gasteiger::PossibleAtomTypesForAtom
• AddAssemblyConstraints() : protocols::domain_assembly::AddAssemblyConstraints
• AddAtom() : core::chemical::AddAtom , core::scoring::sc::MolecularSurfaceCalculator
• AddAtomAlias() : core::chemical::AddAtomAlias
• AddAtomType() : core::chemical::gasteiger::PossibleAtomTypesForAtom
• AddBehaviorRLT() : core::pack::task::operation::AddBehaviorRLT
• AddBond() : core::chemical::AddBond
• AddBondType() : core::chemical::AddBondType
• AddCavitiesMover() : protocols::simple_moves::AddCavitiesMover
• AddCDRProfileSetsOperation() : protocols::antibody::task_operations::AddCDRProfileSetsOperation
• AddCDRProfilesOperation() : protocols::antibody::task_operations::AddCDRProfilesOperation
• AddChainBreak() : protocols::protein_interface_design::movers::AddChainBreak
• AddChainMover() : protocols::simple_moves::AddChainMover
• AddChi() : core::chemical::AddChi
• AddChiRotamer() : core::chemical::AddChiRotamer
• AddCompositionConstraintMover() : protocols::aa_composition::AddCompositionConstraintMover
• AddConnect() : core::chemical::AddConnect
• AddConnectAndTrackingVirt() : core::chemical::AddConnectAndTrackingVirt
• AddConnectDeleteChildProton() : core::chemical::AddConnectDeleteChildProton
• AddConstraints() : protocols::constraint_generator::AddConstraints
• AddConstraintsToCurrentConformationMover() : protocols::constraint_movers::AddConstraintsToCurrentConformationMover
• addcount() : core::scoring::motif::ResPairMotif
• AddDot() : core::scoring::sc::MolecularSurfaceCalculator
• added_cutpoint_closed_ : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• AddEdgeVisitor() : core::conformation::AddEdgeVisitor< Vertex, Edge >
• addEntry() : protocols::sparta::GDB
• addfilt() : protocols::constel::MasterFilter
• AddGood2BPairEnergyRotamers() : protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers
• AddHelixSequenceConstraintsMover() : protocols::aa_composition::AddHelixSequenceConstraintsMover
• AddHydrogen() : protocols::ligand_docking::AddHydrogen
• AddHydrogens() : protocols::ligand_docking::AddHydrogens
• additional_low_resolution_steps_ : protocols::docking::DockingProtocol
• additional_outputs_returned_ : protocols::antibody::design::AntibodyDesignMover
• additional_residue_types_ : core::pack::palette::CustomBaseTypePackerPalette
• additional_setup_for_floating_base() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• additional_string_output() : core::io::StructFileRep
• additional_string_output_ : core::io::StructFileRep
• additional_task_operations_ : protocols::docking::DockTaskFactory
• AdditionalBackgroundNodesInteractionGraph() : core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >
• AdditionalOutputWrapper() : protocols::rosetta_scripts::AdditionalOutputWrapper
• AdditiveAtomicPolarizability : core::chemical::gasteiger::GasteigerAtomTypeData
• AddJobPairData() : protocols::simple_moves::AddJobPairData
• AddLigandMotifRotamers() : protocols::enzdes::AddLigandMotifRotamers
• addloopgeometry() : protocols::generalized_kinematic_closure::GeneralizedKIC
• addloweranchor() : protocols::generalized_kinematic_closure::GeneralizedKIC
• addLowResStatistics() : protocols::flexpep_docking::FlexPepDockingProtocol
• addmem_ : protocols::membrane::MPQuickRelaxMover , protocols::relax::RangeRelaxMover
• AddMembraneMover() : protocols::membrane::AddMembraneMover
• AddMembraneSpanConstraint() : protocols::membrane::AddMembraneSpanConstraint
• AddMembraneSpanTermZConstraint() : protocols::membrane::AddMembraneSpanTermZConstraint
• AddMHCEpitopeConstraintMover() : protocols::aa_composition::AddMHCEpitopeConstraintMover
• AddMover() : protocols::stepwise::monte_carlo::mover::AddMover
• AddMPLigandMover() : protocols::membrane::AddMPLigandMover
• addnativesolution() : protocols::loop_grower::LoopGrower
• AddNetChargeConstraintMover() : protocols::aa_composition::AddNetChargeConstraintMover
• AddOrDeleteMover() : protocols::stepwise::monte_carlo::mover::AddOrDeleteMover
• AddOrRemoveMatchCsts() : protocols::enzdes::AddOrRemoveMatchCsts
• AddPDBInfoMover() : protocols::simple_moves::AddPDBInfoMover
• AddProperty() : core::chemical::AddProperty
• AddProtonChi() : core::chemical::AddProtonChi
• addRemark() : protocols::sparta::GDB
• AddResidue() : core::scoring::sc::ElectrostaticComplementarityCalculator , core::scoring::sc::MolecularSurfaceCalculator
• AddResidueCouplingConstraint() : protocols::simple_moves::AddResidueCouplingConstraint
• AddResidueLabelMover() : protocols::simple_moves::AddResidueLabelMover
• AddResiduesRotamerSetOperation() : core::pack::rotamer_set::AddResiduesRotamerSetOperation
• address() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• address_ : protocols::canonical_sampling::mc_convergence_checks::PoolData
• address_exists_in_cache() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• address_to_buf() : protocols::canonical_sampling::mc_convergence_checks::DataBuffer
• address_to_string() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• AddRigidBodyLigandConfs() : protocols::enzdes::AddRigidBodyLigandConfs
• adds_any_property() : core::chemical::ResidueTypeFinder
• adds_any_variant() : core::chemical::ResidueTypeFinder
• adds_atoms() : core::chemical::AddAtom , core::chemical::AddAtomAlias , core::chemical::Patch , core::chemical::PatchCase , core::chemical::PatchOperation
• adds_crosslinker_residue() : protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper , protocols::cyclic_peptide::crosslinker::Metal_HelperBase
• adds_properties() : core::chemical::Patch , core::chemical::PatchCase
• adds_properties_enums() : core::chemical::Patch , core::chemical::PatchCase
• adds_property() : core::chemical::AddProperty , core::chemical::PatchOperation
• adds_property_enum() : core::chemical::AddProperty , core::chemical::PatchOperation
• AddSearchPatternRotSetOp() : protocols::hotspot_hashing::AddSearchPatternRotSetOp
• AddSegmentDataMover() : protocols::denovo_design::movers::AddSegmentDataMover
• AddSidechainConstraintsToHotspots() : protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots
• addtailgeometry() : protocols::generalized_kinematic_closure::GeneralizedKIC
• addtime_ : protocols::simple_moves::DumpPdb
• Adduct() : core::chemical::Adduct
• adduct_name() : core::chemical::Adduct
• adduct_name_ : core::chemical::Adduct
• adducts() : core::pack::task::PackerTask , core::pack::task::PackerTask_ , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• adducts_ : core::pack::task::ResidueLevelTask_
• addupperanchor() : protocols::generalized_kinematic_closure::GeneralizedKIC
• addVAR() : protocols::sparta::GDB
• addVirtualResAsRootMembrane() : protocols::topology_broker::MembraneTopologyClaimer
• AddZincSiteConstraints() : protocols::metal_interface::AddZincSiteConstraints
• ADJ_Tab : protocols::sparta::Sparta::SpartaLib
• adjacent_bg_node_indices_ : core::pack::interaction_graph::FirstClassNode< V, E, G >
• adjacent_first_class_node_indices_ : core::pack::interaction_graph::BackgroundNode< V, E, G >
• adjacent_lists_ : protocols::cluster::calibur::Clustering
• adjacent_node_ : core::pack::interaction_graph::NodeBase
• adjacent_node_ind_ : core::pack::interaction_graph::NodeBase
• adjacent_nodes_ : core::pack::interaction_graph::BackgroundNode< V, E, G >
• AdjacentList() : protocols::cluster::calibur::AdjacentList
• adjbb_elec_scale() : core::scoring::FACTSPotential
• adjbb_elec_scale_ : core::scoring::FACTSPotential
• adjbb_solv_scale() : core::scoring::FACTSPotential
• adjbb_solv_scale_ : core::scoring::FACTSPotential
• adjbs_elec_scale() : core::scoring::FACTSPotential
• adjbs_elec_scale_ : core::scoring::FACTSPotential
• adjbs_solv_scale() : core::scoring::FACTSPotential
• adjbs_solv_scale_ : core::scoring::FACTSPotential
• adjFileName : protocols::sparta::Sparta::SpartaLib
• adjust_n_ter_tail_length() : protocols::splice::SpliceInAntibody , protocols::splice::SpliceOutAntibody
• adjust_near_pi() : core::scoring::loop_graph::evaluator::SixDTransRotPotential
• adjust_relax_movemap() : protocols::topology_broker::RigidChunkClaimer , protocols::topology_broker::TopologyBroker , protocols::topology_broker::TopologyClaimer
• adjust_residue_to_minimize_deviation() : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• adjust_stem_positions_by_template() : protocols::splice::SpliceManager
• adjust_stem_positions_by_template_ : protocols::splice::SpliceManager
• adjust_template_jump() : protocols::splice::SpliceInAntibody
• adp_strategy_ : core::scoring::cryst::PhenixInterface , protocols::cryst::FitBfactorsMover
• ads_sec_struct_ : protocols::surface_docking::FullatomRelaxMover
• advance_if_needed() : core::select::Enumerate1WithSelector
• advance_to_next_pose_segment() : protocols::stepwise::modeler::protein::InputStreamWithResidueInfo
• ADVISED_THRESHOLD : protocols::cluster::calibur::PreloadedPDB
• affix_has_inherent_position() : core::chemical::carbohydrates::CarbohydrateInfoManager
• affix_to_patch_map() : core::chemical::carbohydrates::CarbohydrateInfoManager
• affix_to_patch_map_ : core::chemical::carbohydrates::CarbohydrateInfoManager
• affix_to_position_inherency_map() : core::chemical::carbohydrates::CarbohydrateInfoManager
• affix_to_position_inherency_map_ : core::chemical::carbohydrates::CarbohydrateInfoManager
• affix_to_position_map() : core::chemical::carbohydrates::CarbohydrateInfoManager
• affix_to_position_map_ : core::chemical::carbohydrates::CarbohydrateInfoManager
• affixed_numbered_name() : protocols::jd2::JobOutputter
• after : protocols::denovo_design::task_operations::SurroundingSS
• after_minimization_reference_energies_ : protocols::optimize_weights::IterativeOptEDriver
• after_placement_filter_ : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover , protocols::protein_interface_design::movers::PlaceStubMover
• ag_ab_atomic_contacts_ : protocols::antibody::AntibodyFeatures
• ag_residues_ : protocols::antibody::snugdock::SnugDockProtocol
• aggregate_ : protocols::pack_daemon::MultistateFitnessFunction
• aggregate_add() : core::scoring::motif::XformScore
• aggregate_function() : protocols::multistate_design::MultiStateFitnessFunction , protocols::pack_daemon::MultistateFitnessFunction
• aggregate_function_ : protocols::multistate_design::MultiStateFitnessFunction
• aggregate_max() : core::scoring::motif::XformScore
• ahd_cutoff_ : protocols::features::WaterFeatures
• AHdist_long_fade_lookup() : core::scoring::hbonds::HBondDatabase
• AHdist_long_fade_lookup_ : core::scoring::hbonds::HBondDatabase
• AHdist_poly_lookup() : core::scoring::hbonds::HBondDatabase
• AHdist_poly_lookup_ : core::scoring::hbonds::HBondDatabase
• AHdist_short_fade_lookup() : core::scoring::hbonds::HBondDatabase
• AHdist_short_fade_lookup_ : core::scoring::hbonds::HBondDatabase
• Ai() : core::scoring::FACTSResidueInfo
• Ai_ : core::scoring::FACTSResidueInfo
• aid : core::scoring::packstat::Sphere
• AID : protocols::sic_dock::Rose
• aigraph_ : core::io::pose_from_sfr::GeometricRenameIsomorphismCallback , core::io::pose_from_sfr::GeometricRenameVerticiesEquivalent , core::io::pose_from_sfr::GraphvizPropertyWriter
• Ajump_ : protocols::cryst::DockLatticeMover
• akash_dyepos_ : protocols::anchored_design::AnchorMoversData
• ala_constraint_over_strength() : protocols::aa_composition::AddHelixSequenceConstraintsMover
• ala_constraint_over_strength_ : protocols::aa_composition::AddHelixSequenceConstraintsMover
• ala_constraint_under_strength() : protocols::aa_composition::AddHelixSequenceConstraintsMover
• ala_constraint_under_strength_ : protocols::aa_composition::AddHelixSequenceConstraintsMover
• ala_pose_ : protocols::hbnet::HBNet
• ala_pose_loop() : protocols::protein_interface_design::movers::PlaceOnLoop
• AlaScan() : protocols::simple_ddg::AlaScan
• algo_ : core::scoring::cryst::PhenixInterface , protocols::cryst::SetRefinementOptionsMover
• algorithm() : protocols::match::upstream::BuildSet
• algorithm_ : protocols::loops::loop_mover::LoopCM , protocols::match::upstream::BuildSet
• algorithm_inputs() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• algorithm_inputs_ : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• Alias() : protocols::denovo_design::components::Alias
• alias() : protocols::denovo_design::components::StructureData
• alias_name_ : protocols::denovo_design::movers::SetResidueAliasMover
• aliases() : protocols::denovo_design::components::StructureData
• aliases_ : core::chemical::AddAtomAlias , protocols::denovo_design::components::StructureData
• align() : core::fragment::Frame , core::fragment::NonContinuousFrame , core::sequence::Aligner , core::sequence::MCAligner , core::sequence::NWAligner , core::sequence::SWAligner , protocols::backbone_moves::local_backbone_mover::FreePeptide , protocols::fibril::SetupForFibrilMover
• align_ : protocols::comparative_modeling::ExtraThreadingMover , protocols::comparative_modeling::PartialThreadingMover , protocols::comparative_modeling::ThreadingMover , protocols::protein_interface_design::movers::TopologyBrokerMover
• align_all_pose() : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• align_and_calculate_rmsd() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• align_and_output_to_silent_file() : protocols::rna::denovo::RNA_DeNovoProtocol
• align_angle() : protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::topology::HelixPairing
• align_angle_ : protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::topology::HelixPairing
• align_by_domain() : protocols::hybridization::HybridizeProtocol
• align_c() : protocols::sic_dock::Rose
• align_chunk_ : protocols::hybridization::ChunkTrialMover
• align_file_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• align_input_axes_to_symdof_axes_ : protocols::matdes::SymDofMover
• align_model() : protocols::legacy_sewing::Assembly
• align_multipole_axes() : core::scoring::MultipoleElecPotential
• align_n() : protocols::sic_dock::Rose
• align_only_over_base_atoms_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• align_option_ : protocols::hybridization::ChunkTrialMover
• align_output() : core::import_pose::options::RNA_DeNovoProtocolOptions
• align_output_ : core::import_pose::options::RNA_DeNovoProtocolOptions
• align_pdb() : core::import_pose::options::RNA_FragmentMonteCarloOptions
• align_pdb_ : core::import_pose::options::RNA_FragmentMonteCarloOptions
• align_pose() : protocols::rna::AlignmentEnergy , protocols::rna::denovo::RNA_FragmentMonteCarlo , protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• align_pose_ : protocols::rna::AlignmentEnergy , protocols::rna::denovo::RNA_FragmentMonteCarlo , protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker , protocols::stepwise::monte_carlo::StepWiseMonteCarlo , protocols::stepwise::screener::AlignRMSD_Screener
• align_poses() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• align_reference_ : protocols::constraint_generator::CoordinateConstraintGenerator
• align_reference_pose() : protocols::constraint_generator::CoordinateConstraintGenerator
• align_residue_multipole_axes() : core::scoring::MultipoleElecPotential
• align_residues() : protocols::denovo_design::movers::AlignResiduesMover
• align_rmsd_screener_ : protocols::stepwise::screener::IntegrationTestBreaker
• Align_RmsdEvaluator() : protocols::comparative_modeling::Align_RmsdEvaluator
• Align_RotamerEvaluator() : protocols::comparative_modeling::Align_RotamerEvaluator
• align_segment() : protocols::forge::remodel::RemodelGlobalFrame
• align_set_ : protocols::comparative_modeling::AlignmentSet
• align_settings_ : protocols::sewing::hashing::AlignmentFileGeneratorMover
• align_templates_by_domain() : protocols::hybridization::HybridizeProtocol
• align_templates_to_pose_ : protocols::hybridization::CartesianHybridize
• align_to_chunk() : core::import_pose::libraries::RNA_ChunkLibrary
• align_to_com_ : protocols::simple_moves::AlignChainMover
• align_to_current_phore_match() : protocols::ligand_docking::ga_ligand_dock::ConstraintInfo
• align_to_native() : protocols::antibody_legacy::Antibody
• align_to_native_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• align_to_native_pose() : protocols::helical_bundle_predict::HelicalBundlePredictApplication
• align_to_origin() : protocols::cyclic_peptide::SymmetricCycpepAlign
• align_to_pdbname_ : protocols::protein_interface_design::filters::ClashWithTargetFilter
• align_to_quick_alignment_pose() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• align_to_residue() : core::conformation::UltraLightResidue
• align_to_ss_only_ : protocols::hybridization::InsertChunkMover
• align_to_zaxis() : protocols::cyclic_peptide::SymmetricCycpepAlign
• align_torsions_ : core::fragment::rna::FragmentLibrary
• align_trial_counter_ : protocols::hybridization::InsertChunkMover
• align_VDW_rep_screen_pose() : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• align_virtual_atoms_in_carbohydrate_residue() : core::conformation::Conformation
• align_with_offset() : protocols::energy_based_clustering::EnergyBasedClusteringProtocol
• align_working_pose() : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• align_working_to_vdw_atom_id_map : core::pose::rna::VDW_RepScreenInfo
• AlignByResidueSelectorMover() : protocols::fold_from_loops::movers::AlignByResidueSelectorMover
• AlignChainMover() : protocols::simple_moves::AlignChainMover
• aligned() : protocols::star::Extender
• aligned_ : protocols::star::Extender
• AlignedThreadOperation() : protocols::task_operations::AlignedThreadOperation
• AlignEndsMover() : protocols::splice::AlignEndsMover
• Aligner() : core::sequence::Aligner
• AlignEvaluator() : protocols::evaluation::AlignEvaluator
• alignment() : protocols::comparative_modeling::ExtraThreadingMover
• Alignment : protocols::comparative_modeling::MultiThreadingMover
• alignment() : protocols::comparative_modeling::ThreadingJob , protocols::comparative_modeling::ThreadingMover
• alignment2AtomMap() : protocols::hybridization::TMalign
• alignment2strings() : protocols::hybridization::TMalign
• alignment_ : protocols::comparative_modeling::ThreadingJob , protocols::star::Extender
• alignment_anchor_res() : core::pose::full_model_info::FullModelInfo
• alignment_anchor_res_ : core::import_pose::FullModelPoseBuilder
• alignment_atom_id_map_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• alignment_atoms_ : protocols::sewing::data_storage::LigandResidue
• alignment_atoms_in_res() : protocols::energy_based_clustering::EnergyBasedClusteringProtocol
• alignment_atoms_num : protocols::sewing::data_storage::LigandDescription
• alignment_atoms_str : protocols::sewing::data_storage::LigandDescription
• alignment_file() : protocols::evolution::AlignmentAAFinder , protocols::evolution::AlignmentGapInserter , protocols::task_operations::AlignedThreadOperation
• alignment_file_ : protocols::evolution::AlignmentAAFinder , protocols::evolution::AlignmentGapInserter , protocols::task_operations::AlignedThreadOperation
• alignment_generator() : protocols::sewing::hashing::BasisMapGenerator
• alignment_generator_ : protocols::sewing::hashing::BasisMapGenerator
• alignment_id() : core::sequence::SequenceAlignment , protocols::comparative_modeling::ThreadingJob
• alignment_medium_ : core::scoring::nmr::rdc::RDCMultiSet
• alignment_res_string_list_ : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• alignment_settings() : protocols::sewing::hashing::BasisMapGenerator , protocols::sewing::movers::AppendAssemblyMover
• alignment_settings_ : protocols::sewing::hashing::BasisMapGenerator , protocols::sewing::movers::AppendAssemblyMover
• alignment_settings_from_options() : protocols::sewing::hashing::BasisMapGenerator
• alignment_settings_from_tag() : protocols::sewing::hashing::AlignmentFileGeneratorMover
• alignment_str_ : protocols::calc_taskop_filters::RelativePoseFilter
• alignment_torsions_in_res() : protocols::energy_based_clustering::EnergyBasedClusteringProtocol
• AlignmentAAFinder() : protocols::evolution::AlignmentAAFinder
• AlignmentCluster() : protocols::comparative_modeling::AlignmentCluster
• AlignmentClustering() : protocols::comparative_modeling::AlignmentClustering
• AlignmentEnergy() : protocols::rna::AlignmentEnergy
• AlignmentFileGeneratorMover() : protocols::sewing::hashing::AlignmentFileGeneratorMover
• AlignmentGapInserter() : protocols::evolution::AlignmentGapInserter
• AlignmentGenerator() : protocols::sewing::hashing::AlignmentGenerator
• alignments() : protocols::comparative_modeling::AlignmentSet
• Alignments : protocols::comparative_modeling::MultiThreadingMover , protocols::comparative_modeling::ThreadingJobInputter
• alignments() : protocols::jd2::InnerMultiThreadingJob
• alignments_ : protocols::comparative_modeling::MultiThreadingMover , protocols::comparative_modeling::ThreadingJobInputter
• AlignmentSet() : protocols::comparative_modeling::AlignmentSet
• AlignmentSettings() : protocols::sewing::hashing::AlignmentSettings
• AlignPDBInfoToSequences() : protocols::pdbinfo_manipulations::AlignPDBInfoToSequences
• alignPerfectCA() : protocols::loop_grower::SheetSampler
• AlignPoseToInvrotTreeMover() : protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover
• AlignResiduesMover() : protocols::denovo_design::movers::AlignResiduesMover
• AlignRMSD_Screener() : protocols::stepwise::screener::AlignRMSD_Screener
• AlignRmsdTargetEvaluatorCreator() : protocols::comparative_modeling::AlignRmsdTargetEvaluatorCreator
• alignStrand() : protocols::loop_grower::SheetSampler
• ALL : protocols::protein_interface_design::filters::AtomicContactCountFilter
• all_abego_ : protocols::frag_picker::quota::ABEGO_SS_Map , protocols::frag_picker::quota::ABEGO_SS_Pool
• all_add_energy() : protocols::wum::SilentStructStore
• all_ala_C : protocols::seeded_abinitio::GrowPeptides
• all_ala_N : protocols::seeded_abinitio::GrowPeptides
• all_aligned() : core::id::SequenceMapping
• all_atom_inds_ : protocols::match::output::SingleDownstreamResidueWriter
• all_atom_mode_ : protocols::ligand_docking::LigandArea
• all_atom_residue_depth_ : protocols::frag_picker::VallResidue
• all_atoms() : core::chemical::MutableResidueType
• ALL_ATOMS : protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator
• all_basis_pairs_ : protocols::sewing::data_storage::SmartAssembly , protocols::sewing::hashing::Hasher
• all_bb() : core::select::movemap::MoveMapFactory
• all_bb_atoms() : core::chemical::ResidueType , core::conformation::Residue
• all_bb_atoms_ : core::chemical::ResidueType
• all_bb_setting_ : core::select::movemap::MoveMapFactory
• all_bfactors_zero_ : protocols::match::BfactorMPM
• all_boltz_ : protocols::pose_metric_calculators::RotamerBoltzCalculator
• all_bondangles() : core::select::movemap::MoveMapFactory
• all_bondangles_setting_ : core::select::movemap::MoveMapFactory
• all_bondlengths() : core::select::movemap::MoveMapFactory
• all_bondlengths_setting_ : core::select::movemap::MoveMapFactory
• all_branches() : core::select::movemap::MoveMapFactory
• all_branches_setting_ : core::select::movemap::MoveMapFactory
• all_broker_files() : protocols::jd2::archive::Batch
• all_build_points_ : protocols::match::Matcher
• all_bur_unsat_polars_ : protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator
• all_cdr_fold_tree() : protocols::antibody_legacy::Antibody
• all_cdr_loops : protocols::antibody_legacy::Antibody
• all_cdr_VL_VH_fold_tree() : protocols::antibody_legacy::AntibodyModeler
• all_cdrs() : protocols::antibody::AntibodyEnumManager
• all_cdrs_ : protocols::antibody::AntibodyEnumManager
• all_cdrs_and_proto_ : protocols::antibody::AntibodyEnumManager
• all_cdrs_present_ : protocols::antibody::AntibodyInfo
• all_cdrs_present_and_proto_ : protocols::antibody::AntibodyInfo
• all_chi() : core::select::movemap::MoveMapFactory
• all_chi_setting_ : core::select::movemap::MoveMapFactory
• all_combinations() : protocols::denovo_design::components::CompoundPerturber
• All_CSA_lines_ : core::scoring::ChemicalShiftAnisotropy
• All_DC_lines_ : core::scoring::DipolarCoupling
• all_default() : core::id::AtomID_Map< T >
• all_dist_buf_ : protocols::noesy_assign::DistanceScoreMover
• all_dof_map_ : protocols::ub_e2c::ubi_e2c_modeler
• all_downstream_algorithms_ : protocols::match::Matcher
• all_downstream_builders_ : protocols::match::Matcher
• all_energies() : protocols::toolbox::DecoySetEvaluation
• all_energies_ : protocols::toolbox::DecoySetEvaluation
• all_energies_begin() : core::scoring::ScoreFunction
• all_energies_end() : core::scoring::ScoreFunction
• all_frames_ : protocols::topology_broker::DisulfJumpClaimer
• all_gap_ : protocols::task_operations::CrystalContactsOperation
• all_Hbonds_ : protocols::simple_pose_metric_calculators::NumberHBondsCalculator
• all_heavy_unsats_ : protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator
• all_helices_ : protocols::hbnet::HBNetStapleInterface
• all_hits_ : protocols::match::HitNeighborFinder
• all_inputs_ProQ2_ : core::scoring::methods::ProQ_Energy
• all_inputs_ProQM_ : core::scoring::methods::ProQ_Energy
• all_invrots_ : protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover
• all_jacobians_ : protocols::recces::sampler::rna::MC_RNA_KIC_Sampler , protocols::stepwise::sampler::rna::RNA_KinematicCloser
• all_job_nodes_ : protocols::jd3::JobGenealogist
• all_job_results_for_node() : protocols::jd3::JobGenealogist
• all_jobs_assigned_for_preliminary_job_node() : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen
• all_jobs_completed() : protocols::jd3::JobDirectedNode
• all_jobs_completed_ : protocols::jd3::JobDirectedNode
• all_jobs_started() : protocols::jd3::JobDirectedNode
• all_jobs_started_ : protocols::jd3::JobDirectedNode
• all_jump_pairings_ : protocols::topology_broker::DisulfJumpClaimer
• all_jumps() : core::select::movemap::MoveMapFactory
• all_jumps_setting_ : core::select::movemap::MoveMapFactory
• all_lex_states : protocols::match::MatcherOutputStats
• all_loops_ : protocols::antibody::LHRepulsiveRampLegacy , protocols::antibody::LHSnugFitLegacy
• all_loops_closed_ : protocols::loops::loop_mover::IndependentLoopMover
• all_lores_score_final() : protocols::rna::denovo::RNA_FragmentMonteCarlo
• all_lores_score_final_ : protocols::rna::denovo::movers::RNA_DeNovoProtocolMover , protocols::rna::denovo::RNA_FragmentMonteCarlo
• all_metapatch_map_ : core::chemical::PoseResidueTypeSet
• all_methods() : core::scoring::ScoreFunction
• all_methods_ : core::scoring::ScoreFunction
• all_movable_ : protocols::seeded_abinitio::SegmentHybridizer
• all_mutants_ : protocols::pmut_scan::PointMutScanDriver
• all_nmer_pssms_ : core::scoring::methods::NMerPSSMEnergy
• all_nmer_svms_ : core::scoring::methods::NMerSVMEnergy
• all_nmer_svms_ranks_ : core::scoring::methods::NMerSVMEnergy
• all_nu() : core::select::movemap::MoveMapFactory
• all_nu_setting_ : core::select::movemap::MoveMapFactory
• all_pairings_ : protocols::jumping::DisulfPairingLibrary
• all_patch_map_ : core::chemical::PoseResidueTypeSet
• all_peptides_ : protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter
• all_permutations() : protocols::denovo_design::components::DivideAndConqueror
• all_pose_to_output_pose_ID_map_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• all_positions_ : protocols::simple_moves::DumpSingleResidueRotamers
• all_pssm_data_ : protocols::optimize_weights::IterativeOptEDriver
• All_RDC_lines : core::scoring::ResidualDipolarCoupling_Rohl
• All_RDC_lines_ : core::scoring::ResidualDipolarCoupling
• all_ref_poses() : core::import_pose::atom_tree_diffs::AtomTreeDiff , protocols::jd2::AtomTreeDiffJobInputter
• all_result_nodes_ : protocols::jd3::JobGenealogist
• all_results_are_in() : protocols::jd3::dag_node_managers::NodeManager
• all_rna_fragments_file() : core::import_pose::options::RNA_FragmentMonteCarloOptions
• all_rna_fragments_file_ : core::import_pose::options::RNA_FragmentMonteCarloOptions
• all_rot_ : core::pack::annealer::FixbbPwatSimAnnealer
• all_rots_bb_ : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary
• all_sc_atoms() : core::chemical::ResidueType
• all_sc_atoms_ : core::chemical::ResidueType
• all_seeds_ : protocols::seeded_abinitio::CAcstGenerator , protocols::seeded_abinitio::GrowPeptides , protocols::seeded_abinitio::SeedFoldTree , protocols::seeded_abinitio::SeedSetupMover
• all_segments() : protocols::legacy_sewing::Assembly
• all_segments_ : protocols::legacy_sewing::Assembly
• all_settings_to_defualt() : protocols::multistage_rosetta_scripts::MRSJobQueen
• all_sort_silent_scores() : protocols::wum::SilentStructStore
• all_ss_ : protocols::frag_picker::quota::ABEGO_SS_Map , protocols::frag_picker::quota::ABEGO_SS_Pool
• ALL_STAGES : protocols::abinitio::ClassicAbinitio , protocols::abinitio::MembraneAbinitio
• all_structs_ : protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashMoverWrapper
• all_suites_ : core::pose::rna::RNA_SuiteName
• all_target_res() : protocols::toolbox::match_enzdes_util::InvrotTarget
• all_target_res_ : protocols::toolbox::match_enzdes_util::InvrotTarget
• all_target_residues() : protocols::toolbox::match_enzdes_util::InvrotTarget , protocols::toolbox::match_enzdes_util::InvrotTreeNode , protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase
• all_threading_start_combinations() : protocols::switches::GraftSwitchMover
• all_turn_residues_are_on_the_same_chain() : protocols::features::BetaTurnDetection
• all_types_with_variants_aa_already_cached() : core::chemical::ResidueTypeSetCache
• all_types_with_variants_residuetypecops_already_cached() : core::chemical::ResidueTypeSetCache
• all_unsat_polars_ : protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator
• all_vs_bb_energies_ : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• all_vs_bb_energy_alt_conf_ : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• all_vs_bb_energy_curr_conf_ : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• all_waste_is_discarded() : protocols::jd3::dag_node_managers::NodeManager
• all_water_weights_ : core::scoring::geometric_solvation::WaterWeightGridSet
• allaas_ : protocols::hbnet::HBNet
• AllAtomNormalization() : protocols::qsar::scoring_grid::AllAtomNormalization
• allcdr_map_ : protocols::antibody::CDRsMinPackMin
• AlleleMatrix() : core::scoring::mhc_epitope_energy::AlleleMatrix
• alleles_ : core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix
• allGroups_ : protocols::task_operations::LinkResidues
• alllevel() : core::sequence::ABEGOManager
• AllMethods : core::scoring::ScoreFunction
• AllMethodsIterator : core::scoring::ScoreFunction
• allocate_appropriate_memory() : core::scoring::Membrane_FAEmbed , core::scoring::methods::LK_hack
• allocate_buffers() : protocols::canonical_sampling::AsyncMPITemperingBase , protocols::canonical_sampling::ParallelTempering
• allocate_grid_of_occluded_sites() : core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy
• allocate_segments() : protocols::sewing::hashing::Hasher
• allocateSpaceForRMSD() : protocols::cluster::calibur::Clustering
• Allocator : protocols::mean_field::jagged_array< T, A >
• allocator_type : protocols::mean_field::jagged_array< T, A >
• allow_all_aa() : protocols::splice::Splice
• allow_all_aa_ : protocols::splice::Splice
• allow_all_aas() : protocols::task_operations::ProteinInterfaceDesignOperation
• allow_all_aas_ : protocols::seeded_abinitio::SeedSetupMover , protocols::task_operations::ProteinInterfaceDesignOperation
• allow_anchor_repack_ : protocols::anchored_design::AnchorMoversData
• allow_base_pair_only_centroid_screen() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• allow_base_pair_only_centroid_screen_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• allow_base_pair_only_screen() : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• allow_base_pair_only_screen_ : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• allow_beta_cys_ : protocols::denovo_design::DisulfidizeMover
• allow_bulge() : core::import_pose::options::RNA_FragmentMonteCarloOptions
• allow_bulge_ : core::import_pose::options::RNA_FragmentMonteCarloOptions
• allow_bulge_at_chainbreak() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• allow_bulge_at_chainbreak_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• allow_chain_boundary_jump_partner_right_at_fixed_BP_ : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• allow_chi_copy_ : protocols::simple_moves::ReturnSidechainMover
• allow_chi_during_relax_ : protocols::forge::remodel::RemodelMover::instruction_flags
• allow_chunk_library_inputter() : protocols::jd3::chunk_library::ChunkLibraryJobQueen
• allow_claim() : protocols::topology_broker::FibrilModelingClaimer , protocols::topology_broker::RigidChunkClaimer , protocols::topology_broker::TopologyClaimer
• allow_consecutive_bulges() : core::import_pose::options::RNA_FragmentMonteCarloOptions
• allow_consecutive_bulges_ : core::import_pose::options::RNA_FragmentMonteCarloOptions
• allow_cyclic_ : protocols::denovo_design::connection::AreConnectablePredicate
• allow_d_cys_ : protocols::denovo_design::DisulfidizeMover
• allow_delete() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• allow_delete_ : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• allow_design() : protocols::task_operations::DesignAroundOperation , protocols::task_operations::SelectResiduesWithinChainOperation
• allow_design_ : protocols::task_operations::DesignAroundOperation , protocols::task_operations::SelectResiduesWithinChainOperation
• allow_design_around() : protocols::task_operations::DatabaseThread , protocols::task_operations::ThreadSequenceOperation
• allow_design_around_ : protocols::task_operations::DatabaseThread , protocols::task_operations::ThreadSequenceOperation
• allow_dof() : core::conformation::symmetry::SymDof
• allow_duplicates : protocols::environment::claims::ResidueElement
• allow_even_trades() : protocols::task_operations::PruneBuriedUnsatsOperation
• allow_even_trades_ : protocols::task_operations::PruneBuriedUnsats_RotamerSetsOperation , protocols::task_operations::PruneBuriedUnsatsOperation
• allow_fixed_res_at_moving_res_ : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• allow_fragment_moves_in_bps() : core::import_pose::options::RNA_FragmentMonteCarloOptions
• allow_fragment_moves_in_bps_ : core::import_pose::options::RNA_FragmentMonteCarloOptions
• allow_full_model_inputter() : protocols::jd3::full_model::FullModelJobQueen
• allow_hbond() : core::scoring::hbonds::HBondSet
• allow_insert_res() : core::import_pose::RNA_DeNovoParameters
• allow_insert_res_ : core::import_pose::RNA_DeNovoParameters
• allow_internal_hinge_moves() : protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions
• allow_internal_hinge_moves_ : protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions
• allow_internal_local_moves() : protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions
• allow_internal_local_moves_ : protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions
• allow_l_cys_ : protocols::denovo_design::DisulfidizeMover
• allow_no_hbnets_ : protocols::hbnet::HBNet
• allow_onebody_networks_ : protocols::hbnet::HBNetStapleInterface
• allow_overlap_ : protocols::ligand_docking::CompoundTranslate
• allow_phosphate_virtualization() : core::pack::task::rna::RNA_ResidueLevelTask
• allow_phosphate_virtualization_ : core::pack::task::rna::RNA_ResidueLevelTask
• allow_pose_inputter() : protocols::jd3::standard::StandardJobQueen
• allow_pose_outputter() : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::standard::StandardJobQueen
• allow_pure_movers() : protocols::environment::Environment
• allow_rama_mismatches() : protocols::antibody::clusters::CDRClusterMatcher
• allow_rama_mismatches_ : protocols::antibody::clusters::CDRClusterMatcher
• allow_reading_cancelled_decoys() : protocols::jd2::archive::Batch
• allow_reading_cancelled_decoys_ : protocols::jd2::archive::Batch
• allow_rebuild_bulge_mode() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• allow_rebuild_bulge_mode_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• allow_repack_ : protocols::antibody::H3RefineCCD
• allow_repacking() : protocols::task_operations::SelectResiduesWithinChainOperation
• allow_repacking_ : protocols::task_operations::SelectResiduesWithinChainOperation
• allow_scoring() : core::scoring::MembraneTopology
• allow_scoring_ : core::scoring::MembraneTopology
• allow_split_off() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• allow_split_off_ : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• allow_submotif_split() : protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions
• allow_submotif_split_ : protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions
• allow_syn_pyrimidine() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• allow_syn_pyrimidine_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• allow_tmh_scoring() : core::scoring::MembraneTopology
• allow_tmh_scoring_ : core::scoring::MembraneTopology
• allow_virtual_ : core::conformation::symmetry::SymmData
• allow_virtual_o2prime_hydrogens() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::modeler::packer::StepWisePacker , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• allow_virtual_o2prime_hydrogens_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::modeler::packer::StepWisePacker , protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker , protocols::stepwise::modeler::StepWiseMinimizer , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• allow_virtual_side_chains() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions , protocols::stepwise::modeler::packer::StepWisePacker , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• allow_virtual_side_chains_ : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions , protocols::stepwise::modeler::packer::StepWisePacker , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• allowable_sequence_sep_ : core::scoring::methods::LinearBranchEnergy , core::scoring::methods::LinearChainbreakEnergy
• allowed_aas_ : core::pack::task::operation::DisallowIfNonnative , core::pack::task::operation::DisallowIfNonnativeRLT , protocols::calc_taskop_movers::DesignRepackMover , protocols::matdes::SchemePlaceMotifsMover
• allowed_aas_per_jump_ : protocols::protein_interface_design::movers::MapHotspot
• allowed_bulge_res() : core::import_pose::options::RNA_FragmentMonteCarloOptions
• allowed_bulge_res_ : core::import_pose::options::RNA_FragmentMonteCarloOptions
• allowed_canonicals_by_position_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• allowed_closure_attempts() : protocols::forge::remodel::RemodelLoopMover
• allowed_closure_attempts_ : protocols::forge::remodel::RemodelLoopMover
• allowed_current_slide() : protocols::symmetry::SymmetrySlider
• allowed_cuts() : protocols::splice::SpliceManager
• allowed_cuts_ : protocols::splice::Splice , protocols::splice::SpliceIn , protocols::splice::SpliceManager
• allowed_deviation_ : protocols::simple_moves::StructProfileMover
• allowed_deviation_for_turn_type_id_ : protocols::features::strand_assembly::SandwichFeatures
• allowed_deviation_loops_ : protocols::simple_moves::StructProfileMover
• allowed_dof_helix_indices_ : protocols::helical_bundle::BundleGridSamplerHelper
• allowed_dof_jumps_ : core::conformation::symmetry::SymDof
• allowed_dof_types_ : protocols::helical_bundle::BundleGridSamplerHelper
• allowed_failure_before_extend_ : protocols::LoopRebuild
• allowed_failure_before_stop : protocols::LoopRebuild
• allowed_failure_before_stop_ : protocols::LoopRebuild
• allowed_host_pos_ : protocols::protein_interface_design::movers::PlaceStubMover
• allowed_loop_abegos_ : protocols::pose_length_moves::ConnectChainsMover , protocols::pose_length_moves::FixAllLoopsMover , protocols::pose_length_moves::NearNativeLoopCloser
• allowed_noncanonicals_by_position_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• allowed_output_modes() : core::simple_metrics::metrics::SequenceMetric
• allowed_output_modes_as_vector() : core::simple_metrics::metrics::SequenceMetric
• allowed_positions_ : protocols::loops::loop_closure::kinematic_closure::KinematicWrapper
• allowed_res_name3_at_position() : protocols::toolbox::match_enzdes_util::EnzConstraintIO , protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• allowed_res_name3s() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• allowed_res_types() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• allowed_res_types_ : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• allowed_res_types_pointers() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• allowed_res_types_pointers_ : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• allowed_residue_types() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• allowed_residue_types_ : core::pack::task::ResidueLevelTask_
• allowed_residue_types_begin() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• allowed_residue_types_end() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• allowed_restypes() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• allowed_separation_ : protocols::antibody::CloseOneCDRLoop , protocols::antibody_legacy::CloseOneMover
• allowed_seqpos() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• allowed_seqpos_ : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• allowed_surface_aa() : protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover
• allowed_time_ : core::optimization::GA_Minimizer
• allowed_torsion_indices_ : protocols::helical_bundle::BackboneGridSamplerHelper
• allowed_types() : protocols::dna::DnaInterfacePacker , protocols::motifs::BuildPosition
• allowed_types_ : protocols::dna::DnaInterfacePacker , protocols::motifs::BuildPosition
• AllowedSeqposForGeomCst() : protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst
• allowSeqShiftMoves_ : protocols::rbsegment_relax::AutoRBMover
• AllowSlideJumpMap_ : protocols::symmetry::SymmetrySlider
• allowSSFragInserts_ : protocols::rbsegment_relax::AutoRBMover
• allprotein_tf_ : protocols::flexpep_docking::FlexPepDockingProtocol
• AllResFilter() : core::pack::task::operation::AllResFilter
• AllResiduesChanged() : protocols::abinitio::AllResiduesChanged , protocols::hybridization::AllResiduesChanged
• allRs_ : protocols::cryst::MakeLatticeMover
• allsc() : protocols::protein_interface_design::movers::SaveAndRetrieveSidechains
• allsc_ : protocols::protein_interface_design::movers::SaveAndRetrieveSidechains
• AllStructureDistanceBoundVector : protocols::noesy_assign::DistanceScoreMover
• allTs_ : protocols::cryst::MakeLatticeMover
• aln_ : protocols::comparative_modeling::Align_RotamerEvaluator , protocols::evaluation::AlignEvaluator , protocols::hybridization::HybridizeProtocol
• aln_files_ : protocols::protein_interface_design::filters::RmsdFilter
• alns : protocols::comparative_modeling::AlignmentCluster
• alns_ : protocols::jd2::InnerMultiThreadingJob
• alpha() : core::io::CrystInfo , core::optimization::lbfgs_iteration_data , core::pose::Pose , core::scoring::CSA , core::scoring::FACTSRsdTypeInfo , core::scoring::fiber_diffraction::Hankel , protocols::cryst::Spacegroup , protocols::cryst::WallpaperGroup , protocols::dna::DNABase , protocols::protein_interface_design::Transformation , protocols::stepwise::sampler::rigid_body::EulerAngles , Transformation
• alpha_ : core::io::CrystInfo , core::scoring::CSA , core::scoring::FACTSRsdTypeInfo , core::scoring::nmr::NMRTensor , protocols::cryst::Spacegroup , protocols::cryst::WallpaperGroup , protocols::dna::DNABase , protocols::rigid::WholeBodyRotationMover , protocols::simple_moves::UniformRotationMover , protocols::stepwise::sampler::rigid_body::EulerAngles
• alpha_aform() : core::chemical::rna::RNA_FittedTorsionInfo
• alpha_alpha : protocols::denovo_design::components::IdealAbegoGenerator
• alpha_atom_names_ : core::scoring::dna::DNATorsionPotential
• alpha_beta_pattern_ : protocols::ncbb::SecStructFinder , protocols::ncbb::SecStructMinimizeMover , protocols::ncbb::SecStructMinimizeMultiFunc
• alpha_components() : core::scoring::dna::DNATorsionPotential
• alpha_components_ : core::scoring::dna::DNATorsionPotential
• alpha_fade_ : core::scoring::rna::RNA_TorsionPotential
• alpha_potential_ : core::scoring::rna::RNA_TorsionPotential
• alpha_to_beta() : protocols::ncbb::SecStructFinder
• alphabet() : core::sequence::ChemicalShiftSequence , core::sequence::SequenceProfile
• alphabet_ : core::scoring::constraints::ResidueCouplingConstraint , core::sequence::ChemicalShiftSequence , core::sequence::SequenceProfile , protocols::simple_moves::AddResidueCouplingConstraint
• alphamax : core::pose::rna::RNA_SuiteName
• alphamin : core::pose::rna::RNA_SuiteName
• alphas_ : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• already_completed_job_count_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• already_connected() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• already_in_queue() : protocols::match::output::UpstreamHitCacher
• already_instantiated_in_pose() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• already_listed_in_obligate_pair() : core::import_pose::RNA_DeNovoSetup , protocols::rna::denovo::movers::RNA_DeNovoProtocolMover
• already_prepped_for_simA_ : core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode
• already_virtualized_res_list_ : protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler
• also_check_fix_disulf() : protocols::frag_picker::CS2ndShift
• alt : core::scoring::sc::_PROBE
• alt_atom_hbonds_ : core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G > , core::pack::interaction_graph::NPDHBondNode< V, E, G > , core::pack::interaction_graph::NPDHBSimpleNode
• alt_bb() : protocols::flexpack::interaction_graph::FlexbbNode
• alt_bg_bg_exhpobeolap_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• alt_codes_ : core::io::NomenclatureManager
• alt_dots_cache_ : core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G >
• alt_e_up_to_date() : protocols::flexpack::interaction_graph::FlexbbEdge
• alt_e_up_to_date_ : protocols::flexpack::interaction_graph::FlexbbEdge
• alt_energy() : protocols::flexpack::interaction_graph::FlexbbEdge
• alt_energy_ : protocols::flexpack::interaction_graph::FlexbbEdge
• alt_hbonds_ : core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G > , core::pack::interaction_graph::NPDHBondNode< V, E, G > , core::pack::interaction_graph::NPDHBSimpleNode
• alt_loc() : core::pose::PDBInfo
• alt_rot() : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• alt_rot_inds_ : protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
• alt_rot_matrix() : protocols::mean_field::MeanField
• alt_rot_matrix_ : protocols::mean_field::MeanField
• alt_rots_ : protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
• alt_sc_centroid() : core::pack::interaction_graph::SimpleNode
• alt_sc_centroid_ : core::pack::interaction_graph::SimpleNode
• alt_sc_radius() : core::pack::interaction_graph::SimpleNode
• alt_sc_radius_ : core::pack::interaction_graph::SimpleNode
• alt_state_atom_atom_overlaps_ : core::pack::interaction_graph::HPatchEdge< V, E, G >
• alt_state_being_considered_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >
• alt_state_dots_matches_current_state_dots_ : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G >
• alt_state_energy() : core::pack::interaction_graph::SymmMinimalistEdge
• alt_state_energy_ : core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmMinimalistEdge
• alt_state_exolap_hphobes_ : core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G > , core::pack::interaction_graph::HPatchEdge< V, E, G >
• alt_state_exp_hphobes() : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G >
• alt_state_exp_hphobes_ : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G >
• alt_state_hphobes() : core::pack::interaction_graph::HPatchNode< V, E, G >
• alt_state_inv_dots() : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G >
• alt_state_inv_dots_ : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G >
• alt_state_rotamer() : core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::NPDHBondNode< V, E, G >
• alt_state_rotamer_dots_ : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G >
• alt_state_rotamer_op() : core::pack::interaction_graph::NPDHBondNode< V, E, G >
• alt_state_sparse_mat_info_ : core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode
• alt_state_total_hASA_ : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G >
• altcrossover_ : protocols::ligand_docking::ga_ligand_dock::GALigandDock , protocols::ligand_docking::ga_ligand_dock::GAOptimizer
• alter_espGrid() : protocols::pockets::PocketGrid
• alter_espGrid_with_bound_ligand() : protocols::pockets::PocketGrid
• alter_foldtree_ : protocols::antibody::CDRsMinPackMin
• alter_rotamer_set() : core::pack::rotamer_set::AddResiduesRotamerSetOperation , core::pack::rotamer_set::DeleteAllRotamerSetOperation , core::pack::rotamer_set::RotamerSetOperation , core::pack::rotamer_set::UnboundRotamersOperation , protocols::matdes::MotifHitsRotamersOperation , protocols::splice::SampleRotamersFromPDB_RotamerSetOperation , protocols::task_operations::LimitAromaChi2_RotamerSetOperation , protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers , protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO , protocols::toolbox::rotamer_set_operations::SpecialRotamerRSO
• alter_rotamer_set_from_db() : protocols::splice::SampleRotamersFromPDB_RotamerSetOperation
• alter_rotamer_set_from_pdb() : protocols::splice::SampleRotamersFromPDB_RotamerSetOperation
• alter_rotamer_sets() : core::pack::rotamer_set::RotamerSetsOperation , protocols::task_operations::PruneBuriedUnsats_RotamerSetsOperation
• altered_residues_ : protocols::fold_from_loops::movers::NubInitioLoopClosureMover
• alternate_hbs() : core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G > , core::pack::interaction_graph::NPDHBondNode< V, E, G >
• alternate_hbs_for_atom() : core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G > , core::pack::interaction_graph::NPDHBondNode< V, E, G >
• alternate_hbs_for_atoms() : core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G > , core::pack::interaction_graph::NPDHBondNode< V, E, G >
• alternate_one_body_energy_ : core::pack::interaction_graph::SimpleNode
• alternate_pose_ : protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
• alternate_pose_energy_ : protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
• alternate_residue_ : core::pack::interaction_graph::SimpleNode
• alternate_state() : protocols::flexpack::interaction_graph::FlexbbNode
• alternate_state_ : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode , protocols::flexpack::interaction_graph::FlexbbNode
• alternate_state_info() : protocols::flexpack::interaction_graph::FlexbbNode
• alternate_state_info_ : protocols::flexpack::interaction_graph::FlexbbNode
• alternate_state_is_being_considered() : protocols::flexpack::interaction_graph::FlexbbNode
• alternate_state_is_being_considered_ : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode , protocols::flexpack::interaction_graph::FlexbbNode
• alternate_state_one_body_energy() : protocols::flexpack::interaction_graph::FlexbbNode
• alternate_state_one_body_energy_ : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode , protocols::flexpack::interaction_graph::FlexbbNode
• alternate_state_total_energy() : protocols::flexpack::interaction_graph::FlexbbNode
• alternate_state_total_energy_ : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode , protocols::flexpack::interaction_graph::FlexbbNode
• alternate_state_two_body_energies() : protocols::flexpack::interaction_graph::FlexbbNode
• alternate_state_two_body_energies_ : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode , protocols::flexpack::interaction_graph::FlexbbNode
• alternative_decoys_out() : protocols::jd2::archive::Batch
• AlternativePairings() : protocols::abinitio::AlternativePairings
• AlterSpecDisruptionDriver() : protocols::pmut_scan::AlterSpecDisruptionDriver
• altitude_max : protocols::hotspot_hashing::SphericalRotationSearchPattern
• altitude_min : protocols::hotspot_hashing::SphericalRotationSearchPattern
• altitude_rotation_sampling : protocols::hotspot_hashing::SphericalRotationSearchPattern
• altLoc : core::io::AtomInformation , core::pose::PDBInfo::AtomRecord
• always_rotamer_one_ : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph
• am_ : core::fragment::picking_old::vall::eval::ABEGOEval
• amb_hnq_ : protocols::relax::AtomCoordinateCstMover
• AmberPeriodicFunc() : core::scoring::func::AmberPeriodicFunc
• AmbigCSScore() : protocols::frag_picker::scores::AmbigCSScore
• ambiguity() : protocols::ligand_docking::ga_ligand_dock::AtomProperties , protocols::noesy_assign::FloatingResonance , protocols::noesy_assign::Resonance
• ambiguity_ : protocols::ligand_docking::ga_ligand_dock::AtomProperties
• ambiguous() : protocols::noesy_assign::CrossPeak
• ambiguous_hnq() : protocols::relax::AtomCoordinateCstMover
• ambiguous_hnq_ : protocols::constraint_generator::CoordinateConstraintGenerator
• AmbiguousConstraint() : core::scoring::constraints::AmbiguousConstraint
• AmbiguousConstraintCreator() : core::scoring::constraints::AmbiguousConstraintCreator
• AmbiguousMultiConstraint() : protocols::constraints_additional::AmbiguousMultiConstraint
• AmbiguousNMRConstraint() : core::scoring::constraints::AmbiguousNMRConstraint
• AmbiguousNMRConstraintCreator() : core::scoring::constraints::AmbiguousNMRConstraintCreator
• AmbiguousNMRDistanceConstraint() : core::scoring::constraints::AmbiguousNMRDistanceConstraint
• AmbiguousNMRDistanceConstraintCreator() : core::scoring::constraints::AmbiguousNMRDistanceConstraintCreator
• amide_mm_ : protocols::chemically_conjugated_docking::UBQ_GTPaseMover
• amino_acid_type_ : protocols::sewing::data_storage::SmartSewingResidue
• amino_acids_ : core::scoring::constraints::ResidueCouplingConstraint
• aminoAcidList : protocols::forge::remodel::LineObject
• AminoAcidNeighborSparseMatrix() : core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >
• amoeba_type_lookup() : core::scoring::MultipoleElecPotential , core::scoring::VdWTinkerPotential
• amp_scaling_factors_ : core::scoring::geometric_solvation::OccludedHbondSolEnergy
• amplitude : core::chemical::rna::GaussianParameter , protocols::dna::DNABase
• amplitude_ : protocols::dna::DNABase
• aN : protocols::sparta::Sparta::SpartaLib
• ana_deriv() : core::optimization::DerivCheckDataPoint , core::optimization::DOF_DataPoint
• ana_deriv_ : core::optimization::DerivCheckDataPoint , core::optimization::DOF_DataPoint
• analytic_etable_derivatives() : core::scoring::etable::Etable
• analytic_etable_evaluation : core::init::pre_talaris_2013_behavior_settings , core::scoring::etable::Etable , core::scoring::etable::EtableOptions , core::scoring::methods::EnergyMethodOptions
• analytic_lj_generic_form() : core::scoring::etable::Etable
• analytic_ljatr_cubic_poly_ramp_to_zero() : core::scoring::etable::Etable
• analytic_ljatr_cubic_poly_ramp_to_zero_deriv() : core::scoring::etable::Etable
• analytic_ljrep_linearized() : core::scoring::etable::Etable
• analytic_lk_derivatives() : core::scoring::etable::Etable
• analytic_lk_energy() : core::scoring::etable::Etable
• analytic_lk_evaluation() : core::scoring::etable::Etable
• analytic_lk_evaluation_individual() : core::scoring::etable::Etable
• analytic_parameters_ : core::scoring::etable::Etable
• analytic_params_for_pair() : core::scoring::etable::Etable
• AnalyticEtableEnergy() : core::scoring::etable::AnalyticEtableEnergy
• AnalyticEtableEvaluator() : core::scoring::etable::AnalyticEtableEvaluator
• analyze() : protocols::multistage_rosetta_scripts::cluster::metrics::JumpMetric , protocols::multistage_rosetta_scripts::cluster::metrics::SequenceMetric
• analyze_and_filter() : protocols::chemically_conjugated_docking::UBQ_GTPaseMover
• analyze_trajectory() : protocols::ligand_docking::ga_ligand_dock::EntropyEstimator
• AnalyzeLoopModeling() : protocols::pose_length_moves::AnalyzeLoopModeling
• analyzer_ : protocols::monte_carlo::MonteCarloInterface
• aname1_ : protocols::enzdes::DiffAtomSasaFilter
• aname2_ : protocols::enzdes::DiffAtomSasaFilter
• anb : core::scoring::packstat::CavityBall
• ancestor_name_ : core::chemical::ChangeAncestory
• Anchor() : protocols::anchored_design::Anchor
• anchor_ : core::scoring::func::MixtureFunc , protocols::anchored_design::AnchorMoversData
• anchor_at_res1() : protocols::membrane::MembranePositionFromTopologyMover
• anchor_at_res1_ : protocols::membrane::MembranePositionFromTopologyMover
• anchor_atom() : core::pack::rotamer_set::WaterAnchorInfo
• anchor_atom_dest_ : protocols::comparative_modeling::StealLigandMover
• anchor_atom_id_ : protocols::seeded_abinitio::CoordinateCst
• anchor_atom_name_ : core::pack::rotamer_set::WaterAnchorInfo
• anchor_atom_source_ : protocols::comparative_modeling::StealLigandMover
• anchor_chain_ : protocols::topology_broker::DensityScoringClaimer , protocols::topology_broker::MetalloClaimer
• anchor_end() : protocols::anchored_design::AnchorMoversData
• anchor_insert_only_ : protocols::hybridization::InsertChunkMover
• anchor_loop_index_ : protocols::anchored_design::AnchorMoversData
• anchor_noise_constraints_mode_ : protocols::anchored_design::AnchorMoversData
• anchor_noise_constraints_setup() : protocols::anchored_design::AnchorMoversData
• anchor_offset() : protocols::multistate_design::PartitionAggregateFunction
• anchor_offset_ : protocols::dna::DnaInterfaceMultiStateDesign , protocols::multistate_design::PartitionAggregateFunction , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• anchor_positions_ : protocols::hybridization::HybridizeFoldtreeDynamic
• anchor_res() : protocols::splice::SpliceManager
• anchor_res_ : protocols::protein_interface_design::movers::SetAtomTree , protocols::seeded_abinitio::CoordinateCst , protocols::splice::SpliceManager
• anchor_reses_ : protocols::hybridization::WeightedFragmentSmoothTrialMover , protocols::hybridization::WeightedFragmentTrialMover
• anchor_residue() : core::pack::rotamer_set::WaterAnchorInfo
• anchor_residue_ : core::conformation::symmetry::SymmData , core::pack::rotamer_set::WaterAnchorInfo , protocols::topology_broker::DensityScoringClaimer , protocols::topology_broker::MetalloClaimer
• anchor_residues_ : protocols::hybridization::AllResiduesChanged
• anchor_resnum() : protocols::protein_interface_design::movers::TaskAwareCsts
• anchor_resnum_ : protocols::protein_interface_design::movers::TaskAwareCsts
• anchor_rsd_ : protocols::membrane::AddMembraneMover
• anchor_rsd_selectors_ : protocols::cyclic_peptide::PeptideStubMover
• anchor_specified() : protocols::seeded_abinitio::SeedFoldTree
• anchor_specified_ : protocols::seeded_abinitio::GrowPeptides , protocols::seeded_abinitio::SeedFoldTree
• anchor_start() : protocols::anchored_design::AnchorMoversData
• anchor_sugar_modeling() : protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator
• anchor_sugar_modeling_ : protocols::stepwise::screener::AnchorSugarScreener
• anchor_sugar_solution_number() : protocols::stepwise::screener::AnchorSugarScreener
• anchor_sugar_solution_number_ : protocols::stepwise::screener::AnchorSugarScreener
• anchor_via_constraints_ : protocols::anchored_design::AnchorMoversData
• anchored_graft_mover_ : protocols::antibody::AntibodyCDRGrafter , protocols::antibody::design::AntibodyDesignMover
• anchored_loop() : protocols::anchored_design::AnchorMoversData
• AnchoredDesignMover() : protocols::anchored_design::AnchoredDesignMover
• AnchoredGraftMover() : protocols::grafting::AnchoredGraftMover
• AnchoredPerturbMover() : protocols::anchored_design::AnchoredPerturbMover
• AnchoredRefineMover() : protocols::anchored_design::AnchoredRefineMover
• anchorfile_ : protocols::anchored_design::Anchor
• AnchorMoversData() : protocols::anchored_design::AnchorMoversData
• anchors() : protocols::protein_interface_design::filters::BoltzmannFilter
• anchors_ : protocols::protein_interface_design::filters::BoltzmannFilter , protocols::seeded_abinitio::GrowPeptides , protocols::seeded_abinitio::SeedFoldTree
• AnchorSugarScreener() : protocols::stepwise::screener::AnchorSugarScreener
• AND : protocols::denovo_design::components::CompoundPerturber
• and_extrachi_cutoff() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• and_linmem_ig() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• and_max_rotbump_energy() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• and_with() : protocols::match::Bool3DGrid , protocols::match::BumpGrid
• AndJumpSelector() : core::select::jump_selector::AndJumpSelector
• AndResidueSelector() : core::select::residue_selector::AndResidueSelector
• AndSelector() : protocols::pose_selectors::AndSelector
• ang123_ : protocols::toolbox::match_enzdes_util::LigandConformer
• ang_cst_ : core::scoring::constraints::BackboneStubConstraint
• ang_D1D2D3_ : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• ang_max_ : protocols::simple_filters::MPSpanAngleFilter
• ang_min_ : protocols::simple_filters::MPSpanAngleFilter
• ang_significance_threshold_ : protocols::rna::movers::RNAIdealizeMover
• ang_U1D2 : protocols::toolbox::match_enzdes_util::SingleConstraint
• ang_U1D2_samples() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• ang_U1D2_samples_ : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• ang_U2D1 : protocols::toolbox::match_enzdes_util::SingleConstraint
• ang_U2D1_samples() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• ang_U2D1_samples_ : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• angle() : core::pack::dunbrack::cenrot::CentroidRotamerSampleData , core::scoring::constraints::AngleConstraint , core::scoring::packstat::trace , protocols::cartesian::MD_Angle , protocols::cartesian::MD_HarmonicDihedral , protocols::constraint_generator::HydrogenBondingAtom , protocols::fold_from_loops::filters::ConstraintFulfilmentFilter , protocols::fold_from_loops::selectors::ConstraintResidueSelector , protocols::ligand_docking::Transform_info , protocols::ligand_docking::TransformEnsemble_info , protocols::loophash::BackboneDB , protocols::make_rot_lib::CentroidRotNum , protocols::matdes::GetRBDOFValues , protocols::simple_moves::SetTorsion , protocols::simple_moves::sidechain_moves::SetChiMover
• angle1_ : protocols::cyclic_peptide::PeptideCyclizeMover
• angle1_func() : protocols::constraint_generator::HydrogenBondConstraintGenerator
• angle1_func_ : protocols::constraint_generator::HydrogenBondConstraintGenerator , protocols::cyclic_peptide::PeptideCyclizeMover
• angle2_ : protocols::cyclic_peptide::PeptideCyclizeMover
• angle2_func() : protocols::constraint_generator::HydrogenBondConstraintGenerator
• angle2_func_ : protocols::constraint_generator::HydrogenBondConstraintGenerator , protocols::cyclic_peptide::PeptideCyclizeMover
• angle_ : core::pack::dunbrack::cenrot::CentroidRotamerSampleData , protocols::constraint_generator::HydrogenBondingAtom , protocols::fold_from_loops::filters::ConstraintFulfilmentFilter , protocols::fold_from_loops::selectors::ConstraintResidueSelector , protocols::matdes::GetRBDOFValues , protocols::membrane::FlipMover , protocols::membrane::TiltMover , protocols::membrane_benchmark::PeptideOrientationMover , protocols::rigid::RollMover , protocols::simple_moves::SetTorsion , protocols::simple_moves::sidechain_moves::SetChiMover
• angle_assigned_ : protocols::cyclic_peptide::PeptideCyclizeMover
• angle_atom_ : core::chemical::AddConnect , core::scoring::methods::GoapRsdType
• angle_constraint_energy() : core::scoring::constraints::ConstraintEdge
• angle_constraint_energy_ : core::scoring::constraints::ConstraintEdge
• angle_constraints_ : protocols::metal_interface::AddZincSiteConstraints
• angle_conv() : protocols::stepwise::sampler::screener::RNA_TorsionScreener
• angle_cutoff_ : protocols::features::ModelFeatures , protocols::membrane::MPLipidAccessibility
• ANGLE_CUTOFF_HIGH : core::scoring::methods::LK_SigmoidalFunc
• ANGLE_CUTOFF_LOW : core::scoring::methods::LK_SigmoidalFunc
• ANGLE_DELTA : core::pack::dunbrack::SingleResidueDunbrackLibrary
• angle_deltas_ : protocols::matdes::SymDofMover
• angle_diff() : protocols::make_rot_lib::MakeRotLibMover
• angle_disp() : protocols::backrub::BackrubSegment
• angle_disp_ : protocols::backrub::BackrubSegment
• angle_exponent() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphOptions , core::select::util::SelectResiduesByLayer
• angle_exponent_ : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphOptions , core::select::util::SelectResiduesByLayer
• angle_length_relax_rounds() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• angle_length_relax_rounds_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• angle_lookup_ : core::scoring::GenericBondedPotential
• angle_magnitude() : protocols::rigid::RigidBodyDeterministicSpinMover
• angle_magnitude_ : protocols::rigid::RigidBodyDeterministicSpinMover
• angle_max() : protocols::simple_moves::BackboneMover
• angle_max_ : protocols::membrane::MPQuickRelaxMover , protocols::recces::sampler::MC_OneTorsion , protocols::recces::sampler::rna::MC_RNA_KIC_Sampler , protocols::relax::RangeRelaxMover , protocols::simple_filters::HelixHelixAngleFilter , protocols::simple_moves::BackboneMover , protocols::simple_moves::bb_sampler::SmallBBSampler , protocols::surface_docking::FullatomRelaxMover
• angle_min_ : protocols::recces::sampler::MC_OneTorsion , protocols::recces::sampler::rna::MC_RNA_KIC_Sampler , protocols::simple_filters::HelixHelixAngleFilter
• angle_or_dist_ : protocols::simple_filters::HelixHelixAngleFilter
• angle_or_score_ : protocols::simple_filters::MPSpanAngleFilter
• angle_parameter : core::scoring::methods::ResidueCartBondedParameters
• angle_parameters() : core::scoring::methods::ResidueCartBondedParameters
• angle_params_ : core::scoring::methods::ResidueCartBondedParameters
• angle_pot_ : core::scoring::GenericBondedPotential
• angle_range_ : protocols::recces::sampler::rna::MC_RNA_Suite
• angle_range_bb() : protocols::recces::options::RECCES_Options
• angle_range_bb_ : protocols::recces::options::RECCES_Options , protocols::recces::scratch::ThermalMinimizer , protocols::recces::scratch::ThermalSamplingMover
• angle_range_chi() : protocols::recces::options::RECCES_Options
• angle_range_chi_ : protocols::recces::options::RECCES_Options , protocols::recces::scratch::ThermalMinimizer , protocols::recces::scratch::ThermalSamplingMover
• angle_range_free_bb() : protocols::recces::options::RECCES_Options
• angle_range_free_bb_ : protocols::recces::options::RECCES_Options
• angle_range_free_chi() : protocols::recces::options::RECCES_Options
• angle_range_free_chi_ : protocols::recces::options::RECCES_Options
• angle_range_loop_bb_ : protocols::recces::scratch::ThermalSamplingMover
• angle_relax_rounds() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• angle_relax_rounds_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• angle_resl_ : core::scoring::motif::MotifHash , core::scoring::motif::XformScore , core::scoring::motif::XfragSet
• angle_sampling_ : protocols::hotspot_hashing::LSMSearchPattern
• angle_sd1_ : core::scoring::rna::RNA_SugarCloseEnergy
• angle_sd2_ : core::scoring::rna::RNA_SugarCloseEnergy
• angle_sd_ : core::scoring::rna::RNA_SugarCloseEnergy , protocols::constraint_generator::HydrogenBondConstraintGenerator
• angle_shift_factor() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphOptions , core::select::util::SelectResiduesByLayer
• angle_shift_factor_ : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphOptions , core::select::util::SelectResiduesByLayer
• angle_sigma2_ : protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential
• angle_steps_ : protocols::matdes::SymDofMover , protocols::matdes::SymDofMoverSampler
• angle_table_ : core::scoring::methods::GoapEnergy
• angle_thresh_ : protocols::simple_filters::SymmetricMotifFilter
• angle_threshold() : protocols::cyclic_peptide::CycpepSymmetryFilter , protocols::cyclic_peptide::SymmetricCycpepAlign
• angle_threshold_ : protocols::cyclic_peptide::CycpepSymmetryFilter , protocols::cyclic_peptide::SymmetricCycpepAlign
• angle_tolerance_ : protocols::fldsgn::SheetConstraintGenerator , protocols::fold_from_loops::constraint_generator::AutomaticSheetConstraintGenerator
• angle_weight() : protocols::fold_from_loops::NubInitioMover
• angle_with_x_axis_proj_y() : protocols::symmetry::DetectSymmetry
• angle_with_y_axis_proj_x() : protocols::symmetry::DetectSymmetry
• angle_with_y_axis_proj_z() : protocols::symmetry::DetectSymmetry
• angle_with_z_axis_proj_y() : protocols::symmetry::DetectSymmetry
• angle_wt_ : protocols::simple_filters::SymmetricMotifFilter
• angle_wts_ : protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential
• angleA_ : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• angleB_ : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• AngleConstraint() : core::scoring::constraints::AngleConstraint
• AngleConstraintCreator() : core::scoring::constraints::AngleConstraintCreator
• AngleInfo : core::fragment::BBTorsionAndAnglesSRFD
• anglelist : protocols::cartesian::MolecularDynamics
• AngleMap : protocols::sparta::Sparta::SpartaLib
• angles : core::scoring::carbohydrates::CHIDihedralSamplingData , core::scoring::carbohydrates::OmegaPreferenceSamplingData , protocols::loophash::BBData
• angles_ : core::fragment::BBTorsionAndAnglesSRFD , core::scoring::sasa::LeGrandSasa , protocols::matdes::SymDofMover , protocols::matdes::SymDofMoverSampler , protocols::pockets::PocketConstraint
• angles_range_max_ : protocols::matdes::SymDofMover , protocols::matdes::SymDofMoverSampler
• angles_range_min_ : protocols::matdes::SymDofMover , protocols::matdes::SymDofMoverSampler
• AngleToVector() : protocols::simple_filters::AngleToVector
• angsplines_ : core::scoring::CenRotEnvPairPotential
• ANGSTROM_LIMIT_ : core::scoring::epr_deer::DEERIO
• angstroms : protocols::ligand_docking::Translate_info
• angstroms_ : protocols::ligand_docking::TetherLigand
• angth : protocols::kinmatch::KRSQuery
• AngularMomentumQuantumNumber : core::chemical::ElectronConfiguration
• AngularMomentumQuantumNumber_strings() : core::chemical::ElectronConfiguration
• animate() : core::conformation::ResidueKinWriter , protocols::match::output::ResidueKinemageWriter , protocols::match::output::WriteUpstreamHitKinemage
• animate_ : core::conformation::ResidueKinWriter , protocols::match::output::ResidueKinemageWriter , protocols::match::output::WriteUpstreamHitKinemage
• aniso_ : protocols::electron_density::VoxelSpacingRefinementMover
• ann : protocols::environment::EnvClaimBroker::BrokerResult
• ANN() : protocols::sparta::ANN
• ann_ : protocols::environment::EnvClaimBroker , protocols::environment::Environment
• ANN_CS_OUTPUT_FULL : protocols::sparta::Sparta::SpartaLib
• ANN_IN_MTX : protocols::sparta::ANN , protocols::sparta::Sparta::SpartaLib
• ANN_IN_MTX_LEVEL1 : protocols::sparta::ANN
• ANN_IN_MTX_LEVEL2 : protocols::sparta::ANN
• ANN_Matrix : protocols::sparta::ANN
• ANN_OUT_MTX_LEVEL1 : protocols::sparta::ANN
• ANN_OUT_MTX_LEVEL2 : protocols::sparta::ANN
• ANN_Vector : protocols::sparta::ANN
• anneal_missing() : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• anneal_step_ : protocols::monte_carlo::GenericSimulatedAnnealer
• AnnealableGraphBase() : core::pack::interaction_graph::AnnealableGraphBase
• AnnealableGraphBaseCOP : protocols::minimization_packing::PackRotamersMover
• AnnealableGraphBaseOP : core::pack::annealer::FixbbCoupledRotamerSimAnnealer , core::pack::annealer::FixbbLinkingRotamerSimAnnealer , core::pack::annealer::FixbbPwatSimAnnealer , core::pack::annealer::FixbbSimAnnealer , core::pack::annealer::SequenceSymmetricAnnealer , core::pack::annealer::SmartFixbbSimAnnealer , protocols::minimization_packing::PackRotamersMover
• annealer_file() : core::pack::annealer::DebuggingAnnealer
• annealing_ : protocols::rna::setup::RNA_CSA_JobDistributor
• annotate() : protocols::environment::claims::EnvClaim
• annotate_fold_tree() : protocols::environment::EnvClaimBroker
• annotated_name() : core::conformation::Residue
• annotated_seq_from_IUPAC_map_ : core::io::NomenclatureManager
• annotated_seq_from_modomics_map_ : core::io::NomenclatureManager
• annotated_sequence() : core::conformation::Conformation , core::pose::Pose , protocols::topology_broker::claims::SequenceClaim
• annotated_sequence_ : protocols::topology_broker::claims::SequenceClaim
• annotated_sequence_from_IUPAC_sequence() : core::io::NomenclatureManager
• annotated_sequence_from_modomics_oneletter_sequence() : core::io::NomenclatureManager
• annotated_sequence_used_for_atom_id_maps_ : protocols::stepwise::modeler::align::StepWisePoseAligner
• AnnotatedFragData() : core::fragment::AnnotatedFragData
• AnnotatedSequence() : core::sequence::AnnotatedSequence
• AnnotatingSelectors : protocols::environment::claims::EnvClaim
• annotations() : core::io::rna::RDAT , protocols::environment::Environment , protocols::environment::ProtectedConformation
• annotations_ : core::io::rna::RDAT , protocols::environment::ProtectedConformation
• anomer() : core::chemical::carbohydrates::CarbohydrateInfo
• anomer_ : core::chemical::carbohydrates::CarbohydrateInfo
• anomeric : core::chemical::carbohydrates::RootData
• anomeric_carbon() : core::chemical::carbohydrates::CarbohydrateInfo
• anomeric_carbon_ : core::chemical::carbohydrates::CarbohydrateInfo
• anomeric_carbon_index() : core::chemical::carbohydrates::CarbohydrateInfo
• anomeric_carbon_index_ : core::chemical::carbohydrates::CarbohydrateInfo
• anomeric_carbon_name() : core::chemical::carbohydrates::CarbohydrateInfo
• anomeric_carbon_name_ : core::chemical::carbohydrates::CarbohydrateInfo
• anomeric_position_from_code() : core::chemical::carbohydrates::CarbohydrateInfoManager
• anomeric_pseudotorsion() : core::chemical::carbohydrates::CarbohydrateInfo
• anomeric_pseudotorsion_ : core::chemical::carbohydrates::CarbohydrateInfo
• anomeric_sidechain_index() : core::chemical::carbohydrates::CarbohydrateInfo
• anomeric_sidechain_index_ : core::chemical::carbohydrates::CarbohydrateInfo
• ANTI : core::scoring::dssp::Pairing
• anti_ : protocols::abinitio::AlternativePairings
• Antibody() : protocols::antibody_legacy::Antibody
• antibody_build_ : protocols::antibody_legacy::CDRH3Modeler
• antibody_DB() : protocols::splice::SpliceInAntibody , protocols::splice::SpliceOutAntibody
• antibody_DB_ : protocols::splice::SpliceInAntibody , protocols::splice::SpliceOutAntibody
• antibody_in_ : protocols::antibody_legacy::AntibodyModeler , protocols::antibody_legacy::CDRH3Modeler
• antibody_info_ : protocols::antibody::snugdock::SnugDock , protocols::antibody::snugdock::SnugDockProtocol
• antibody_modeling_insert_ter() : protocols::antibody_legacy::CDRH3Modeler
• antibody_refine_ : protocols::antibody_legacy::CDRH3Modeler
• antibody_region_enum_to_string() : protocols::antibody::AntibodyEnumManager
• antibody_region_string_to_enum() : protocols::antibody::AntibodyEnumManager
• antibody_region_to_enum_ : protocols::antibody::AntibodyEnumManager
• antibody_region_to_string_ : protocols::antibody::AntibodyEnumManager
• AntibodyCDRGrafter() : protocols::antibody::AntibodyCDRGrafter
• AntibodyDatabaseManager() : protocols::antibody::AntibodyDatabaseManager
• AntibodyDesignEnumManager() : protocols::antibody::design::AntibodyDesignEnumManager
• AntibodyDesignMover() : protocols::antibody::design::AntibodyDesignMover
• AntibodyEnumManager() : protocols::antibody::AntibodyEnumManager
• AntibodyFeatures() : protocols::antibody::AntibodyFeatures
• AntibodyInfo() : protocols::antibody::AntibodyInfo
• AntibodyModeler() : protocols::antibody_legacy::AntibodyModeler
• AntibodyModelerProtocol() : protocols::antibody::AntibodyModelerProtocol
• AntibodyNumberingConverterMover() : protocols::antibody::AntibodyNumberingConverterMover
• AntibodyNumberingParser() : protocols::antibody::AntibodyNumberingParser
• AntibodyRegionSelector() : protocols::antibody::residue_selector::AntibodyRegionSelector
• AntibodySeqDesignTFCreator() : protocols::antibody::design::AntibodySeqDesignTFCreator
• antigen_chains_ : protocols::antibody::constraints::ParatopeSiteConstraintMover
• antigen_present() : protocols::antibody::AntibodyInfo
• antipar_ : core::scoring::dssp::StrandPairing
• antiparallel() : core::scoring::dssp::StrandPairing , protocols::abinitio::AlternativePairings
• antiparallel_weight_ : core::scoring::SecondaryStructureWeights
• any() : core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::HBondBonusOptions
• ANY_AA__TGT_ATOM : protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator
• any_active_enmeths() : core::scoring::MinimizationEdge
• any_exposed_dots() : protocols::vardist_solaccess::VarSolDRotamerDots
• any_intrares_energies() : core::scoring::ScoreFunction
• any_intrares_energies_ : core::scoring::ScoreFunction
• any_lr_residue_pair_energy() : core::scoring::ScoreFunction
• any_neighbors_for_residue() : core::scoring::constraints::CstEnergyContainer , core::scoring::DenseEnergyContainer , core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer , core::scoring::LREnergyContainer , core::scoring::OneToAllEnergyContainer , core::scoring::PolymerBondedEnergyContainer
• any_unassigned() : core::pack::scmin::SidechainStateAssignment
• any_upper_neighbors_for_residue() : core::scoring::constraints::CstEnergyContainer , core::scoring::DenseEnergyContainer , core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer , core::scoring::LREnergyContainer , core::scoring::OneToAllEnergyContainer , core::scoring::PolymerBondedEnergyContainer
• any_vertex_state_unassigned() : core::pack::interaction_graph::AnnealableGraphBase , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::MultiplexedAnnealableGraph , core::pack::interaction_graph::ResidueArrayAnnealingEvaluator
• AnyResFilter() : core::pack::task::operation::AnyResFilter
• AObondedatoms_ : core::chemical::orbitals::AssignOrbitals
• AOD_orb_orb_splines_ : core::scoring::orbitals::OrbitalsLookup
• AOdist_ : core::chemical::orbitals::AssignOrbitals
• AOH_Haro_scOrbH_splines_ : core::scoring::orbitals::OrbitalsLookup
• AOH_Hpol_bbOrbH_splines_ : core::scoring::orbitals::OrbitalsLookup
• AOH_Hpol_scOrbH_splines_ : core::scoring::orbitals::OrbitalsLookup
• AOhybridization_ : core::chemical::orbitals::AssignOrbitals
• APBS_CONFIG_EXT : core::scoring::PoissonBoltzmannPotential , protocols::pb_potential::SetupPoissonBoltzmannPotential
• APBS_DX_EXT : core::scoring::PoissonBoltzmannPotential , protocols::pb_potential::SetupPoissonBoltzmannPotential
• apbs_path_ : core::scoring::PoissonBoltzmannPotential
• APBS_PQR_EXT : core::scoring::PoissonBoltzmannPotential , protocols::pb_potential::SetupPoissonBoltzmannPotential
• APBSConfig() : core::scoring::APBSConfig
• APBSResult() : core::scoring::APBSResult
• APBSWrapper() : core::scoring::APBSWrapper
• APCluster() : protocols::cluster::APCluster
• apfc_list() : core::scoring::custom_pair_distance::RespairInteractions
• apfc_list_ : core::scoring::custom_pair_distance::RespairInteractions
• apol_calcenergy : core::scoring::APBSConfig::I_PARAM
• apol_calcforce : core::scoring::APBSConfig::I_PARAM
• apolar_ : core::pack::task::operation::ResidueTypeFilter
• apolar_res_set_ : protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter
• APolarHydrogenFilter() : core::chemical::APolarHydrogenFilter
• append() : core::scoring::epr_deer::DEERDataCache , core::scoring::epr_deer::DEERDistanceDistribution , core::scoring::lkball::LKB_ResiduesInfo , protocols::network::NetworkQueue::WorkUnit , protocols::simple_moves::LoadPDBMover
• append_ : protocols::simple_moves::LoadPDBMover
• append_aa_composition_setup_files() : core::scoring::methods::EnergyMethodOptions
• append_Aform_residue() : core::import_pose::RNA_HelixAssembler
• append_atom() : core::io::ResidueInformation , core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• append_atom_info_to_sfr() : core::io::pose_to_sfr::PoseToStructFileRepConverter
• append_atoms() : core::io::ResidueInformation
• append_attributes() : protocols::rotamer_recovery::RRComparerAutomorphicRMSDCreator , protocols::rotamer_recovery::RRComparerChiDiff , protocols::rotamer_recovery::RRComparerChiDiffCreator , protocols::rotamer_recovery::RRComparerCreator , protocols::rotamer_recovery::RRComparerElecDensDiffCreator , protocols::rotamer_recovery::RRComparerRotBinsCreator , protocols::rotamer_recovery::RRProtocolCreator , protocols::rotamer_recovery::RRProtocolMinPackCreator , protocols::rotamer_recovery::RRProtocolMoverCreator , protocols::rotamer_recovery::RRProtocolPackRotamersCreator , protocols::rotamer_recovery::RRProtocolReferenceStructure , protocols::rotamer_recovery::RRProtocolReferenceStructureCreator , protocols::rotamer_recovery::RRProtocolRelaxCreator , protocols::rotamer_recovery::RRProtocolRotamerTrialsCreator , protocols::rotamer_recovery::RRProtocolRTMinCreator , protocols::rotamer_recovery::RRReporterCreator , protocols::rotamer_recovery::RRReporterHumanCreator , protocols::rotamer_recovery::RRReporterSimpleCreator , protocols::rotamer_recovery::RRReporterSQLiteCreator
• append_attributes_for_tag_parsing() : core::io::silent::SilentFileOptions
• append_by_bond() : protocols::cyclic_peptide::PeptideStubMover
• append_by_jump() : protocols::cyclic_peptide::PeptideStubMover
• append_char() : core::sequence::Sequence
• append_choices() : protocols::genetic_algorithm::PositionSpecificRandomizer
• append_combine_history() : protocols::simple_moves::CombinePoseMover
• append_common_tag_subelements() : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::standard::StandardJobQueen , protocols::multistage_rosetta_scripts::MRSJobQueen
• append_comparer_attributes() : protocols::rotamer_recovery::RotamerRecoveryFactory
• append_downstream_atom_to_active_site_required_list() : protocols::match::MatcherTask
• append_fragment() : protocols::frags::SingleResidueTorsionFragmentLibrary
• append_gap() : core::sequence::Sequence
• append_hairpin() : core::scoring::Hairpins
• append_hbond() : core::scoring::hbonds::HBondSet
• append_index() : core::select::residue_selector::ResidueIndexSelector
• append_input_source() : protocols::jd3::InnerLarvalJob
• append_job_results_that_should_be_discarded() : protocols::jd3::dag_node_managers::NodeManager
• append_job_tag_subelements() : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::standard::StandardJobQueen , protocols::multistage_rosetta_scripts::MRSJobQueen
• append_ligand_docking_scores() : protocols::ligand_docking::LigandDockProtocol
• append_ligands_subelement() : protocols::sewing::hashing::AlignmentFileGeneratorMover
• append_metal_vsites() : protocols::ligand_docking::ga_ligand_dock::ConstraintInfo
• append_mhc_epitope_setup_files() : core::scoring::methods::EnergyMethodOptions
• append_model() : protocols::legacy_sewing::Assembly , protocols::legacy_sewing::ContinuousAssembly , protocols::legacy_sewing::DisembodiedAssembly
• append_movie_frame() : protocols::legacy_sewing::LegacyAssemblyMover
• append_n_residues_ : protocols::ncbb::oop::OopCreatorMover
• append_netcharge_setup_files() : core::scoring::methods::EnergyMethodOptions
• append_op() : core::pack::task::operation::OperateOnResidueSubset
• append_other_pose() : protocols::stepwise::monte_carlo::mover::AddMover
• append_outputter() : protocols::jd3::output::MultipleOutputter
• append_peptide() : core::environment::FoldTreeSketch
• append_polymer_residue_after_seqpos() : core::conformation::Conformation , core::conformation::symmetry::SymmetricConformation , core::pose::Pose , protocols::environment::ProtectedConformation
• append_pose_by_jump() : core::pose::Pose
• append_protocol_attributes() : protocols::rotamer_recovery::RotamerRecoveryFactory
• append_reporter_attributes() : protocols::rotamer_recovery::RotamerRecoveryFactory
• append_res() : core::pose::PDBInfo
• append_residue() : core::conformation::Conformation , core::environment::FoldTreeSketch , core::fragment::picking_old::vall::VallSection , core::kinematics::FoldTree , protocols::stepwise::monte_carlo::mover::AddMover
• append_residue_by_atoms() : core::pose::Pose
• append_residue_by_bond() : core::conformation::Conformation , core::pose::Pose
• append_residue_by_chemical_bond() : core::kinematics::FoldTree
• append_residue_by_jump() : core::conformation::Conformation , core::conformation::symmetry::MirrorSymmetricConformation , core::conformation::symmetry::SymmetricConformation , core::pose::Pose , protocols::environment::ProtectedConformation
• append_residue_info_to_sfr() : core::io::pose_to_sfr::PoseToStructFileRepConverter
• append_residue_to_sfr() : core::io::pose_to_sfr::PoseToStructFileRepConverter
• append_residues_cterminally() : protocols::seeded_abinitio::GrowPeptides
• append_residues_nterminally() : protocols::seeded_abinitio::GrowPeptides
• append_rotamer_operation() : core::pack::task::PackerTask , core::pack::task::PackerTask_ , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• append_rotamerset_operation() : core::pack::task::PackerTask , core::pack::task::PackerTask_ , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• append_rotamersets_operation() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• append_schema_attributes() : core::import_pose::ImportPoseOptions , core::io::StructFileReaderOptions , core::io::StructFileRepOptions , core::scoring::etable::EtableOptions , core::scoring::hbonds::HBondOptions
• append_secondary_outputter() : protocols::jd3::output::StandardResultOutputter
• append_segments() : protocols::legacy_sewing::Assembly
• append_seq() : core::environment::SequenceAnnotation
• append_specification() : protocols::jd3::output::MultipleOutputSpecification
• append_to_additional_string_output() : core::io::StructFileRep
• append_to_edge_map() : protocols::sewing::hashing::EdgeMapGenerator
• append_to_fragment_store() : protocols::indexed_structure_store::BinaryFragmentStoreBackend , protocols::indexed_structure_store::FragmentStoreProvider
• append_to_network_vector() : protocols::hbnet::HBNet
• append_to_tag() : protocols::stepwise::screener::TagDefinition
• append_trace_data() : core::scoring::epr_deer::DEERDecayData
• append_trace_data_and_calculate() : core::scoring::epr_deer::DEERDecayData
• append_two_body_energy_computations_to_work_vector() : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::symmetry::SymmetricRotamerSets
• append_twobody_energy() : protocols::hbnet::NetworkState
• append_unitbox() : protocols::simple_filters::ResidueDepthCalculator
• append_upstream_resiue_as_defining_active_site() : protocols::match::MatcherTask
• append_virtual_anchor() : protocols::rna::denovo::RNA_DeNovoPoseInitializer
• AppendAssemblyMover() : protocols::sewing::movers::AppendAssemblyMover
• AppendMainchainAtom() : core::chemical::AppendMainchainAtom
• AppendResidueRotamerSet() : core::pack::task::operation::AppendResidueRotamerSet
• AppendRotamer() : core::pack::task::operation::AppendRotamer
• AppendRotamerSet() : core::pack::task::operation::AppendRotamerSet
• applicable() : protocols::evaluation::PoseEvaluator , protocols::evaluation::SingleValuePoseEvaluator< T > , protocols::simple_filters::CamShiftEvaluator , protocols::simple_filters::ExternalEvaluator , protocols::simple_filters::PalesEvaluator , protocols::simple_filters::ScoreEvaluator , protocols::sparta::ChemicalShiftEvaluator
• applied_fullatom_pert_ : protocols::ub_e2c::ubi_e2c_modeler
• applies_to() : core::chemical::Metapatch , core::chemical::Patch , core::chemical::PatchCase
• applies_to_placeholder() : core::chemical::ChiralFlipNaming , core::chemical::PatchOperation , core::chemical::Set_AA , core::chemical::SetIO_String
• apply() : core::chemical::AddAtom , core::chemical::AddAtomAlias , core::chemical::AddBond , core::chemical::AddBondType , core::chemical::AddChi , core::chemical::AddChiRotamer , core::chemical::AddConnect , core::chemical::AddConnectAndTrackingVirt , core::chemical::AddConnectDeleteChildProton , core::chemical::AddProperty , core::chemical::AddProtonChi , core::chemical::AppendMainchainAtom , core::chemical::ChangeAncestory , core::chemical::ChangeBondType , core::chemical::ChiralFlipAtoms , core::chemical::ChiralFlipNaming , core::chemical::ClearChiRotamers , core::chemical::ConnectSulfurAndMakeVirtualProton , core::chemical::DeleteActCoordAtom , core::chemical::DeleteAtom , core::chemical::DeleteChildProton , core::chemical::DeleteMetalbindingAtom , core::chemical::DeleteProperty , core::chemical::DeleteTerminalChi , core::chemical::DeleteVariantType , core::chemical::NCAARotLibBBTorsions , core::chemical::NCAARotLibNumRotamerBins , core::chemical::NCAARotLibPath , core::chemical::Patch , core::chemical::PatchCase , core::chemical::PatchOperation , core::chemical::PrependMainchainAtom , core::chemical::RamaPreproFilename , core::chemical::RamaPreproResname , core::chemical::RedefineChi , core::chemical::RemoveRotamerSpecifications , core::chemical::RenameAtom , core::chemical::ReplaceMainchainAtom , core::chemical::ReplaceProtonWithBromine , core::chemical::ReplaceProtonWithChlorine , core::chemical::ReplaceProtonWithEthyl , core::chemical::ReplaceProtonWithFluorine , core::chemical::ReplaceProtonWithHydroxyl , core::chemical::ReplaceProtonWithIodine , core::chemical::ReplaceProtonWithMethoxy , core::chemical::ReplaceProtonWithMethyl , core::chemical::ReplaceProtonWithTrifluoromethyl , core::chemical::ResetBondLength , core::chemical::Set_AA , core::chemical::SetAllAtomsRepulsive , core::chemical::SetAtomicCharge , core::chemical::SetAtomType , core::chemical::SetBackboneHeavyatom , core::chemical::SetDisulfideAtomName , core::chemical::SetFormalCharge , core::chemical::SetICoor , core::chemical::SetInterchangeabilityGroup_String , core::chemical::SetIO_String , core::chemical::SetMMAtomType , core::chemical::SetNbrAtom , core::chemical::SetNbrRadius , core::chemical::SetNetFormalCharge , core::chemical::SetOrientAtom , core::chemical::SetPolymerConnectAtom , core::chemical::SetVirtualShadow , core::chemical::VirtualizeAll , core::chemical::VirtualizeSidechain , core::fragment::BBTorsionAndAnglesSRFD , core::fragment::BBTorsionSRFD , core::fragment::DownJumpSRFD , core::fragment::FragData , core::fragment::FragID , core::fragment::Frame , core::fragment::IndependentBBTorsionSRFD , core::fragment::SecstructSRFD , core::fragment::SingleResidueFragData , core::fragment::UpJumpSRFD , core::import_pose::RNA_HelixAssembler , core::pack::task::operation::AddBehaviorRLT , core::pack::task::operation::AppendResidueRotamerSet , core::pack::task::operation::AppendRotamer , core::pack::task::operation::AppendRotamerSet , core::pack::task::operation::ClashBasedRepackShell , core::pack::task::operation::DesignRestrictions , core::pack::task::operation::DisallowIfNonnative , core::pack::task::operation::DisallowIfNonnativeRLT , core::pack::task::operation::EnableMultiCoolAnnealer , core::pack::task::operation::EnableSmartAnnealer , core::pack::task::operation::ExtraChiCutoff , core::pack::task::operation::ExtraChiCutoffRLT , core::pack::task::operation::ExtraRotamers , core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::operation::ExtraRotamersGenericRLT , core::pack::task::operation::FillAUTOTaskOperation , core::pack::task::operation::IncludeCurrent , core::pack::task::operation::IncludeCurrentRLT , core::pack::task::operation::InitializeExtraRotsFromCommandline , core::pack::task::operation::InitializeFromCommandline , core::pack::task::operation::InitializeFromOptionCollection , core::pack::task::operation::KeepSequenceSymmetry , core::pack::task::operation::NoRepackDisulfides , core::pack::task::operation::OperateOnCertainResidues , core::pack::task::operation::OperateOnResidueSubset , core::pack::task::operation::OptCysHG , core::pack::task::operation::OptH , core::pack::task::operation::PreserveCBeta , core::pack::task::operation::PreserveCBetaRLT , core::pack::task::operation::PreventRepacking , core::pack::task::operation::PreventRepackingRLT , core::pack::task::operation::ProhibitResidueProperties , core::pack::task::operation::ProhibitSpecifiedBaseResidueTypes , core::pack::task::operation::ReadResfile , core::pack::task::operation::ReadResfileAndObeyLengthEvents , core::pack::task::operation::ReplicateTask , core::pack::task::operation::ResLvlTaskOperation , core::pack::task::operation::RestrictAbsentCanonicalAAS , core::pack::task::operation::RestrictAbsentCanonicalAASExceptNativeRLT , core::pack::task::operation::RestrictAbsentCanonicalAASRLT , core::pack::task::operation::RestrictInteractionGraphThreadsOperation , core::pack::task::operation::RestrictResidueToRepacking , core::pack::task::operation::RestrictToRepacking , core::pack::task::operation::RestrictToRepackingRLT , core::pack::task::operation::RestrictToResidueProperties , core::pack::task::operation::RestrictToSpecifiedBaseResidueTypes , core::pack::task::operation::RestrictYSDesign , core::pack::task::operation::RotamerExplosion , core::pack::task::operation::SetRotamerCouplings , core::pack::task::operation::SetRotamerLinks , core::pack::task::operation::TaskOperation , core::pack::task::operation::UseMultiCoolAnnealer , core::pack::task::residue_selector::ClashBasedShellSelector , core::pose::copydofs::CopyDofs , core::pose::rna::RNA_IdealCoord , core::scoring::TMscore , core::scoring::TMscoreStore , core::select::jump_selector::AndJumpSelector , core::select::jump_selector::InterchainJumpSelector , core::select::jump_selector::JumpIndexSelector , core::select::jump_selector::JumpSelector , core::select::jump_selector::NotJumpSelector , core::select::jump_selector::OrJumpSelector , core::select::residue_selector::AndResidueSelector , core::select::residue_selector::AsymmetricUnitSelector , core::select::residue_selector::BinSelector , core::select::residue_selector::BondedResidueSelector , core::select::residue_selector::ChainSelector , core::select::residue_selector::CloseContactResidueSelector , core::select::residue_selector::DensityFitResidueSelector , core::select::residue_selector::FalseResidueSelector , core::select::residue_selector::GlycanLayerSelector , core::select::residue_selector::GlycanPositionSelector , core::select::residue_selector::GlycanResidueSelector , core::select::residue_selector::InterGroupInterfaceByVectorSelector , core::select::residue_selector::JumpDownstreamSelector , core::select::residue_selector::JumpUpstreamSelector , core::select::residue_selector::LayerSelector , core::select::residue_selector::NeighborhoodResidueSelector , core::select::residue_selector::NotResidueSelector , core::select::residue_selector::NumNeighborsSelector , core::select::residue_selector::OrResidueSelector , core::select::residue_selector::PhiSelector , core::select::residue_selector::PrimarySequenceNeighborhoodSelector , core::select::residue_selector::RandomGlycanFoliageSelector , core::select::residue_selector::RandomResidueSelector , core::select::residue_selector::ResidueIndexSelector , core::select::residue_selector::ResidueInMembraneSelector , core::select::residue_selector::ResidueInSequenceMotifSelector , core::select::residue_selector::ResidueNameSelector , core::select::residue_selector::ResiduePDBInfoHasLabelSelector , core::select::residue_selector::ResiduePropertySelector , core::select::residue_selector::ResidueSelector , core::select::residue_selector::ResidueSpanSelector , core::select::residue_selector::ReturnResidueSubsetSelector , core::select::residue_selector::ScoreTermValueBasedSelector , core::select::residue_selector::SecondaryStructureSelector , core::select::residue_selector::SliceResidueSelector , core::select::residue_selector::SSElementSelector , core::select::residue_selector::SymmetricalResidueSelector , core::select::residue_selector::TrueResidueSelector , core::simple_metrics::CompositeRealMetric , core::simple_metrics::CompositeStringMetric , core::simple_metrics::PerResidueRealMetric , core::simple_metrics::PerResidueStringMetric , core::simple_metrics::RealMetric , core::simple_metrics::SimpleMetric , core::simple_metrics::StringMetric , protocols::aa_composition::AddCompositionConstraintMover , protocols::aa_composition::AddHelixSequenceConstraintsMover , protocols::aa_composition::AddMHCEpitopeConstraintMover , protocols::aa_composition::AddNetChargeConstraintMover , protocols::aa_composition::ClearCompositionConstraintsMover , protocols::abinitio::AbrelaxMover , protocols::abinitio::abscript::AbscriptLoopCloserCM , protocols::abinitio::abscript::AbscriptMover , protocols::abinitio::abscript::AbscriptStageMover , protocols::abinitio::abscript::ConstraintPreparer , protocols::abinitio::abscript::FragmentCM , protocols::abinitio::abscript::RigidChunkCM , protocols::abinitio::abscript::StructPerturberCM , protocols::abinitio::ClassicAbinitio , protocols::abinitio::ComputeTotalDistCst , protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::DomainAssembly , protocols::abinitio::FoldConstraints , protocols::abinitio::FragmentSampler , protocols::abinitio::JumpingFoldConstraintsWrapper , protocols::abinitio::KinematicAbinitio , protocols::abinitio::KinematicTaskControl , protocols::abinitio::MembraneAbinitio , protocols::abinitio::PcaEvaluator , protocols::abinitio::Protocol , protocols::abinitio::ResolutionSwitcher , protocols::abinitio::ShowViolation , protocols::abinitio::Stage1Sampler , protocols::analysis::GlycanInfoMover , protocols::analysis::InterfaceAnalyzerMover , protocols::analysis::LoopAnalyzerMover , protocols::analysis::PackStatMover , protocols::analysis::simple_metrics::RunSimpleMetricsMover , protocols::anchored_design::AnchoredDesignMover , protocols::anchored_design::AnchoredPerturbMover , protocols::anchored_design::AnchoredRefineMover , protocols::antibody::AntibodyCDRGrafter , protocols::antibody::AntibodyModelerProtocol , protocols::antibody::AntibodyNumberingConverterMover , protocols::antibody::CDRsMinPackMin , protocols::antibody::CloseOneCDRLoop , protocols::antibody::constraints::CDRDihedralConstraintMover , protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover , protocols::antibody::constraints::ParatopeSiteConstraintMover , protocols::antibody::design::AntibodyDesignMover , protocols::antibody::design::MutateFrameworkForCluster , protocols::antibody::design::ResnumFromStringsWithRangesSelector , protocols::antibody::GraftCDRLoopsProtocol , protocols::antibody::GraftedStemOptimizer , protocols::antibody::GraftOneCDRLoop , protocols::antibody::H3CterInsert , protocols::antibody::H3PerturbCCD , protocols::antibody::H3RefineCCD , protocols::antibody::LHRepulsiveRamp , protocols::antibody::LHRepulsiveRampLegacy , protocols::antibody::LHSnugFitLegacy , protocols::antibody::RefineBetaBarrel , protocols::antibody::residue_selector::AntibodyRegionSelector , protocols::antibody::residue_selector::CDRResidueSelector , protocols::antibody::snugdock::SnugDock , protocols::antibody::snugdock::SnugDockProtocol , protocols::antibody::task_operations::AddCDRProfileSetsOperation , protocols::antibody::task_operations::AddCDRProfilesOperation , protocols::antibody::task_operations::DisableAntibodyRegionOperation , protocols::antibody::task_operations::DisableCDRsOperation , protocols::antibody::task_operations::RestrictToCDRsAndNeighbors , protocols::antibody_legacy::AntibodyModeler , protocols::antibody_legacy::CDRH3Modeler , protocols::antibody_legacy::CloseOneMover , protocols::antibody_legacy::GraftMover , protocols::antibody_legacy::GraftOneMover , protocols::antibody_legacy::LoopRlxMover , protocols::backbone_moves::local_backbone_mover::free_peptide_movers::CircularPermuteFreePeptideMover , protocols::backbone_moves::local_backbone_mover::free_peptide_movers::FreePeptideMover , protocols::backbone_moves::local_backbone_mover::free_peptide_movers::LongAxisRotationFreePeptideMover , protocols::backbone_moves::local_backbone_mover::free_peptide_movers::ShearFreePeptideMover , protocols::backbone_moves::local_backbone_mover::free_peptide_movers::TranslationFreePeptideMover , protocols::backbone_moves::local_backbone_mover::LocalBackboneMover , protocols::backbone_moves::RandomizeBBByRamaPrePro , protocols::backrub::BackrubMover , protocols::backrub::BackrubProtocol , protocols::backrub::BackrubSidechainMover , protocols::calc_taskop_filters::ConservedPosMutationFilter , protocols::calc_taskop_filters::MultipleSigmoids , protocols::calc_taskop_filters::Operator , protocols::calc_taskop_filters::RelativePoseFilter , protocols::calc_taskop_filters::RotamerBoltzmannWeight2 , protocols::calc_taskop_filters::RotamerBoltzmannWeight , protocols::calc_taskop_filters::Sigmoid , protocols::calc_taskop_movers::ConsensusDesignMover , protocols::calc_taskop_movers::CreateSequenceMotifMover , protocols::calc_taskop_movers::DesignRepackMover , protocols::calc_taskop_movers::ForceDisulfidesMover , protocols::canonical_sampling::AsyncMPITemperingBase , protocols::canonical_sampling::CanonicalSamplingMover , protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::mc_convergence_checks::Pool_Evaluator , protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::MetropolisHastingsMover , protocols::canonical_sampling::ParallelTempering , protocols::canonical_sampling::PatchOperation , protocols::canonical_sampling::SidechainMetropolisHastingsMover , protocols::canonical_sampling::SimulatedTempering , protocols::canonical_sampling::TemperatureController , protocols::canonical_sampling::TemperingBase , protocols::canonical_sampling::ThermodynamicObserver , protocols::canonical_sampling::TrajectoryRecorder , protocols::carbohydrates::CreateGlycanSequonMover , protocols::carbohydrates::GlycanSampler , protocols::carbohydrates::GlycanTreeMinMover , protocols::carbohydrates::GlycanTreeModeler , protocols::carbohydrates::IdealizeAnomericHydrogens , protocols::carbohydrates::LinkageConformerMover , protocols::carbohydrates::RingPlaneFlipMover , protocols::carbohydrates::SimpleGlycosylateMover , protocols::carbohydrates::TautomerizeAnomerMover , protocols::chemically_conjugated_docking::UBQ_GTPaseMover , protocols::cluster::AssignToClustersMover , protocols::cluster::GatherPosesMover , protocols::comparative_modeling::Align_RmsdEvaluator , protocols::comparative_modeling::Align_RotamerEvaluator , protocols::comparative_modeling::ExtraThreadingMover , protocols::comparative_modeling::LoopRelaxMover , protocols::comparative_modeling::LoopRelaxThreadingMover , protocols::comparative_modeling::MultiThreadingMover , protocols::comparative_modeling::PartialThreadingMover , protocols::comparative_modeling::RecoverSideChainsMover , protocols::comparative_modeling::StealLigandMover , protocols::comparative_modeling::StealSideChainsMover , protocols::comparative_modeling::ThreadingMover , protocols::constraint_filters::ConstraintScoreCutoffFilter , protocols::constraint_filters::ConstraintScoreFilter , protocols::constraint_filters::SavePoseConstraintToFileFilter , protocols::constraint_filters::ShowConstraintsFilter , protocols::constraint_generator::AddConstraints , protocols::constraint_generator::AtomPairConstraintGenerator , protocols::constraint_generator::ConstraintGenerator , protocols::constraint_generator::CoordinateConstraintGenerator , protocols::constraint_generator::DihedralConstraintGenerator , protocols::constraint_generator::DistanceConstraintGenerator , protocols::constraint_generator::HydrogenBondConstraintGenerator , protocols::constraint_generator::MembraneSpanConstraintGenerator , protocols::constraint_generator::MetalContactsConstraintGenerator , protocols::constraint_generator::RemoveConstraints , protocols::constraint_generator::ResidueTypeConstraintGenerator , protocols::constraint_generator::TerminiConstraintGenerator , protocols::constraint_movers::AddConstraintsToCurrentConformationMover , protocols::constraint_movers::ClearConstraintsMover , protocols::constraint_movers::ConstraintSetMover , protocols::constraint_movers::CstInfoMover , protocols::constraint_movers::ResidueTypeConstraintMover , protocols::constraints_additional::CombinedConstraintEvaluator , protocols::constraints_additional::ConstraintEvaluator , protocols::contact_map::ContactMap , protocols::coupled_moves::CoupledMovesProtocol , protocols::cryst::CrystRMS , protocols::cryst::DockLatticeMover , protocols::cryst::FitBfactorsMover , protocols::cryst::LoadDensityMapMover , protocols::cryst::MakeLatticeMover , protocols::cryst::MakeLayerMover , protocols::cryst::RecomputeDensityMapMover , protocols::cryst::ReportGradientsMover , protocols::cryst::SetCrystWeightMover , protocols::cryst::SetRefinementOptionsMover , protocols::cryst::TagPoseWithRefinementStatsMover , protocols::cryst::UpdateCrystInfo , protocols::cryst::UpdateSolventMover , protocols::cutoutdomain::CutOutDomain , protocols::cyclic_peptide::CreateAngleConstraint , protocols::cyclic_peptide::CreateDistanceConstraint , protocols::cyclic_peptide::CreateTorsionConstraint , protocols::cyclic_peptide::CrosslinkerMover , protocols::cyclic_peptide::CycpepSymmetryFilter , protocols::cyclic_peptide::DeclareBond , protocols::cyclic_peptide::FlipChiralityMover , protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter , protocols::cyclic_peptide::PeptideCyclizeMover , protocols::cyclic_peptide::PeptideInternalHbondsFilter , protocols::cyclic_peptide::PeptideStubMover , protocols::cyclic_peptide::RamaMutationSelector , protocols::cyclic_peptide::SymmetricCycpepAlign , protocols::cyclic_peptide::TryDisulfPermutations , protocols::ddg::ddGMover , protocols::denovo_design::architects::DeNovoArchitect , protocols::denovo_design::components::ExtendedPoseBuilder , protocols::denovo_design::components::NullPoseFolder , protocols::denovo_design::components::PoseFolder , protocols::denovo_design::components::RandomTorsionPoseFolder , protocols::denovo_design::components::RemodelLoopMoverPoseFolder , protocols::denovo_design::components::StructureDataPerturber , protocols::denovo_design::connection::ConnectionArchitect , protocols::denovo_design::constraints::FileConstraintGenerator , protocols::denovo_design::filters::CavityVolumeFilter , protocols::denovo_design::filters::ExposedHydrophobicsFilter , protocols::denovo_design::filters::PreProlineFilter , protocols::denovo_design::filters::SSPredictionFilter , protocols::denovo_design::filters::SSShapeComplementarityFilter , protocols::denovo_design::movers::AddSegmentDataMover , protocols::denovo_design::movers::AlignResiduesMover , protocols::denovo_design::movers::BridgeChainsMover , protocols::denovo_design::movers::BuildDeNovoBackboneMover , protocols::denovo_design::movers::DeclareStructureDataCovalentBondMover , protocols::denovo_design::movers::ExtendChainMover , protocols::denovo_design::movers::FastDesign , protocols::denovo_design::movers::FoldTreeFromFoldGraphMover , protocols::denovo_design::movers::MakeAsymmetricStructureDataMover , protocols::denovo_design::movers::RotateSegmentMover , protocols::denovo_design::movers::SealFoldTreeMover , protocols::denovo_design::movers::SetPoseSecstructFromStructureDataMover , protocols::denovo_design::movers::SetResidueAliasMover , protocols::denovo_design::residue_selectors::NamedSegmentSelector , protocols::denovo_design::residue_selectors::PairedSheetResidueSelector , protocols::denovo_design::task_operations::ConsensusLoopDesignOperation , protocols::design_opt::GreedyOptMutationMover , protocols::dna::DesignProteinBackboneAroundDNA , protocols::dna::DnaInterfaceMinMover , protocols::dna::DnaInterfaceMultiStateDesign , protocols::dna::DnaInterfacePacker , protocols::dna::RestrictDesignToProteinDNAInterface , protocols::dna::SeparateDnaFromNonDna , protocols::dna::WatsonCrickRotamerCouplings , protocols::dna_dock::DNAClashCheckFilter , protocols::dna_dock::PropagateClashCheckFilter , protocols::docking::ConformerSwitchMover , protocols::docking::DockingEnsemblePrepackProtocol , protocols::docking::DockingHighRes , protocols::docking::DockingHighResFilter , protocols::docking::DockingHighResLegacy , protocols::docking::DockingInitialPerturbation , protocols::docking::DockingLowRes , protocols::docking::DockingLowResFilter , protocols::docking::DockingPrepackProtocol , protocols::docking::DockingProtocol , protocols::docking::DockingSlideIntoContact , protocols::docking::DockMCMCycle , protocols::docking::DockMCMProtocol , protocols::docking::DockMinMover , protocols::docking::DockSetupMover , protocols::docking::EllipsoidalRandomizationMover , protocols::docking::FaDockingSlideIntoContact , protocols::docking::InterfaceSidechainMinMover , protocols::docking::membrane::MPDockingMover , protocols::docking::membrane::MPDockingSetupMover , protocols::docking::membrane::MPFindInterfaceMover , protocols::docking::membrane::QuickRelaxPartnersSeparately , protocols::docking::SidechainMinMover , protocols::docking::SlideIntoContact , protocols::docking::stateless::SaneDockingProtocol , protocols::docking::TemperedDocking , protocols::domain_assembly::AddAssemblyConstraints , protocols::domain_assembly::AssembleLinkerMover , protocols::domain_assembly::CombineChainsMover , protocols::domain_assembly::PostDockAssemblyScorer , protocols::electron_density::BfactorFittingMover , protocols::electron_density::DockIntoDensityMover , protocols::electron_density::ReportFSC , protocols::electron_density::ScaleMapIntensities , protocols::electron_density::SetupForDensityScoringMover , protocols::electron_density::VoxelSpacingRefinementMover , protocols::environment::claims::EnvLabelSelector , protocols::environment::CoMTrackerCM , protocols::environment::EnvMover , protocols::environment::ScriptCM , protocols::enzdes::AddLigandMotifRotamers , protocols::enzdes::AddOrRemoveMatchCsts , protocols::enzdes::AddRigidBodyLigandConfs , protocols::enzdes::ApplyRandomStoredRBConf , protocols::enzdes::BackboneSampler , protocols::enzdes::DetectProteinLigandInterface , protocols::enzdes::DiffAtomSasaFilter , protocols::enzdes::DiversifyStoredRBConfs , protocols::enzdes::EnzdesFixBBProtocol , protocols::enzdes::EnzdesFlexBBProtocol , protocols::enzdes::EnzdesScorefileFilter , protocols::enzdes::EnzRepackMinimize , protocols::enzdes::EnzScoreFilter , protocols::enzdes::GenerateStoredRBConfs , protocols::enzdes::LigBurialFilter , protocols::enzdes::LigDSasaFilter , protocols::enzdes::LigInterfaceEnergyFilter , protocols::enzdes::MinimizeStoredRBConfs , protocols::enzdes::ModifyStoredRBConfs , protocols::enzdes::PackRotamersMoverPartGreedy , protocols::enzdes::PredesignPerturbMover , protocols::enzdes::ProteinLigandInterfaceUpweighter , protocols::enzdes::RemoveLigandFilter , protocols::enzdes::RepackLigandSiteWithoutLigandMover , protocols::enzdes::RepackWithoutLigandFilter , protocols::enzdes::ResidueConformerFilter , protocols::enzdes::SecondaryMatchProtocol , protocols::enzdes::SetCatalyticResPackBehavior , protocols::enzdes::UpdateEnzdesHeaderMover , protocols::enzymatic_movers::EnzymaticMover , protocols::evaluation::AlignEvaluator , protocols::evaluation::MetaPoseEvaluator , protocols::evaluation::PoseEvaluator , protocols::evaluation::SingleValuePoseEvaluator< T > , protocols::evaluation::TimeEvaluator , protocols::evolution::AASynthesisFitnessCost , protocols::evolution::AlignmentAAFinder , protocols::evolution::AlignmentGapInserter , protocols::evolution::EvolutionaryDynamicsMover , protocols::evolution::NucleotideMutation , protocols::farnesyl::InstallFarnesylMover , protocols::farnesyl::SampleFarnesylMover , protocols::features::InterfaceDdGMover , protocols::features::ProteinSilentReport , protocols::features::Report , protocols::features::ReportToDB , protocols::features::TrajectoryReportToDB , protocols::fibril::SetupForFibrilMover , protocols::filters::CalculatorFilter , protocols::filters::CombinedFilter , protocols::filters::CompoundFilter , protocols::filters::ContingentFilter , protocols::filters::FalseFilter , protocols::filters::Filter , protocols::filters::FilterCollection , protocols::filters::IfThenFilter , protocols::filters::MoveBeforeFilter , protocols::filters::ReplicateFilter , protocols::filters::StochasticFilter , protocols::filters::TimeFilter , protocols::filters::TrueFilter , protocols::filters::VectorPoseFilter , protocols::fldsgn::BluePrintBDR , protocols::fldsgn::CircularPermutation , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::filters::FragQualFilter , protocols::fldsgn::filters::HelixBendFilter , protocols::fldsgn::filters::HelixKinkFilter , protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::filters::HSSTripletFilter , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::fldsgn::filters::NcontactsFilter , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter , protocols::fldsgn::filters::SecondaryStructureCountFilter , protocols::fldsgn::filters::SecondaryStructureFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter , protocols::fldsgn::filters::SheetTopologyFilter , protocols::fldsgn::filters::StrandCurvatureByLevels , protocols::fldsgn::filters::StrandHelixGeometryFilter , protocols::fldsgn::MatchResiduesMover , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::fldsgn::SheetConstraintGenerator , protocols::flexpack::FlexPacker , protocols::flexpep_docking::FlexPepDockingAbInitio , protocols::flexpep_docking::FlexPepDockingLowRes , protocols::flexpep_docking::FlexPepDockingProtocol , protocols::floppy_tail::FloppyTailMover , protocols::flxbb::CombinedTaskOperation , protocols::flxbb::FilterStructs , protocols::flxbb::FilterStructs_Packstat , protocols::flxbb::FilterStructs_TotalCharge , protocols::flxbb::FlxbbDesign , protocols::flxbb::FlxbbDesignPack , protocols::flxbb::InterlockAroma , protocols::flxbb::LayerDesignOperation , protocols::fold_from_loops::constraint_generator::AutomaticSheetConstraintGenerator , protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator , protocols::fold_from_loops::filters::ConstraintFulfilmentFilter , protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter , protocols::fold_from_loops::filters::ScorePoseSegmentFromResidueSelectorFilter , protocols::fold_from_loops::movers::AlignByResidueSelectorMover , protocols::fold_from_loops::movers::DisplayPoseLabelsMover , protocols::fold_from_loops::movers::LabelPoseFromResidueSelectorMover , protocols::fold_from_loops::movers::MoveMapFactoryToNamedMoveMapMover , protocols::fold_from_loops::movers::NubInitioLoopClosureMover , protocols::fold_from_loops::movers::ReleaseConstraintFromResidueMover , protocols::fold_from_loops::movers::ResidueLabelsToPymolSelectionMover , protocols::fold_from_loops::movers::SavePDBInfoMover , protocols::fold_from_loops::movers::SplitAndMixPoseMover , protocols::fold_from_loops::NubInitioMover , protocols::fold_from_loops::selectors::ConstraintResidueSelector , protocols::fold_from_loops::selectors::CutpointResidueSelector , protocols::fold_from_loops::selectors::ProteinResidueSelector , protocols::fold_from_loops::utils::Nub , protocols::forge::components::BDR , protocols::forge::components::VarLengthBuild , protocols::forge::constraints::InvrotTreeRCG , protocols::forge::constraints::RemoveRemodelCsts , protocols::forge::remodel::RemodelAccumulator , protocols::forge::remodel::RemodelConstraintGenerator , protocols::forge::remodel::RemodelDesignMover , protocols::forge::remodel::RemodelEnzdesCstModule , protocols::forge::remodel::RemodelGlobalFrame , protocols::forge::remodel::RemodelLigandHandler , protocols::forge::remodel::RemodelLoopMover , protocols::forge::remodel::RemodelMover , protocols::forge::remodel::RemodelRotamerLinks , protocols::frag_picker::FragmentScoreFilter , protocols::frag_picker::nonlocal::NonlocalFrags , protocols::frags::TorsionFragmentMover , protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter , protocols::generalized_kinematic_closure::GeneralizedKIC , protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber , protocols::generalized_kinematic_closure::selector::GeneralizedKICselector , protocols::grafting::AnchoredGraftMover , protocols::grafting::CCDEndsGraftMover , protocols::grafting::simple_movers::DeleteRegionMover , protocols::grafting::simple_movers::InsertPoseIntoPoseMover , protocols::grafting::simple_movers::KeepRegionMover , protocols::grafting::simple_movers::ReplaceRegionMover , protocols::hbnet::ConstrainHBondNetwork , protocols::hbnet::HBNet , protocols::hbnet::HBNetScore , protocols::hbnet::UnsatSelector , protocols::helical_bundle::BackboneGridSampler , protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::BundleReporterFilter , protocols::helical_bundle::FitSimpleHelix , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::PerturbBundle , protocols::helical_bundle::PerturbBundleHelix , protocols::helix_capper::HelixNCapperMover , protocols::hotspot_hashing::AddSearchPatternRotSetOp , protocols::hotspot_hashing::movers::PlaceProbeMover , protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionSampler , protocols::hybridization::CartesianHybridize , protocols::hybridization::CartesianSampler , protocols::hybridization::ChunkTrialMover , protocols::hybridization::DomainAssembly , protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol , protocols::hybridization::InsertChunkMover , protocols::hybridization::MRMover , protocols::hybridization::TMalign , protocols::hybridization::WeightedFragmentSmoothTrialMover , protocols::hybridization::WeightedFragmentTrialMover , protocols::hydrate::Hydrate , protocols::idealize::IdealizeMover , protocols::indel::IndelOptimizationMover , protocols::indexed_structure_store::filters::FragmentLookupFilter , protocols::indexed_structure_store::movers::DirectSegmentLookupMover , protocols::indexed_structure_store::movers::SegmentSequenceProfileMover , protocols::kinematic_closure::BalancedKicMover , protocols::kinematic_closure::ClosureSolution , protocols::legacy_sewing::LegacyAddStartnodeFragments , protocols::legacy_sewing::LegacyAppendAssemblyMover , protocols::legacy_sewing::LegacyAssemblyConstraintsMover , protocols::legacy_sewing::LegacyAssemblyMover , protocols::legacy_sewing::LegacyReadNativeRotamersFile , protocols::legacy_sewing::LegacyReadRepeatNativeRotamersFile , protocols::ligand_docking::AddHydrogen , protocols::ligand_docking::AddHydrogens , protocols::ligand_docking::AtomCountFilter , protocols::ligand_docking::ChainExistsFilter , protocols::ligand_docking::CompleteConnectionsFilter , protocols::ligand_docking::CompoundTranslate , protocols::ligand_docking::ComputeLigandRDF , protocols::ligand_docking::FinalMinimizer , protocols::ligand_docking::ga_ligand_dock::EntropyEstimator , protocols::ligand_docking::ga_ligand_dock::GALigandDock , protocols::ligand_docking::ga_ligand_dock::LigandAligner , protocols::ligand_docking::GrowLigand , protocols::ligand_docking::HBondAcceptorFilter , protocols::ligand_docking::HBondDonorFilter , protocols::ligand_docking::HeavyAtomFilter , protocols::ligand_docking::HighResDocker , protocols::ligand_docking::HighResEnsemble , protocols::ligand_docking::InterfaceScoreCalculator , protocols::ligand_docking::LigandBaseProtocol , protocols::ligand_docking::LigandDesign , protocols::ligand_docking::LigandDockMain , protocols::ligand_docking::LigandDockProtocol , protocols::ligand_docking::MinimizeBackbone , protocols::ligand_docking::MinimizeLigand , protocols::ligand_docking::MolarMassFilter , protocols::ligand_docking::MolecularMassFilter , protocols::ligand_docking::ProtLigEnsemble , protocols::ligand_docking::RandomConformerMover , protocols::ligand_docking::RandomConformers , protocols::ligand_docking::RigidSearchMover , protocols::ligand_docking::Rotate , protocols::ligand_docking::Rotates , protocols::ligand_docking::SlideTogether , protocols::ligand_docking::StartFrom , protocols::ligand_docking::TetherLigand , protocols::ligand_docking::Transform , protocols::ligand_docking::TransformEnsemble , protocols::ligand_docking::Translate , protocols::ligand_docking::UnconstrainedTorsionsMover , protocols::ligand_docking::WriteLigandMolFile , protocols::loop_build::LoopBuildMover , protocols::loop_build::LoopmodelWrapper , protocols::loop_grower::FragmentExtension , protocols::loop_grower::LoopComparator , protocols::loop_grower::LoopGrower , protocols::loop_grower::LoopPartialSolution , protocols::loop_grower::SheetSampler , protocols::loop_modeling::LoopMover , protocols::loophash::FastGapMover , protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashLibrary , protocols::loophash::LoopHashMoverWrapper , protocols::loophash::LoopHashRelaxProtocol , protocols::loophash::Mover_LoopHashRefine , protocols::LoopRebuild , protocols::LoopRefine , protocols::loops::filters::LoopAnalyzerFilter , protocols::loops::FoldTreeFromLoops , protocols::loops::loop_closure::ccd::CCDLoopClosureMover , protocols::loops::loop_closure::ccd::LoopClosure , protocols::loops::loop_closure::ccd::ShortLoopClosure , protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure , protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover , protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::loops::loop_closure::kinematic_closure::KinematicWrapper , protocols::loops::loop_mover::IndependentLoopMover , protocols::loops::loop_mover::LoopCM , protocols::loops::loop_mover::LoopMover , protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub , protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::loops::loop_mover::refine::LoopMover_Refine_KIC , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer , protocols::loops::loop_mover::refine::RepackTrial , protocols::loops::loop_mover::refine::ShearMinCCDTrial , protocols::loops::loop_mover::refine::SmallMinCCDTrial , protocols::loops::loops_definers::LoopsDatabaseDefiner , protocols::loops::loops_definers::LoopsDefiner , protocols::loops::loops_definers::LoopsExplicitDefiner , protocols::loops::loops_definers::LoopsFileDefiner , protocols::loops::loops_definers::LoopsStringDefiner , protocols::magnesium::MgHydrater , protocols::magnesium::MgMinimizer , protocols::magnesium::MgMonteCarlo , protocols::magnesium::MgOrbitalFrameFinder , protocols::magnesium::MgScanner , protocols::magnesium::MgWaterHydrogenPacker , protocols::make_rot_lib::MakeRotLibMover , protocols::match::MatcherMover , protocols::matdes::BuildingBlockInterfaceOperation , protocols::matdes::ClashCheckFilter , protocols::matdes::ExtractSubposeMover , protocols::matdes::GetRBDOFValues , protocols::matdes::InterfacePackingFilter , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::OligomericAverageDegreeFilter , protocols::matdes::SchemePlaceMotifsMover , protocols::matdes::SymDofMover , protocols::matdes::SymUnsatHbondFilter , protocols::md::CartesianMD , protocols::md::MDBase , protocols::mean_field::GenMeanFieldMover , protocols::medal::MedalExchangeMover , protocols::medal::MedalMover , protocols::membrane::AddMembraneMover , protocols::membrane::AddMembraneSpanConstraint , protocols::membrane::AddMembraneSpanTermZConstraint , protocols::membrane::AddMPLigandMover , protocols::membrane::AqueousPoreFinder , protocols::membrane::benchmark::MakeCanonicalHelix , protocols::membrane::benchmark::SampleTiltAngles , protocols::membrane::FlipMover , protocols::membrane::HelixFromSequence , protocols::membrane::MembranePositionFromTopologyMover , protocols::membrane::MPLipidAccessibility , protocols::membrane::MPMutateRelaxMover , protocols::membrane::MPQuickRelaxMover , protocols::membrane::OptimizeMembranePositionMover , protocols::membrane::OptimizeProteinEmbeddingMover , protocols::membrane::RandomPositionRotationMover , protocols::membrane::RandomPositionTranslationMover , protocols::membrane::RotationMover , protocols::membrane::SetMembraneCenterMover , protocols::membrane::SetMembraneNormalMover , protocols::membrane::SetMembranePositionMover , protocols::membrane::SpinAroundPartnerMover , protocols::membrane::TiltMover , protocols::membrane::TransformIntoMembraneMover , protocols::membrane::TranslationMover , protocols::membrane::TranslationRotationMover , protocols::membrane::visualize::VisualizeEmbeddingMover , protocols::membrane::visualize::VisualizeMembraneMover , protocols::membrane_benchmark::MembraneEnergyLandscapeSampler , protocols::membrane_benchmark::PeptideOrientationMover , protocols::metal_interface::ZincHeterodimerMover , protocols::minimization_packing::BoltzmannRotamerMover , protocols::minimization_packing::DisulfideOptimizationMover , protocols::minimization_packing::EnergyCutRotamerTrialsMinMover , protocols::minimization_packing::EnergyCutRotamerTrialsMover , protocols::minimization_packing::GreenPacker , protocols::minimization_packing::MinMover , protocols::minimization_packing::MinPackMover , protocols::minimization_packing::PackRotamersMover , protocols::minimization_packing::PertMinMover , protocols::minimization_packing::RepackSidechainsMover , protocols::minimization_packing::RotamerizeMover , protocols::minimization_packing::RotamerTrialsMinMover , protocols::minimization_packing::RotamerTrialsMover , protocols::minimization_packing::SaneMinMover , protocols::minimization_packing::SetReturningPackRotamersMover , protocols::minimization_packing::symmetry::TaskAwareSymMinMover , protocols::minimization_packing::TaskAwareMinMover , protocols::monte_carlo::GenericMonteCarloMover , protocols::monte_carlo::GenericSimulatedAnnealer , protocols::monte_carlo::MonteCarloRecover , protocols::monte_carlo::MonteCarloReset , protocols::monte_carlo::MonteCarloTest , protocols::monte_carlo::ResetBaselineMover , protocols::motif_grafting::movers::MotifGraftMover , protocols::motifs::MotifDnaPacker , protocols::moves::ChangeFoldTreeMover , protocols::moves::CompositionMover , protocols::moves::CycleMover , protocols::moves::CyclicMover , protocols::moves::DsspMover , protocols::moves::FilterMover , protocols::moves::FilterReportAsPoseExtraScoresMover , protocols::moves::FilterReporterMover , protocols::moves::IfMover , protocols::moves::IteratedConvergenceMover , protocols::moves::JumpOutMover , protocols::moves::MCShowMover , protocols::moves::MonteCarloUtil , protocols::moves::Mover , protocols::moves::MoverContainer , protocols::moves::MoverForPoseList , protocols::moves::NullMover , protocols::moves::PDBDumpMover , protocols::moves::ProfilerMover , protocols::moves::PyMOLMover , protocols::moves::RampingMover , protocols::moves::RandomMover , protocols::moves::RepeatMover , protocols::moves::SequenceMover , protocols::moves::StructureRestrictor , protocols::moves::SwitchMover , protocols::moves::TrialMover , protocols::moves::VectorPoseMover , protocols::moves::WhileMover , protocols::mpi_refinement::Clusterer , protocols::mpi_refinement::Serial_Refine , protocols::mpi_refinement::StructAvrgMover , protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopCreatorMover , protocols::ncbb::oop::OopDockDesignProtocol , protocols::ncbb::ResidueReplacementRebuildMover , protocols::ncbb::SecStructFinder , protocols::ncbb::SecStructMinimizeMover , protocols::network::UIMover , protocols::nmr::ParaNMRScoreMover , protocols::nmr::pcs::PCSLigandTransformMover , protocols::nmr::pre::PREMover , protocols::noesy_assign::DistanceScoreMover , protocols::nonlocal::BiasedFragmentMover , protocols::nonlocal::HelixRotate , protocols::nonlocal::SheetTranslate , protocols::nonlocal::SingleFragmentMover , protocols::normalmode::NormalModeMinimizer , protocols::normalmode::NormalModeRelaxMover , protocols::optimize_weights::ScaleAnnealerTemperatureOperation , protocols::pack_interface::ProteinProteinInterfaceUpweighter , protocols::parser::FragmentReader , protocols::pb_potential::SetupPoissonBoltzmannPotential , protocols::pdbinfo_manipulations::AlignPDBInfoToSequences , protocols::peptide_deriver::PeptideDeriverFilter , protocols::pose_creation::ExtendedPoseMover , protocols::pose_creation::MakeJunctionsMover , protocols::pose_creation::MakePolyXMover , protocols::pose_creation::MergePDBatOverlapMover , protocols::pose_creation::MergePDBMover , protocols::pose_creation::PoseFromSequenceMover , protocols::pose_creation::SliceToMiniProteinMover , protocols::pose_length_moves::AnalyzeLoopModeling , protocols::pose_length_moves::ConnectChainsMover , protocols::pose_length_moves::FixAllLoopsMover , protocols::pose_length_moves::InsertResMover , protocols::pose_length_moves::NearNativeLoopCloser , protocols::protein_interface_design::filters::AtomicContactCountFilter , protocols::protein_interface_design::filters::AverageDegreeFilter , protocols::protein_interface_design::filters::BindingStrainFilter , protocols::protein_interface_design::filters::BoltzmannFilter , protocols::protein_interface_design::filters::ClashWithTargetFilter , protocols::protein_interface_design::filters::DesignableResiduesFilter , protocols::protein_interface_design::filters::DisulfideFilter , protocols::protein_interface_design::filters::FilterScanFilter , protocols::protein_interface_design::filters::FNatFilter , protocols::protein_interface_design::filters::HbondsToAtomFilter , protocols::protein_interface_design::filters::HbondsToResidueFilter , protocols::protein_interface_design::filters::InterfaceHolesFilter , protocols::protein_interface_design::filters::IRmsdFilter , protocols::protein_interface_design::filters::LRmsdFilter , protocols::protein_interface_design::filters::RelativeSegmentFilter , protocols::protein_interface_design::filters::RmsdFilter , protocols::protein_interface_design::filters::RmsdSimpleFilter , protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter , protocols::protein_interface_design::filters::SSamountFilter , protocols::protein_interface_design::filters::StubScoreFilter , protocols::protein_interface_design::filters::Torsion , protocols::protein_interface_design::movers::AddChainBreak , protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots , protocols::protein_interface_design::movers::BackrubDDMover , protocols::protein_interface_design::movers::BestHotspotCstMover , protocols::protein_interface_design::movers::BuildAlaPose , protocols::protein_interface_design::movers::DesignMinimizeHbonds , protocols::protein_interface_design::movers::DisulfideMover , protocols::protein_interface_design::movers::DockAndRetrieveSidechains , protocols::protein_interface_design::movers::DockWithHotspotMover , protocols::protein_interface_design::movers::FavorNativeResiduePreCycle , protocols::protein_interface_design::movers::FavorNonNativeResiduePreCycle , protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover , protocols::protein_interface_design::movers::HotspotHasherMover , protocols::protein_interface_design::movers::InterfaceRecapitulationMover , protocols::protein_interface_design::movers::LoopFinder , protocols::protein_interface_design::movers::LoopLengthChange , protocols::protein_interface_design::movers::LoopMoverFromCommandLine , protocols::protein_interface_design::movers::LoopOver , protocols::protein_interface_design::movers::LoopRemodel , protocols::protein_interface_design::movers::MapHotspot , protocols::protein_interface_design::movers::PatchdockTransform , protocols::protein_interface_design::movers::PeptideStapleDesignMover , protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::protein_interface_design::movers::PlacementMinimizationMover , protocols::protein_interface_design::movers::PlaceOnLoop , protocols::protein_interface_design::movers::PlaceSimultaneouslyMover , protocols::protein_interface_design::movers::PlaceStubMover , protocols::protein_interface_design::movers::PrepackMover , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover , protocols::protein_interface_design::movers::RandomMutation , protocols::protein_interface_design::movers::RepackMinimize , protocols::protein_interface_design::movers::SaveAndRetrieveSidechains , protocols::protein_interface_design::movers::SetAtomTree , protocols::protein_interface_design::movers::SetTemperatureFactor , protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover , protocols::protein_interface_design::movers::SetupHotspotConstraintsMover , protocols::protein_interface_design::movers::ShoveResidueMover , protocols::protein_interface_design::movers::SpinMover , protocols::protein_interface_design::movers::SubroutineMover , protocols::protein_interface_design::movers::TaskAwareCsts , protocols::protein_interface_design::movers::TopologyBrokerMover , protocols::protein_interface_design::movers::TryRotamers , protocols::protein_interface_design::movers::VLB , protocols::protein_interface_design::Revert , protocols::qsar::qsarMover , protocols::qsar::RenderGridsToKinemage , protocols::quantum_annealing::ExternalPackerResultLoader , protocols::rbsegment_relax::AutoRBMover , protocols::rbsegment_relax::CCDMoveWrapper , protocols::rbsegment_relax::FragInsertAndAlignMover , protocols::rbsegment_relax::GaussianRBSegmentMover , protocols::rbsegment_relax::HelicalGaussianMover , protocols::rbsegment_relax::IdealizeHelicesMover , protocols::rbsegment_relax::MakeStarTopologyMover , protocols::rbsegment_relax::OptimizeThreadingMover , protocols::rbsegment_relax::RBSegmentMover , protocols::rbsegment_relax::RBSegmentRelax , protocols::rbsegment_relax::SequenceShiftMover , protocols::rbsegment_relax::StrandTwistingMover , protocols::RBSegmentRelaxImpl , protocols::recces::RECCES_Mover , protocols::recces::sampler::MC_Any , protocols::recces::sampler::MC_Comb , protocols::recces::sampler::MC_OneTorsion , protocols::recces::sampler::rna::MC_RNA_KIC_Sampler , protocols::recces::sampler::rna::MC_RNA_OneJump , protocols::recces::sampler::rna::MC_RNA_Sugar , protocols::recces::scratch::ThermalMinimizer , protocols::recces::scratch::ThermalSamplingMover , protocols::recon_design::FindConsensusSequence , protocols::recon_design::FitnessFilter , protocols::recon_design::MSDMover , protocols::relax::AcceptToBestMover , protocols::relax::AtomCoordinateCstMover , protocols::relax::CentroidRelax , protocols::relax::ClassicRelax , protocols::relax::FastRelax , protocols::relax::LocalRelax , protocols::relax::membrane::MPFastRelaxMover , protocols::relax::membrane::MPRangeRelaxMover , protocols::relax::MiniRelax , protocols::relax::RangeRelaxMover , protocols::relax::RepeatProteinRelax , protocols::residue_selectors::HBondSelector , protocols::residue_selectors::LigandMetalContactSelector , protocols::residue_selectors::NativeSelector , protocols::residue_selectors::StoredResidueSubsetSelector , protocols::residue_selectors::StoreResidueSubsetMover , protocols::residue_selectors::TaskSelector , protocols::rigid::MembraneCenterPerturbationMover , protocols::rigid::MembraneNormalPerturbationMover , protocols::rigid::MovePoseToMembraneCenterMover , protocols::rigid::RigidBodyDeterministicSpinMover , protocols::rigid::RigidBodyDofPerturbMover , protocols::rigid::RigidBodyDofRandomizeMover , protocols::rigid::RigidBodyDofRandomTransMover , protocols::rigid::RigidBodyDofSeqPerturbMover , protocols::rigid::RigidBodyDofSeqRandomizeMover , protocols::rigid::RigidBodyDofSeqTransMover , protocols::rigid::RigidBodyDofTransMover , protocols::rigid::RigidBodyMotionMover , protocols::rigid::RigidBodyMover , protocols::rigid::RigidBodyPerturbMover , protocols::rigid::RigidBodyPerturbNoCenterMover , protocols::rigid::RigidBodyPerturbRandomJumpMover , protocols::rigid::RigidBodyRandomizeMover , protocols::rigid::RigidBodySpinMover , protocols::rigid::RigidBodyTiltMover , protocols::rigid::RigidBodyTransMover , protocols::rigid::RollMover , protocols::rigid::RotateJumpAxisMover , protocols::rigid::UniformRigidBodyCM , protocols::rigid::UniformRigidBodyMover , protocols::rigid::UniformSphereTransMover , protocols::rigid::WholeBodyRotationMover , protocols::rigid::WholeBodyTranslationMover , protocols::rna::denovo::coarse::CoarseRNA_LoopCloser , protocols::rna::denovo::coarse::MultipleDomainMover , protocols::rna::denovo::movers::RNA_DeNovoMasterMover , protocols::rna::denovo::movers::RNA_DeNovoProtocolMover , protocols::rna::denovo::movers::RNA_FragmentMover , protocols::rna::denovo::movers::RNA_HelixMover , protocols::rna::denovo::movers::RNA_Minimizer , protocols::rna::denovo::movers::RNA_Relaxer , protocols::rna::denovo::movers::RNP_HighResMover , protocols::rna::denovo::output::RNA_FragmentMonteCarloOutputter , protocols::rna::denovo::RNA_DeNovoProtocol , protocols::rna::denovo::RNA_FragmentMonteCarlo , protocols::rna::movers::ERRASER2Protocol , protocols::rna::movers::ErraserMinimizerMover , protocols::rna::movers::RNA_DeNovoOptimizer , protocols::rna::movers::RNA_LoopCloser , protocols::rna::movers::RNAIdealizeMover , protocols::rna::movers::RNAThreadAndMinimizeMover , protocols::rna::setup::RNA_CSA_JobDistributor , protocols::rna::setup::RNA_JobDistributor , protocols::rna::setup::RNA_MonteCarloJobDistributor , protocols::rosetta_scripts::AdditionalOutputWrapper , protocols::rosetta_scripts::MultipleOutputWrapper , protocols::rosetta_scripts::MultiplePoseMover , protocols::rosetta_scripts::ParsedProtocol , protocols::rosetta_scripts::SavePoseMover , protocols::rotamer_recovery::RotamerRecoveryMover , protocols::RotamerDump::RotamerDumpMover , protocols::score_filters::GeometryFilter , protocols::score_filters::ScoreCutoffFilter , protocols::score_filters::ScoreTypeFilter , protocols::seeded_abinitio::CAcstGenerator , protocols::seeded_abinitio::CloseFold , protocols::seeded_abinitio::CoordinateCst , protocols::seeded_abinitio::DefineMovableLoops , protocols::seeded_abinitio::GrowPeptides , protocols::seeded_abinitio::SeedFoldTree , protocols::seeded_abinitio::SeedSetupMover , protocols::seeded_abinitio::SegmentHybridizer , protocols::seeded_abinitio::SwapSegment , protocols::sewing::hashing::AlignmentFileGeneratorMover , protocols::sewing::movers::AppendAssemblyMover , protocols::sewing::movers::AssemblyMover , protocols::sewing::movers::LigandBindingAssemblyMover , protocols::simple_ddg::AlaScan , protocols::simple_ddg::ddG , protocols::simple_ddg::DdgFilter , protocols::simple_ddg::DdGScan , protocols::simple_ddg::InterfaceBindingEnergyDensityFilter , protocols::simple_ddg::SSElementBisectddGFilter , protocols::simple_filters::AbinitioBaseFilter , protocols::simple_filters::AngleToVector , protocols::simple_filters::AtomicContactFilter , protocols::simple_filters::AtomicDistanceFilter , protocols::simple_filters::AveragePathLengthFilter , protocols::simple_filters::BatchEvaluator , protocols::simple_filters::BatchNrEvaluator , protocols::simple_filters::BuriedSurfaceAreaFilter , protocols::simple_filters::BuriedUnsatHbondFilter , protocols::simple_filters::ChainBreak , protocols::simple_filters::ChainCountFilter , protocols::simple_filters::ChiWellRmsdEvaluator , protocols::simple_filters::COFilter , protocols::simple_filters::ContactMapEvaluator , protocols::simple_filters::ContactMolecularSurfaceFilter , protocols::simple_filters::DeltaFilter , protocols::simple_filters::DisulfideEntropyFilter , protocols::simple_filters::DomainInterfaceFilter , protocols::simple_filters::EnergyPerResidueFilter , protocols::simple_filters::EvaluatedTrialMover , protocols::simple_filters::ExpiryFilter , protocols::simple_filters::ExternalEvaluator , protocols::simple_filters::FileExistFilter , protocols::simple_filters::FileRemoveFilter , protocols::simple_filters::HelixHelixAngleFilter , protocols::simple_filters::HolesFilter , protocols::simple_filters::InterfaceHbondsFilter , protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter , protocols::simple_filters::InterfaceSasaFilter , protocols::simple_filters::InterRepeatContactFilter , protocols::simple_filters::IntraRepeatContactFilter , protocols::simple_filters::JScoreEvaluator , protocols::simple_filters::JumpEvaluator , protocols::simple_filters::JumpNrEvaluator , protocols::simple_filters::LeastNativeLike9merFilter , protocols::simple_filters::LongestContinuousPolarSegmentFilter , protocols::simple_filters::LoopRmsdEvaluator , protocols::simple_filters::MembAccesResidueLipophilicityFilter , protocols::simple_filters::MotifScoreFilter , protocols::simple_filters::MPSpanAngleFilter , protocols::simple_filters::MutationsFilter , protocols::simple_filters::NeighborTypeFilter , protocols::simple_filters::NetChargeFilter , protocols::simple_filters::NMerPSSMEnergyFilter , protocols::simple_filters::NMerSVMEnergyFilter , protocols::simple_filters::NonSequentialNeighborsFilter , protocols::simple_filters::PackerNeighborGraphFilter , protocols::simple_filters::PackStatFilter , protocols::simple_filters::PDDFScoreFilter , protocols::simple_filters::PoseComment , protocols::simple_filters::PoseInfoFilter , protocols::simple_filters::PoseMetricEvaluator< T > , protocols::simple_filters::PredictedBurialEvaluator , protocols::simple_filters::RangeFilter , protocols::simple_filters::RDC_Evaluator , protocols::simple_filters::ReadPoseExtraScoreFilter , protocols::simple_filters::RepeatParameterFilter , protocols::simple_filters::ReportFilter , protocols::simple_filters::ResidueBurialFilter , protocols::simple_filters::ResidueChiralityFilter , protocols::simple_filters::ResidueCountFilter , protocols::simple_filters::ResidueDepthFilter , protocols::simple_filters::ResidueDistanceFilter , protocols::simple_filters::ResidueIEFilter , protocols::simple_filters::ResidueLipophilicityFilter , protocols::simple_filters::ResidueSelectionDistanceFilter , protocols::simple_filters::ResidueSetChainEnergyFilter , protocols::simple_filters::ResiduesInInterfaceFilter , protocols::simple_filters::RGFilter , protocols::simple_filters::RmsdEvaluator , protocols::simple_filters::SaveResfileToDiskFilter , protocols::simple_filters::SAXSScoreFilter , protocols::simple_filters::ScoreEvaluator , protocols::simple_filters::SecretionPredictionFilter , protocols::simple_filters::SelectGdtEvaluator , protocols::simple_filters::SelectMaxsubEvaluator , protocols::simple_filters::SelectRDC_Evaluator , protocols::simple_filters::SelectRmsdEvaluator , protocols::simple_filters::SequenceDistance , protocols::simple_filters::ShapeComplementarityFilter , protocols::simple_filters::SheetFilter , protocols::simple_filters::SidechainRmsdFilter , protocols::simple_filters::SimpleHbondsToAtomFilter , protocols::simple_filters::SimpleMetricFilter , protocols::simple_filters::SpanTopologyMatchPoseFilter , protocols::simple_filters::SSElementLengthFilter , protocols::simple_filters::SSElementMotifContactFilter , protocols::simple_filters::SSMotifFinder , protocols::simple_filters::StemFinder , protocols::simple_filters::StructuralSimilarityEvaluator , protocols::simple_filters::SymmetricMotifFilter , protocols::simple_filters::SymmetricRmsdEvaluator , protocols::simple_filters::TaskAwareSASAFilter , protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::simple_filters::TerminusDistanceFilter , protocols::simple_filters::TMsAACompFilter , protocols::simple_filters::TMsSpanMembraneFilter , protocols::simple_filters::TotalSasaFilter , protocols::simple_filters::TruncatedScoreEvaluator , protocols::simple_moves::a3b_hbs::A3BHbsPatcher , protocols::simple_moves::AddCavitiesMover , protocols::simple_moves::AddChainMover , protocols::simple_moves::AddJobPairData , protocols::simple_moves::AddPDBInfoMover , protocols::simple_moves::AddResidueCouplingConstraint , protocols::simple_moves::AddResidueLabelMover , protocols::simple_moves::AlignChainMover , protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockMoveRbJumpMover , protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockRbTrialMover , protocols::simple_moves::BackboneMover , protocols::simple_moves::BBConRotMover , protocols::simple_moves::BBDihedralSamplerMover , protocols::simple_moves::BBGaussianMover , protocols::simple_moves::bin_transitions::InitializeByBins , protocols::simple_moves::bin_transitions::PerturbByBins , protocols::simple_moves::ChainSplitMover , protocols::simple_moves::ChangeAndResetFoldTreeMover , protocols::simple_moves::chiral::ChiralMover , protocols::simple_moves::ClassicFragmentMover , protocols::simple_moves::CombinePoseMover , protocols::simple_moves::ConcatenatePosesMover , protocols::simple_moves::ConstrainToIdealMover , protocols::simple_moves::ContingentAcceptMover , protocols::simple_moves::ConvertRealToVirtualMover , protocols::simple_moves::ConvertVirtualToRealMover , protocols::simple_moves::CopyDofMover , protocols::simple_moves::CopyRotamerMover , protocols::simple_moves::CoupledMover , protocols::simple_moves::CutChainMover , protocols::simple_moves::CyclizationMover , protocols::simple_moves::DeleteChainMover , protocols::simple_moves::DeleteChainsMover , protocols::simple_moves::DisulfideInsertionMover , protocols::simple_moves::DME_FilterMover , protocols::simple_moves::DumpPdb , protocols::simple_moves::DumpSingleResidueRotamers , protocols::simple_moves::ExplicitWaterMover , protocols::simple_moves::FavorSequenceProfile , protocols::simple_moves::FavorSymmetricSequence , protocols::simple_moves::FoldTreeFromMotif , protocols::simple_moves::FragmentMover , protocols::simple_moves::hbs::HbsPatcher , protocols::simple_moves::LoadPDBMover , protocols::simple_moves::LoadUnboundRotMover , protocols::simple_moves::MembraneTopology , protocols::simple_moves::MissingDensityToJumpMover , protocols::simple_moves::ModifyVariantTypeMover , protocols::simple_moves::MutateResidue , protocols::simple_moves::oop::OopMover , protocols::simple_moves::oop::OopPatcher , protocols::simple_moves::oop::OopRandomPuckMover , protocols::simple_moves::oop::OopRandomSmallMover , protocols::simple_moves::PDBReloadMover , protocols::simple_moves::PeptideStapleMover , protocols::simple_moves::PeriodicBoxMover , protocols::simple_moves::PoseFromPoseResourceMover , protocols::simple_moves::ProlineFixMover , protocols::simple_moves::PSSM2BfactorMover , protocols::simple_moves::RandomOmegaFlipMover , protocols::simple_moves::RandomTorsionMover , protocols::simple_moves::rational_mc::RationalMonteCarlo , protocols::simple_moves::RepeatPropagationMover , protocols::simple_moves::ReportEffectivePKA , protocols::simple_moves::ReportXYZ , protocols::simple_moves::RepulsiveOnlyMover , protocols::simple_moves::ResetFoldTree , protocols::simple_moves::ResetFullModelInfoMover , protocols::simple_moves::ReturnSidechainMover , protocols::simple_moves::RingConformationMover , protocols::simple_moves::SaveSequenceToCommentsMover , protocols::simple_moves::ScoreMover , protocols::simple_moves::SequenceProfileMover , protocols::simple_moves::SetTorsion , protocols::simple_moves::SetupMetalsMover , protocols::simple_moves::ShakeStructureMover , protocols::simple_moves::ShortBackrubMover , protocols::simple_moves::sidechain_moves::SetChiMover , protocols::simple_moves::sidechain_moves::SidechainMCMover , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase , protocols::simple_moves::SimpleThreadingMover , protocols::simple_moves::StorePoseSnapshot , protocols::simple_moves::StructProfileMover , protocols::simple_moves::SuperimposeMover , protocols::simple_moves::SwitchChainOrderMover , protocols::simple_moves::SwitchResidueTypeSetMover , protocols::simple_moves::TailsScoreMover , protocols::simple_moves::TorsionDOFMover , protocols::simple_moves::TorsionSetMover , protocols::simple_moves::triazolamer::TriazolamerMover , protocols::simple_moves::triazolamer::TriazolamerRandomSmallMover , protocols::simple_moves::Tumble , protocols::simple_moves::UniformRotationMover , protocols::simple_moves::UniformTranslationMover , protocols::simple_moves::VirtualRootMover , protocols::simple_moves::WriteFiltersToPose , protocols::simple_moves::WriteSSEMover , protocols::simple_task_operations::DockingNoRepack1 , protocols::simple_task_operations::DockingNoRepack2 , protocols::simple_task_operations::RestrictToInterface , protocols::simple_task_operations::RestrictToLoops , protocols::simple_task_operations::RestrictToLoopsAndNeighbors , protocols::sparta::ChemicalShiftEvaluator , protocols::splice::AlignEndsMover , protocols::splice::DesignInterfacesOperation , protocols::splice::FindEndpointsOperation , protocols::splice::RBInMover , protocols::splice::RBOutMover , protocols::splice::RotLibOut , protocols::splice::SampleRotamersFromPDB , protocols::splice::Splice , protocols::splice::SpliceIn , protocols::splice::SpliceInAntibody , protocols::splice::SpliceInTail , protocols::splice::SpliceOut , protocols::splice::SpliceOutAntibody , protocols::splice::TailSegmentMover , protocols::star::StarAbinitio , protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer , protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup , protocols::stepwise::modeler::align::StepWiseClusterer , protocols::stepwise::modeler::align::StepWisePoseAligner , protocols::stepwise::modeler::packer::SideChainCopier , protocols::stepwise::modeler::packer::StepWisePacker , protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker , protocols::stepwise::modeler::precomputed::PrecomputedLibraryMover , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_MultiPoseCloser , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger , protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler , protocols::stepwise::modeler::rna::bulge::BulgeApplyMover , protocols::stepwise::modeler::rna::bulge::BulgeUnApplyMover , protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker , protocols::stepwise::modeler::rna::o2prime::O2PrimePacker , protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler , protocols::stepwise::modeler::rna::phosphate::PhosphateMover , protocols::stepwise::modeler::rna::sugar::SugarInstantiateMover , protocols::stepwise::modeler::rna::sugar::SugarVirtualizeMover , protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator , protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler , protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList , protocols::stepwise::modeler::StepWiseConnectionSampler , protocols::stepwise::modeler::StepWiseMinimizer , protocols::stepwise::modeler::StepWiseModeler , protocols::stepwise::monte_carlo::mover::AddMover , protocols::stepwise::monte_carlo::mover::AddOrDeleteMover , protocols::stepwise::monte_carlo::mover::DeleteMover , protocols::stepwise::monte_carlo::mover::FromScratchMover , protocols::stepwise::monte_carlo::mover::ResampleMover , protocols::stepwise::monte_carlo::mover::StepWiseMasterMover , protocols::stepwise::monte_carlo::mover::VaryLoopLengthMover , protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo , protocols::stepwise::monte_carlo::rna::RNA_O2PrimeMover , protocols::stepwise::monte_carlo::rna::RNA_TorsionMover , protocols::stepwise::monte_carlo::StepWiseMonteCarlo , protocols::stepwise::sampler::copy_dofs::CopyDofStepWiseSampler , protocols::stepwise::sampler::copy_dofs::ResidueListStepWiseSampler , protocols::stepwise::sampler::input_streams::InputStreamStepWiseSampler , protocols::stepwise::sampler::jump::JumpStepWiseSampler , protocols::stepwise::sampler::protein::ProteinFragmentStepWiseSampler , protocols::stepwise::sampler::protein::ProteinMainChainStepWiseSampler , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueList , protocols::stepwise::sampler::rna::RNA_KIC_Sampler , protocols::stepwise::sampler::rna::RNA_KinematicCloser , protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler , protocols::stepwise::sampler::StepWiseSamplerComb , protocols::stepwise::sampler::StepWiseSamplerOneDOF , protocols::stepwise::sampler::StepWiseSamplerOneTorsion , protocols::stepwise::sampler::StepWiseSamplerOneValue , protocols::stepwise::sampler::StepWiseSamplerRingConformer , protocols::stepwise::sampler::StepWiseSamplerSized , protocols::stepwise::sampler::StepWiseSamplerSizedAny , protocols::stepwise::sampler::StepWiseSamplerSizedComb , protocols::struct_fragment::StructFragmentMover , protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::FullatomRelaxMover , protocols::surface_docking::SurfaceDockingProtocol , protocols::surface_docking::SurfaceOrientMover , protocols::switches::GraftSwitchMover , protocols::symmetric_docking::membrane::MPSymDockMover , protocols::symmetric_docking::SymDockBaseProtocol , protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockingLowRes , protocols::symmetric_docking::SymDockProtocol , protocols::symmetric_docking::SymFoldandDockMoveRbJumpMover , protocols::symmetric_docking::SymFoldandDockRbTrialMover , protocols::symmetric_docking::SymFoldandDockSlideTrialMover , protocols::symmetric_docking::SymInterfaceSidechainMinMover , protocols::symmetric_docking::SymRestrictTaskForDocking , protocols::symmetric_docking::SymSidechainMinMover , protocols::symmetry::DetectSymmetry , protocols::symmetry::ExtractAsymmetricPoseMover , protocols::symmetry::ExtractAsymmetricUnitMover , protocols::symmetry::FaSymDockingSlideTogether , protocols::symmetry::SetupForSequenceSymmetryMover , protocols::symmetry::SetupForSymmetryMover , protocols::symmetry::SetupNCSMover , protocols::symmetry::SymDockingInitialPerturbation , protocols::symmetry::SymDockingSlideIntoContact , protocols::symmetry::SymmetricRMSMover , protocols::symmetry::SymmetrySlider , protocols::task_operations::AlignedThreadOperation , protocols::task_operations::ConservativeDesignOperation , protocols::task_operations::CrystalContactsOperation , protocols::task_operations::DatabaseThread , protocols::task_operations::DesignAroundOperation , protocols::task_operations::DsspDesignOperation , protocols::task_operations::ImportUnboundRotamersOperation , protocols::task_operations::InteractingRotamerExplosion , protocols::task_operations::JointSequenceOperation , protocols::task_operations::LimitAromaChi2Operation , protocols::task_operations::LinkResidues , protocols::task_operations::ModifyAnnealer , protocols::task_operations::MutationSetDesignOperation , protocols::task_operations::pHVariantTaskOperation , protocols::task_operations::PreventChainFromRepackingOperation , protocols::task_operations::PreventResiduesFromRepackingOperation , protocols::task_operations::ProteinInterfaceDesignOperation , protocols::task_operations::PruneBuriedUnsatsOperation , protocols::task_operations::ReadResfileFromDB , protocols::task_operations::ResfileCommandOperation , protocols::task_operations::ResidueProbDesignOperation , protocols::task_operations::RestrictByCalculatorsOperation , protocols::task_operations::RestrictChainToRepackingOperation , protocols::task_operations::RestrictConservedLowDdgOperation , protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation , protocols::task_operations::RestrictIdentitiesOperation , protocols::task_operations::RestrictInterGroupVectorOperation , protocols::task_operations::RestrictNativeResiduesOperation , protocols::task_operations::RestrictNonSurfaceToRepackingOperation , protocols::task_operations::RestrictOperationsBase , protocols::task_operations::RestrictResiduesToRepackingOperation , protocols::task_operations::RestrictToAlignedSegmentsOperation , protocols::task_operations::RestrictToCDRH3Loop , protocols::task_operations::RestrictToInterfaceOperation , protocols::task_operations::RestrictToInterfaceVectorOperation , protocols::task_operations::RestrictToMoveMapChiOperation , protocols::task_operations::RestrictToNeighborhoodOperation , protocols::task_operations::RestrictToTerminiOperation , protocols::task_operations::RetrieveStoredTaskOperation , protocols::task_operations::SelectByDeltaScoreOperation , protocols::task_operations::SelectByDensityFitOperation , protocols::task_operations::SelectBySASAOperation , protocols::task_operations::SelectResiduesWithinChainOperation , protocols::task_operations::SeqprofConsensusOperation , protocols::task_operations::SequenceMotifTaskOperation , protocols::task_operations::SetIGTypeOperation , protocols::task_operations::StoreCombinedStoredTasksMover , protocols::task_operations::StoreCompoundTaskMover , protocols::task_operations::StoreTaskMover , protocols::task_operations::ThreadSequenceOperation , protocols::testing::BenchmarkBuildRotamersMover , protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover , protocols::toolbox::SamplerPlusPlus , protocols::topology_broker::ConstraintEvaluatorWrapper , protocols::topology_broker::RigidBodyRandomTMHMover , protocols::topology_broker::TopologyBroker , protocols::ub_e2c::ubi_e2c_modeler , protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover , protocols::vardist_solaccess::LoadVarSolDistSasaCalculatorMover , protocols::vip::VIP_Mover
• apply_A_LH_foldtree() : protocols::antibody::design::GeneralAntibodyModeler
• apply_abinitio() : protocols::fold_from_loops::NubInitioMover
• apply_Aform_torsions_to_five_prime_phosphate() : protocols::stepwise::modeler::rna::phosphate::PhosphateMover
• apply_Aform_torsions_to_three_prime_phosphate() : protocols::stepwise::modeler::rna::phosphate::PhosphateMover
• apply_after_jump_change() : protocols::rna::denovo::coarse::CoarseRNA_LoopCloser
• apply_allow_insert_res() : core::pose::toolbox::AtomLevelDomainMap
• apply_alpha_aa_rama_check() : protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter
• apply_ambiguous_constraints_ : protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover , protocols::protein_interface_design::movers::SetupHotspotConstraintsMover
• apply_and_return_jump() : protocols::rna::denovo::coarse::MultipleDomainMover
• apply_and_to_subset() : core::select::jump_selector::AndJumpSelector , core::select::residue_selector::AndResidueSelector
• apply_at_all_positions() : protocols::simple_moves::FragmentMover
• apply_at_domain() : protocols::rna::denovo::coarse::MultipleDomainMover
• apply_atom_pair_distance() : protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter
• apply_backbone_bin() : protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter
• apply_basic_filters() : core::chemical::ResidueTypeFinder
• apply_best_fragment() : core::fragment::rna::FullAtomRNA_Fragments , core::fragment::rna::RNA_Fragments
• apply_binder_selector() : protocols::fold_from_loops::utils::Nub
• apply_binder_selector_as_ranges() : protocols::fold_from_loops::utils::Nub
• apply_body() : protocols::docking::DockingInitialPerturbation
• apply_bulge_variants() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• apply_by_jump() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler
• apply_centroid_mode_ : protocols::antibody_legacy::CDRH3Modeler
• apply_check() : protocols::motifs::Motif
• apply_chem_shift_data() : protocols::rna::denovo::RNA_FragmentMonteCarlo
• apply_closure() : protocols::backbone_moves::local_backbone_mover::GapCloser
• apply_closure_trust() : protocols::fold_from_loops::movers::NubInitioLoopClosureMover
• apply_const() : protocols::analysis::GlycanInfoMover , protocols::analysis::InterfaceAnalyzerMover
• apply_constraints() : protocols::hybridization::CartesianSampler
• apply_coord_cst_to_sctip() : protocols::ligand_docking::ga_ligand_dock::GALigandDock
• apply_coords() : core::pose::rna::RNA_IdealCoord
• apply_copy_backbone_dihedrals() : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• apply_current_pose_segment() : protocols::stepwise::modeler::protein::InputStreamWithResidueInfo
• apply_cutpoint_variants() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• apply_default_commands_to_inserts_ : core::pack::task::operation::ReadResfileAndObeyLengthEvents
• apply_delta_torsions_angles() : core::kinematics::jacobian::ModuleType1
• apply_disulfides() : protocols::relax::RelaxProtocolBase
• apply_dof_conformer() : protocols::jumping::ResiduePairJump
• apply_dof_tasks_to_movemap() : protocols::minimization_packing::MinMover
• apply_dofs() : core::pose::copydofs::CopyDofsInfo
• apply_filter() : protocols::rosetta_scripts::ParsedProtocol , protocols::topology_broker::TopologyBroker
• apply_filters_after_patches() : core::chemical::ResidueTypeFinder
• apply_frag() : protocols::hybridization::CartesianHybridize
• apply_fragcsts() : protocols::hybridization::CartesianSampler
• apply_fragment() : protocols::simple_moves::ClassicFragmentMover , protocols::simple_moves::LoggedFragmentMover , protocols::simple_moves::SymmetricFragmentMover , protocols::simple_moves::WobbleMover
• apply_frame() : protocols::hybridization::CartesianHybridize , protocols::hybridization::CartesianSampler , protocols::seeded_abinitio::SegmentHybridizer
• apply_frames() : protocols::simple_moves::ClassicFragmentMover , protocols::simple_moves::FragmentMover , protocols::simple_moves::ResTypeFragmentMover
• apply_from_template_pose() : protocols::simple_moves::CopyRotamerMover
• apply_full_to_sub_mapping() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• apply_fullatom_mode_ : protocols::antibody_legacy::CDRH3Modeler
• apply_func_to_all() : protocols::mean_field::jagged_array< T, A >
• apply_func_to_each_col() : protocols::mean_field::jagged_array< T, A >
• apply_func_to_each_elem() : protocols::mean_field::jagged_array< T, A >
• apply_helper() : protocols::pose_creation::MergePDBatOverlapMover , protocols::simple_filters::EnergyPerResidueFilter , protocols::simple_task_operations::RestrictToLoops
• apply_holes() : protocols::vip::VIP_Mover
• apply_if_reasonable() : protocols::kinematic_closure::ClosureSolution
• apply_internal_coordinates() : protocols::kinematic_closure::ClosureProblem
• apply_large_frags_ : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• apply_legacy() : protocols::stepwise::monte_carlo::mover::StepWiseMasterMover
• apply_linked_constraints() : protocols::recon_design::MSDMover
• apply_loop_bump_check() : protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter
• apply_lowest_delta_torsion_selector() : protocols::generalized_kinematic_closure::selector::GeneralizedKICselector
• apply_lowest_energy_selector() : protocols::generalized_kinematic_closure::selector::GeneralizedKICselector
• apply_lowest_rmsd_selector() : protocols::generalized_kinematic_closure::selector::GeneralizedKICselector
• apply_metapatches_recursively() : core::chemical::ResidueTypeFinder
• apply_metropolis_criterion() : protocols::helical_bundle_predict::HelicalBundlePredictApplication
• apply_mover() : protocols::monte_carlo::GenericSimulatedAnnealer , protocols::rosetta_scripts::ParsedProtocol , protocols::stepwise::screener::SampleApplier , protocols::stepwise::screener::StepWiseScreener
• apply_mover_if_defined() : protocols::moves::CompositionMover
• apply_movers() : protocols::denovo_design::movers::BuildDeNovoBackboneMover
• apply_mpi() : protocols::filters::VectorPoseFilter , protocols::moves::VectorPoseMover , protocols::recon_design::FindConsensusSequence , protocols::recon_design::FitnessFilter , protocols::recon_design::MSDMover
• apply_multi() : protocols::electron_density::DockIntoDensityMover
• apply_multi_sequence() : protocols::pdbinfo_manipulations::AlignPDBInfoToSequences
• apply_no_remarks() : protocols::fold_from_loops::movers::LabelPoseFromResidueSelectorMover
• apply_nucleoside_torsion() : protocols::stepwise::monte_carlo::rna::RNA_TorsionMover
• apply_nucleoside_torsion_Aform() : protocols::stepwise::monte_carlo::rna::RNA_TorsionMover
• apply_offset_ : core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup
• apply_on_pose() : protocols::normalmode::NormalModeRelaxMover
• apply_or_to_subset() : core::select::jump_selector::OrJumpSelector , core::select::residue_selector::OrResidueSelector
• apply_parsed_protocol_mpi() : protocols::jd2::VectorPoseJobDistributor
• apply_parsed_protocol_serial() : protocols::jd2::VectorPoseJobDistributor
• apply_patch() : core::chemical::ResidueTypeSet
• apply_patch_from_file() : core::scoring::ScoreFunction
• apply_patches_recursively() : core::chemical::ResidueTypeFinder
• apply_peptide_plane_variants() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• apply_peptide_plane_variants_OLD() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• apply_perturb_backbone_by_bins() : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• apply_perturb_dihedral_bbg() : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• apply_perturbations() : protocols::generalized_kinematic_closure::GeneralizedKIC
• apply_pose_is_mutant_ : protocols::features::InterfaceDdGMover
• apply_preferences_and_discouragements() : core::chemical::ResidueTypeFinder
• apply_probability() : protocols::rosetta_scripts::ParsedProtocol
• apply_probability_ : protocols::rosetta_scripts::ParsedProtocol
• apply_profile() : protocols::indexed_structure_store::movers::SegmentSequenceProfileMover
• apply_profile_ : protocols::indexed_structure_store::movers::SegmentSequenceProfileMover
• apply_protein_patches() : protocols::mainchain_potential::GenerateMainchainPotential
• apply_pucker() : core::pose::rna::RNA_IdealCoord
• apply_rama_prepro_check() : protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter
• apply_random() : protocols::loophash::LoopHashLibrary
• apply_random_fragment() : core::fragment::rna::FullAtomRNA_Fragments , core::fragment::rna::RNA_Fragments , protocols::rna::denovo::coarse::CoarseRNA_Fragments
• apply_random_nucleoside_torsion() : protocols::stepwise::monte_carlo::rna::RNA_TorsionMover
• apply_random_selector() : protocols::generalized_kinematic_closure::selector::GeneralizedKICselector
• apply_random_suite_torsion() : protocols::stepwise::monte_carlo::rna::RNA_TorsionMover
• apply_randomize_alpha_backbone_by_rama() : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• apply_randomize_backbone_by_bins() : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• apply_randomize_backbone_by_rama_prepro() : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• apply_ranked_fragment() : protocols::enzdes::EnzdesFlexibleRegion
• apply_remarks() : protocols::fold_from_loops::movers::LabelPoseFromResidueSelectorMover
• apply_repeat() : protocols::legacy_sewing::LegacyAssemblyConstraintsMover
• apply_residue() : protocols::ligand_docking::RandomConformers
• apply_residue_alternative_sampler_ : protocols::stepwise::screener::SampleApplier
• apply_rigid_body_moves() : protocols::ligand_docking::HighResDocker
• apply_rigid_body_only() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives
• apply_rotation_offset_to_pose_() : protocols::pockets::PlaidFingerprint
• apply_sample_cis_peptide_bond() : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• apply_selector() : protocols::fold_from_loops::utils::Nub
• apply_selector_as_ranges() : protocols::fold_from_loops::utils::Nub
• apply_selector_to_native_ : core::simple_metrics::metrics::SequenceSimilarityMetric
• apply_self_energies_ : protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover , protocols::protein_interface_design::movers::SetupHotspotConstraintsMover
• apply_sequence_mapping() : core::kinematics::FoldTree
• apply_set_backbone_bin() : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• apply_set_bondangle() : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• apply_set_bondlength() : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• apply_set_dihedral() : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• apply_sheets() : protocols::loop_grower::LoopPartialSolution
• apply_single_sequence() : protocols::pdbinfo_manipulations::AlignPDBInfoToSequences
• apply_solutions() : protocols::rna::denovo::coarse::CoarseRNA_LoopCloser , protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser
• apply_ss() : core::fragment::DownJumpSRFD , core::fragment::FragData , core::fragment::FragID , core::fragment::Frame , core::fragment::SecstructSRFD , core::fragment::SingleResidueFragData , core::fragment::UpJumpSRFD
• apply_suite_torsion() : protocols::stepwise::monte_carlo::rna::RNA_TorsionMover
• apply_suite_torsion_Aform() : protocols::stepwise::monte_carlo::rna::RNA_TorsionMover
• apply_terminus_variants_at_protein_rna_boundaries() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• apply_to() : protocols::jumping::JumpSample
• apply_to_cdr() : protocols::antibody::AntibodyCDRGrafter , protocols::antibody::design::AntibodyDesignMover
• apply_to_centroid_ : protocols::abinitio::ResolutionSwitcher
• apply_to_pose() : protocols::backbone_moves::local_backbone_mover::FreePeptide , protocols::backbone_moves::local_backbone_mover::Residue , protocols::loophash::BackboneSegment
• apply_to_res() : protocols::carbohydrates::GlycanSampler
• apply_to_rotpack() : protocols::minimization_packing::PackRotamersMoverLazy
• apply_transform() : protocols::electron_density::DockIntoDensityMover , protocols::hybridization::CartesianSampler
• apply_transform_downstream() : core::conformation::Residue
• apply_transform_Rx_plus_v() : core::conformation::Conformation , core::conformation::Residue , core::conformation::symmetry::SymmetricConformation , core::pose::Pose
• apply_transformation() : core::conformation::symmetry::SymmetricConformation , protocols::simple_filters::RepeatParameterFilter
• apply_transformation_norecompute() : core::conformation::symmetry::SymmetricConformation
• apply_user_defined_reweighting_() : core::scoring::ScoreFunctionFactory
• apply_vdw_cut_ : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• apply_virtual_phosphate_variants() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• apply_virtual_res_variant() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• apply_virtual_res_variant_at_dinucleotide_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• apply_without_merge() : protocols::fold_from_loops::movers::SplitAndMixPoseMover
• applyANNTransformation() : protocols::sparta::ANN
• applyForces_BeeMan() : protocols::cartesian::MolecularDynamics
• applyForces_ConjugateGradient() : protocols::cartesian::MolecularDynamics
• applyForces_LangevinIntegration() : protocols::cartesian::MolecularDynamics
• ApplyRandomStoredRBConf() : protocols::enzdes::ApplyRandomStoredRBConf
• applyRotation() : protocols::rbsegment_relax::RBSegmentMover
• applySpin() : protocols::rbsegment_relax::RBSegmentMover
• applyTransformation() : protocols::rbsegment_relax::RBSegmentMover
• applyTranslation() : protocols::rbsegment_relax::RBSegmentMover
• applyVecAverage() : protocols::sparta::ANN
• applyVecNormalization() : protocols::sparta::ANN
• approved() : protocols::topology_broker::claims::DofClaim
• approved_ : protocols::topology_broker::claims::DofClaim
• approximate_buried_unsat_penalty_assume_const_backbone() : core::scoring::methods::EnergyMethodOptions
• approximate_buried_unsat_penalty_assume_const_backbone_ : core::scoring::methods::EnergyMethodOptions
• approximate_buried_unsat_penalty_burial_atomic_depth() : core::scoring::methods::EnergyMethodOptions
• approximate_buried_unsat_penalty_burial_atomic_depth_ : core::scoring::methods::EnergyMethodOptions
• approximate_buried_unsat_penalty_burial_probe_radius() : core::scoring::methods::EnergyMethodOptions
• approximate_buried_unsat_penalty_burial_probe_radius_ : core::scoring::methods::EnergyMethodOptions
• approximate_buried_unsat_penalty_burial_resolution() : core::scoring::methods::EnergyMethodOptions
• approximate_buried_unsat_penalty_burial_resolution_ : core::scoring::methods::EnergyMethodOptions
• approximate_buried_unsat_penalty_hbond_bonus_cross_chain() : core::scoring::methods::EnergyMethodOptions
• approximate_buried_unsat_penalty_hbond_bonus_cross_chain_ : core::scoring::methods::EnergyMethodOptions
• approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb() : core::scoring::methods::EnergyMethodOptions
• approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_ : core::scoring::methods::EnergyMethodOptions
• approximate_buried_unsat_penalty_hbond_energy_threshold() : core::scoring::methods::EnergyMethodOptions
• approximate_buried_unsat_penalty_hbond_energy_threshold_ : core::scoring::methods::EnergyMethodOptions
• approximate_buried_unsat_penalty_natural_corrections1() : core::scoring::methods::EnergyMethodOptions
• approximate_buried_unsat_penalty_natural_corrections1_ : core::scoring::methods::EnergyMethodOptions
• approximate_buried_unsat_penalty_oversat_penalty() : core::scoring::methods::EnergyMethodOptions
• approximate_buried_unsat_penalty_oversat_penalty_ : core::scoring::methods::EnergyMethodOptions
• APPROXIMATE_UNSAT_POSE_INFO : core::pose::datacache::CacheableDataType
• approximate_vdw_radii_ : core::scoring::AtomVDW
• approximate_vdw_radius() : core::scoring::AtomVDW
• ApproximateBuriedUnsatPenalty() : core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty
• AqueousPoreFinder() : protocols::membrane::AqueousPoreFinder
• AqueousPoreParameters() : core::conformation::membrane::AqueousPoreParameters
• aquireNextQueue() : protocols::viewer::triangleIterator
• aramid_backbones_are_compatible() : core::pack::palette::PackerPalette
• ARBITRARY_FLOAT_DATA : core::pose::datacache::CacheableDataType
• ARBITRARY_STRING_DATA : core::pose::datacache::CacheableDataType
• arc_ : protocols::jd2::archive::SortPredicate
• arccos_() : protocols::sparta::PDB
• architect() : protocols::denovo_design::movers::BridgeChainsMover , protocols::denovo_design::movers::ExtendChainMover
• architect_ : protocols::denovo_design::components::ConnectionPerturber , protocols::denovo_design::components::HelixPerturber , protocols::denovo_design::movers::BridgeChainsMover , protocols::denovo_design::movers::BuildDeNovoBackboneMover , protocols::denovo_design::movers::ExtendChainMover
• architect_group_name() : protocols::denovo_design::architects::DeNovoArchitectFactory
• architect_name() : protocols::denovo_design::architects::DeNovoMotifArchitect , protocols::denovo_design::architects::PoseArchitect
• ArchitectCreatorMap : protocols::denovo_design::architects::DeNovoArchitectFactory
• architects_ : protocols::denovo_design::architects::CompoundArchitect
• archive_rank() : protocols::jd2::archive::MPIArchiveJobDistributor
• archive_rank_ : protocols::jd2::archive::ArchiveManager , protocols::jd2::archive::MPIArchiveJobDistributor
• ArchiveBase() : protocols::jd2::archive::ArchiveBase
• archived_starting_task_ : protocols::forge::remodel::RemodelDesignMover
• ArchiveManager() : protocols::jd2::archive::ArchiveManager
• arcs_ : core::scoring::packstat::trace
• are_aa_pres() : protocols::constel::PresenceCommon
• are_atoms_pres() : protocols::constel::PresenceCommon
• are_colliding() : protocols::match::downstream::DownstreamAlgorithm
• are_normally_bonded() : core::scoring::bin_transitions::BinTransitionCalculator
• are_they_neighbors() : core::scoring::ScoreFunction
• are_torsions_allowed() : protocols::simple_moves::BackboneMover
• area : core::scoring::packstat::CavityBall , core::scoring::packstat::LR_AtomData , core::scoring::packstat::LR_MP_AtomData , core::scoring::sc::_DOT , core::scoring::sc::_RESULTS
• area_cav_ball_required_exposed : core::scoring::packstat::SasaOptions
• AreaAccumulator() : core::scoring::packstat::AreaAccumulator
• AreConnectablePredicate() : protocols::denovo_design::connection::AreConnectablePredicate
• arg_cation_pi_his_can_be_pi() : core::scoring::methods::EnergyMethodOptions
• arg_cation_pi_his_can_be_pi_ : core::scoring::methods::EnergyMethodOptions
• arg_sweep_cutoff_ : protocols::enzdes::DetectProteinLigandInterface
• arg_sweep_interface_ : protocols::enzdes::DetectProteinLigandInterface
• argc_ : protocols::rpc::BasicCmdLineInit
• ArgCationPiEnergy() : core::scoring::methods::ArgCationPiEnergy
• ArgIndices : protocols::pack_daemon::VectorFunction2 , protocols::pack_daemon::VectorFunction
• argstring_ : core::pack::task::TARGET
• argv_ : protocols::rpc::BasicCmdLineInit
• ArithmeticASTExpression : protocols::pack_daemon::IterativeVectorExpression
• ArithmeticASTExpressionOP : protocols::pack_daemon::DynamicAggregateFunction , protocols::pack_daemon::EntityFunc
• Armijo() : core::optimization::ArmijoLineMinimization
• armijo_max_step_limit() : core::optimization::MinimizerOptions
• armijo_max_step_limit_ : core::optimization::MinimizerOptions
• ArmijoLineMinimization() : core::optimization::ArmijoLineMinimization
• aro_specified_ : core::pack::task::EX
• aroC_scale_factor_ : core::scoring::carbon_hbonds::CarbonHBondPotential
• aroma_ : core::chemical::Bond
• aromatic_ : core::pack::task::operation::ResidueTypeFilter
• aromatic_dG_fraction : protocols::analysis::InterfaceData
• aromatic_dSASA_fraction : protocols::analysis::InterfaceData
• aromatic_motifs() : protocols::motifs::MotifDnaPacker
• aromatic_motifs_ : protocols::motifs::MotifDnaPacker
• aromatic_nres : protocols::analysis::InterfaceData
• AromaticAtomFilter() : core::chemical::AromaticAtomFilter
• AromaticBackboneRestraintEnergy() : core::scoring::methods::AromaticBackboneRestraintEnergy
• aromaticity() : core::chemical::Bond
• around_shell_ : protocols::simple_filters::EnergyPerResidueFilter
• array : core::scoring::APBSConfig::I_PARAM , core::scoring::APBSConfig::R_PARAM
• Array1aa : protocols::indexed_structure_store::SegmentSequenceProfileResult
• Array2D() : core::scoring::packstat::Array2D
• array_ : core::scoring::EnergyEdge , core::scoring::packstat::Array2D
• array_pool() : core::scoring::EnergyGraph
• array_to_farray() : protocols::canonical_sampling::mc_convergence_checks::DataBuffer
• ArrayXaa : protocols::indexed_structure_store::SegmentSequenceProfileResult
• asked_for_feedback_ : protocols::mpi_refinement::MPI_Refine_Master
• aspartimide_penalty_value() : core::scoring::methods::EnergyMethodOptions
• aspartimide_penalty_value_ : core::scoring::methods::AspartimidePenaltyEnergy , core::scoring::methods::EnergyMethodOptions
• AspartimidePenaltyEnergy() : core::scoring::methods::AspartimidePenaltyEnergy
• assemble_datamatrix() : core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl
• assemble_enzdes_fragdata() : protocols::enzdes::EnzdesFlexibleRegion
• assemble_missing_chain() : protocols::pose_length_moves::ConnectChainsMover
• assemble_next_best_loop_combination() : protocols::enzdes::EnzdesFlexBBProtocol
• assemble_outtag() : protocols::match::output::PDBWriter
• assemble_remark_lines() : protocols::match::output::PDBWriter
• AssembleLinkerMover() : protocols::domain_assembly::AssembleLinkerMover
• Assembly() : protocols::legacy_sewing::Assembly
• assembly_begin() : protocols::legacy_sewing::Assembly
• assembly_end() : protocols::legacy_sewing::Assembly
• assembly_meets_requirements() : protocols::sewing::movers::AssemblyMover
• assembly_mover_subtag_ct_namer() : protocols::sewing::movers::AssemblyMover
• assembly_requirement_ct_namer() : protocols::sewing::requirements::AssemblyRequirementFactory
• assembly_requirement_group_name() : protocols::sewing::requirements::AssemblyRequirementFactory
• assembly_scorefxn_ : protocols::legacy_sewing::LegacyAssemblyMover
• assembly_scorer_ct_namer() : protocols::sewing::scoring::AssemblyScorerFactory
• assembly_scorer_group_name() : protocols::sewing::scoring::AssemblyScorerFactory
• assembly_scorer_types_ : protocols::sewing::scoring::AssemblyScorerFactory
• assembly_scorers_ : protocols::sewing::movers::AssemblyMover
• AssemblyMover() : protocols::sewing::movers::AssemblyMover
• AssemblyRequirement() : protocols::sewing::requirements::AssemblyRequirement
• AssemblyRequirementCreator() : protocols::sewing::requirements::AssemblyRequirementCreator
• AssemblyRequirementCreatorMap : protocols::sewing::requirements::AssemblyRequirementFactory
• AssemblyRequirementFactory() : protocols::sewing::requirements::AssemblyRequirementFactory
• AssemblyRequirementRegistrator() : protocols::sewing::requirements::AssemblyRequirementRegistrator< T >
• AssemblyScorer() : protocols::sewing::scoring::AssemblyScorer
• AssemblyScorerCreator() : protocols::sewing::scoring::AssemblyScorerCreator
• AssemblyScorerCreatorMap : protocols::sewing::scoring::AssemblyScorerFactory
• AssemblyScorerFactory() : protocols::sewing::scoring::AssemblyScorerFactory
• AssemblyScorerRegistrator() : protocols::sewing::scoring::AssemblyScorerRegistrator< T >
• assert_calculators() : protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator , protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator
• assert_is_calc_chem_shift_atom() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• assert_jump_point_in_fixed_res_ : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• assign() : core::pose::rna::RNA_SuiteName , core::scoring::DockingScoreFunction , core::scoring::MinScoreScoreFunction , core::scoring::ScoreFunction , protocols::mean_field::jagged_array< T, A > , protocols::moves::FilterReporterMover , protocols::noesy_assign::NoesyModule , protocols::peptide_deriver::PeptideDeriverFilter , protocols::toolbox::GreedyKCenter , protocols::toolbox::KCluster , protocols::toolbox::KMedoid
• assign_all_amoeba_types() : core::scoring::MultipoleElecPotential , core::scoring::VdWTinkerPotential
• assign_atom() : protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator
• assign_best_rotamer() : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• assign_BMEC() : core::pack::interaction_graph::FASTERInteractionGraph
• assign_chain_ids() : protocols::cyclic_peptide::PeptideStubMover
• assign_chi_for_interpolated_rotamer() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >
• assign_conformer_group_to_residue() : protocols::match::downstream::LigandConformerBuilder
• assign_CSPs() : protocols::ub_e2c::ubi_e2c_modeler
• assign_disulfides() : protocols::fold_from_loops::utils::Nub
• assign_dofs_to_mobile_residues() : core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::SCMinMinimizerMap
• assign_downstream_position_group_for_match() : protocols::match::output::SameSequenceAndDSPositionGrouper
• assign_energy() : core::pack::scmin::SidechainStateAssignment
• assign_entity_sequence_to_variables() : protocols::pack_daemon::EntityFunc
• assign_esp_for_atom_grid_points() : protocols::pockets::ElectrostaticpotentialGrid
• assign_esp_for_protein_grid_points() : protocols::pockets::ElectrostaticpotentialGrid
• assign_esp_for_surface_grid_points() : protocols::pockets::ElectrostaticpotentialGrid
• assign_esp_for_surface_grid_points_by_nn() : protocols::pockets::ElectrostaticpotentialGrid
• assign_exemplars() : protocols::cluster::APCluster
• assign_fragprobs() : protocols::hybridization::FragmentBiasAssigner
• assign_from_res_to_res() : protocols::splice::SpliceIn , protocols::splice::SpliceInAntibody , protocols::splice::SpliceInTail , protocols::splice::SpliceOutAntibody
• assign_group_for_match() : protocols::match::output::MatchGrouper , protocols::match::output::SameChiBinComboGrouper , protocols::match::output::SameRotamerComboGrouper , protocols::match::output::SameSequenceAndDSPositionGrouper , protocols::match::output::SameSequenceGrouper
• assign_haro_derivs_one_way() : core::scoring::orbitals::OrbitalsScore
• assign_hpol_derivs_one_way() : core::scoring::orbitals::OrbitalsScore
• assign_incomplete_ : protocols::loop_grower::FragmentExtension , protocols::loop_grower::LoopComparator
• assign_internal_coordinates() : core::chemical::MutableResidueType
• assign_jobs_to_local_daemon_set() : protocols::pack_daemon::DynamicAggregateFunctionDriver
• assign_jobs_to_remote_daemon_sets() : protocols::pack_daemon::DynamicAggregateFunctionDriver
• assign_labelled_spin() : protocols::noesy_assign::CrossPeak3D
• assign_last_rotamers_to_pose() : protocols::pack_daemon::PackDaemon
• assign_ligand_trans() : protocols::ligand_docking::ga_ligand_dock::LigandConformer
• assign_loop_info() : protocols::mpi_refinement::MPI_Refine_Master
• assign_neighbor_atom() : core::chemical::MutableResidueType
• assign_neighbors() : protocols::loop_grower::DensSkeleton
• assign_new_cluster_tag : protocols::toolbox::ClusterOptions
• assign_non_CSPs() : protocols::ub_e2c::ubi_e2c_modeler
• assign_only_pi_orbitals_to_atom() : core::chemical::orbitals::AssignOrbitals
• assign_orb_H_derivs() : core::scoring::orbitals::OrbitalsScore
• assign_orb_orb_derivs() : core::scoring::orbitals::OrbitalsScore
• assign_orbitals() : core::chemical::orbitals::AssignOrbitals , core::conformation::Residue
• assign_output_index() : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::standard::StandardJobQueen , protocols::multistage_rosetta_scripts::MRSJobQueen
• assign_parameters_to_full_etables() : core::scoring::etable::Etable
• assign_passport() : protocols::environment::Environment
• assign_passports() : protocols::environment::EnvClaimBroker
• assign_phi_psi_omega_from_lookback() : protocols::pose_length_moves::PossibleLoop
• assign_prob_with_rsd_wdw() : protocols::hybridization::FragmentBiasAssigner
• assign_random_chi() : core::pack::dunbrack::DunbrackRotamerSampleData
• assign_random_rotamer() : core::pack::dunbrack::cenrot::CentroidRotamerSampleData , core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >
• assign_random_rotamer_with_bias() : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary , core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N > , core::pack::rotamers::SingleBasicRotamerLibrary , core::pack::rotamers::SingleLigandRotamerLibrary , core::pack::rotamers::SingleResidueRotamerLibrary
• assign_random_rotamer_with_bias_bbdep() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >
• assign_residue_amoeba_type() : core::scoring::MultipoleElecPotential , core::scoring::VdWTinkerPotential
• assign_rosetta_torsions() : core::optimization::MinimizerMap , core::optimization::symmetry::SymMinimizerMap
• assign_rosetta_torsions_and_trim() : core::optimization::CartesianMinimizerMap
• assign_seq() : protocols::pose_creation::MakeJunctionsMover , protocols::pose_creation::MergePDBatOverlapMover
• assign_sp2_orbitals_to_one_bonded_atom() : core::chemical::orbitals::AssignOrbitals
• assign_sp2_sp_orbitals_to_one_bonded_atom() : core::chemical::orbitals::AssignOrbitals
• assign_spin() : protocols::noesy_assign::CrossPeak3D , protocols::noesy_assign::CrossPeak4D , protocols::noesy_assign::CrossPeak
• assign_state() : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode , core::pack::scmin::SidechainStateAssignment , protocols::flexpack::interaction_graph::MinimalistFlexbbNode
• assign_state_energies_to_variables_and_subexpressions() : protocols::pack_daemon::DynamicAggregateFunction
• assign_state_surface() : core::pack::interaction_graph::SurfaceNode< V, E, G >
• assign_state_to_all_nodes_immediately_ : core::pack::annealer::RotamerAssigningAnnealer
• assign_type_data() : protocols::toolbox::KClusterElement
• assign_zero_state() : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::NodeBase , core::pack::interaction_graph::NPDHBondNode< V, E, G > , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode , protocols::flexpack::interaction_graph::MinimalistFlexbbNode
• AssignAtomRadius() : core::scoring::sc::MolecularSurfaceCalculator
• AssignAttentionNumbers() : core::scoring::sc::ContactMolecularSurfaceCalculator , core::scoring::sc::MolecularSurfaceCalculator , core::scoring::sc::ShapeComplementarityCalculator
• assigned() : protocols::noesy_assign::CrossPeak
• assigned_num_ : protocols::loophash::LoopHashLibrary
• assigned_string_ : protocols::loophash::LoopHashLibrary
• assignment() : core::scoring::hbonds::HBDerivAssigner , protocols::noesy_assign::CrossPeak::Spin
• assignment_ : protocols::noesy_assign::EXCN_AssignmentNotFound
• assignment_index() : protocols::noesy_assign::CrossPeak::Spin
• assignments() : protocols::noesy_assign::CrossPeak , protocols::noesy_assign::CrossPeakList , protocols::noesy_assign::PeakAssignmentResidueMap
• assignments_ : protocols::noesy_assign::CrossPeak , protocols::noesy_assign::CrossPeak::Spin , protocols::noesy_assign::CrossPeakList
• AssignmentScaleAndDerivVectID() : core::scoring::hbonds::AssignmentScaleAndDerivVectID
• AssignOrbitals() : core::chemical::orbitals::AssignOrbitals
• AssignToClustersMover() : protocols::cluster::AssignToClustersMover
• assume_atom_ids_invariant_ : protocols::stepwise::modeler::align::StepWiseClusterer
• assume_const_backbone_ : core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty
• assume_non_stem_is_loop : protocols::rna::denovo::RNA_DeNovoPoseInitializer
• astr : core::pack::dunbrack::DunbrackAAParameterSet
• astype1_ : protocols::simple_filters::AtomicDistanceFilter
• astype2_ : protocols::simple_filters::AtomicDistanceFilter
• asym_eval_long_range_twobody_energies() : core::scoring::ScoreFunction
• asym_eval_onebody_energies() : core::scoring::ScoreFunction
• asym_eval_twobody_neighbor_energies() : core::scoring::ScoreFunction
• asym_setup_for_derivatives() : core::scoring::ScoreFunction
• asym_setup_for_minimizing() : core::scoring::ScoreFunction
• AsymFoldandDockClaimer() : protocols::topology_broker::AsymFoldandDockClaimer
• AsymFoldandDockMoveRbJumpMover() : protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockMoveRbJumpMover
• AsymFoldandDockRbTrialMover() : protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockRbTrialMover
• asymm_only_ : protocols::electron_density::ReportFSC , protocols::electron_density::ScaleMapIntensities
• asymm_residues : protocols::hbnet::HBondNetStruct
• asymm_score_ : protocols::pose_creation::MergePDBMover
• asymmdump_ : protocols::loop_grower::FragmentExtension , protocols::loop_grower::LoopGrower , protocols::loop_grower::LoopPartialSolutionStore
• asymmetric_apply() : protocols::cyclic_peptide::CrosslinkerMover
• asymmetric_dof() : core::optimization::symmetry::SymMinimizerMap
• asymmetric_res_ : protocols::topology_broker::SymmetryClaimer
• asymmetric_unit() : core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• asymmetric_unit_ : core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• AsymmetricUnitSelector() : core::select::residue_selector::AsymmetricUnitSelector
• AsyncMPITemperingBase() : protocols::canonical_sampling::AsyncMPITemperingBase
• at() : core::scoring::epr_deer::DEERDataCache , core::scoring::epr_deer::EPRSpinLabel , core::sequence::Sequence , protocols::canonical_sampling::BiasEnergy::Histogram< T > , protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering > , protocols::frag_picker::scores::AdaptiveScoreHistogram , protocols::frag_picker::scores::FragmentScoreMap , protocols::frag_picker::VallChunk , protocols::frag_picker::VallProvider
• at1_type_ : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• at2_type_ : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• at3_type_ : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• at_end() : protocols::match::VoxelSetIterator
• at_inds() : protocols::match::downstream::AtomGeometrySecMatchRPE
• at_inds_ : protocols::match::downstream::AtomGeometrySecMatchRPE
• at_least_one_net_fully_satisfied_ : protocols::hbnet::HBNetStapleInterface
• at_least_one_net_spans_all_helices_ : protocols::hbnet::HBNetStapleInterface
• at_least_one_net_w_aromatic_sc_ : protocols::hbnet::HBNetStapleInterface
• at_start_position_ : core::scoring::nmr::NMRGridSearch
• atcs_for_residues_ : core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap
• aterm() : core::scoring::BondOrderParser
• atm : core::scoring::TorsionParams , protocols::ligand_docking::ga_ligand_dock::Pharmacophore
• atm1() : protocols::simple_filters::AngleToVector
• atm1_ : protocols::simple_filters::AngleToVector
• atm2() : protocols::simple_filters::AngleToVector
• atm2_ : protocols::simple_filters::AngleToVector
• atm_ : core::chemical::ResetBondLength
• atm_coords_ : core::io::silent::BinarySilentStruct
• atm_excluded() : core::scoring::ResidueExclParams
• atm_excluded_ : core::scoring::ResidueExclParams
• atmid() : core::scoring::methods::GoapRsdType
• atmid_ : core::scoring::methods::GoapRsdType
• atmids_ : protocols::ligand_docking::ga_ligand_dock::ConstraintInfo
• atmname_using() : core::scoring::methods::GoapRsdType
• atmname_using_ : core::scoring::methods::GoapRsdType
• atmpairnos_ : core::scoring::ResidueExclParams
• atmplt() : protocols::tcr::TCRmodel
• atmplt_ : protocols::tcr::TCRmodel
• atms : core::scoring::elec::ElecGroup , protocols::ligand_docking::ga_ligand_dock::Pharmacophore
• atms_ : protocols::constraints_additional::BindingSiteConstraint , protocols::constraints_additional::COMCoordinateConstraint , protocols::ligand_docking::ga_ligand_dock::Pharmacophore
• Atom() : core::chemical::Atom
• atom() : core::chemical::MutableResidueType
• Atom() : core::conformation::Atom
• atom() : core::conformation::Residue , core::id::EXCN_AtomNotFound , core::id::NamedAtomID , core::id::NamedStubID , core::id::StubID , core::kinematics::AtomTree
• Atom : core::kinematics::AtomTree , core::kinematics::tree::Atom
• atom() : core::pack::dunbrack::DunbrackConstraint , core::pack::dunbrack::RotamerConstraint , core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::SCMinMinimizerMap , core::scoring::aa_composition_energy::SequenceConstraint , core::scoring::constraints::AmbiguousNMRDistanceConstraint , core::scoring::constraints::AngleConstraint , core::scoring::constraints::AtomPairConstraint , core::scoring::constraints::BackboneStubConstraint , core::scoring::constraints::BackboneStubLinearConstraint , core::scoring::constraints::BasePairConstraint , core::scoring::constraints::BigBinConstraint , core::scoring::constraints::ConstantConstraint , core::scoring::constraints::Constraint , core::scoring::constraints::CoordinateConstraint , core::scoring::constraints::DihedralConstraint , core::scoring::constraints::DihedralPairConstraint , core::scoring::constraints::DistancePairConstraint , core::scoring::constraints::LocalCoordinateConstraint , core::scoring::constraints::MembraneSpanConstraint , core::scoring::constraints::MembraneSpanTermZConstraint , core::scoring::constraints::MultiConstraint , core::scoring::constraints::NonResidueTypeConstraint , core::scoring::constraints::ResidueCouplingConstraint , core::scoring::constraints::ResidueTypeConstraint , core::scoring::constraints::ResidueTypeLinkingConstraint , core::scoring::constraints::RTConstraint , core::scoring::constraints::SequenceProfileConstraint , core::scoring::elec::electrie::ElecAtom , core::scoring::lkball::lkbtrie::LKBAtom , core::scoring::packstat::Circle , core::scoring::packstat::SimplePDB
• ATOM : core::scoring::packstat::SimplePDB_Atom
• atom() : core::scoring::PDatom , core::scoring::power_diagram::PDsphere , core::scoring::sc::_ATOM_RADIUS , core::scoring::sc::_DOT , core::scoring::sc::Atom
• Atom() : core::scoring::sc::Atom
• atom() : core::scoring::trie::RotamerDescriptor< AT, CPDAT > , core::scoring::trie::RotamerDescriptorAtom< AT, CPDAT > , core::scoring::trie::TrieNode< AT, CPDATA > , protocols::constraints_additional::BindingSiteConstraint , protocols::constraints_additional::COMCoordinateConstraint , protocols::constraints_additional::SequenceCouplingConstraint
• Atom : protocols::fldsgn::NcontactsCalculator
• atom() : protocols::legacy_sewing::ModelConstIterator< T > , protocols::legacy_sewing::ModelIterator< T > , protocols::ligand_docking::ga_ligand_dock::atmInfo , protocols::noesy_assign::EXCN_UnknownResonance , protocols::noesy_assign::PeakAssignment , protocols::noesy_assign::Resonance , protocols::pockets::PocketConstraint
• atom1() : core::chemical::sdf::MolFileIOBond , core::id::BondID , core::id::NamedStubID , core::id::StubID , core::scoring::constraints::AngleConstraint , core::scoring::constraints::AtomPairConstraint , core::scoring::constraints::Obsolet_NamedAtomPairConstraint , core::scoring::CSA , core::scoring::DC , core::scoring::lkball::WaterBuilder , core::scoring::RDC , protocols::denovo_design::components::BondInfo , protocols::environment::claims::JumpElement
• atom13() : core::scoring::methods::ProQ_Energy
• atom13_0() : core::scoring::methods::ProQ_Energy
• atom1_ : core::chemical::AddBond , core::chemical::AddBondType , core::chemical::AddChi , core::chemical::ChangeBondType , core::chemical::RedefineChi , core::chemical::sdf::MolFileIOBond , core::scoring::constraints::AngleConstraint , core::scoring::constraints::AtomPairConstraint , core::scoring::constraints::DihedralConstraint , core::scoring::constraints::Obsolet_NamedAtomPairConstraint , core::scoring::CSA , core::scoring::DC , core::scoring::lkball::WaterBuilder , core::scoring::RDC , protocols::cyclic_peptide::CreateAngleConstraint , protocols::cyclic_peptide::CreateDistanceConstraint , protocols::cyclic_peptide::CreateTorsionConstraint , protocols::cyclic_peptide::DeclareBond , protocols::cyclic_peptide::PeptideCyclizeMover , protocols::denovo_design::movers::DeclareStructureDataCovalentBondMover , protocols::simple_moves::TorsionDOFMover , protocols::toolbox::match_enzdes_util::EnzCstTemplateRes , protocols::toolbox::match_enzdes_util::EnzCstTemplateResAtoms , protocols::topology_broker::claims::JumpClaim
• atom1_angle2_ : protocols::cyclic_peptide::PeptideCyclizeMover
• atom1_angle_ : protocols::cyclic_peptide::PeptideCyclizeMover
• atom1_atom2_atom3_angle() : protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder , protocols::toolbox::match_enzdes_util::LigandConformer
• atom1_atom2_distance() : protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder , protocols::toolbox::match_enzdes_util::LigandConformer
• atom1_belongs_in_active_site() : protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder
• atom1_derivs() : core::scoring::lkball::LKB_ResidueInfo
• atom1_dist_ : protocols::cyclic_peptide::PeptideCyclizeMover
• atom1_radius() : protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder
• atom1_torsion_ : protocols::cyclic_peptide::PeptideCyclizeMover
• atom2() : core::chemical::sdf::MolFileIOBond , core::id::BondID , core::id::NamedStubID , core::id::StubID , core::scoring::constraints::AngleConstraint , core::scoring::constraints::AtomPairConstraint , core::scoring::constraints::Obsolet_NamedAtomPairConstraint , core::scoring::CSA , core::scoring::DC , core::scoring::lkball::WaterBuilder , core::scoring::RDC , protocols::constraint_generator::HydrogenBondingAtom , protocols::denovo_design::components::BondInfo , protocols::environment::claims::JumpElement
• atom2_ : core::chemical::AddBond , core::chemical::AddBondType , core::chemical::AddChi , core::chemical::ChangeBondType , core::chemical::RedefineChi , core::chemical::sdf::MolFileIOBond , core::scoring::constraints::AngleConstraint , core::scoring::constraints::AtomPairConstraint , core::scoring::constraints::DihedralConstraint , core::scoring::constraints::Obsolet_NamedAtomPairConstraint , core::scoring::CSA , core::scoring::DC , core::scoring::lkball::WaterBuilder , core::scoring::RDC , protocols::constraint_generator::HydrogenBondingAtom , protocols::cyclic_peptide::CreateAngleConstraint , protocols::cyclic_peptide::CreateDistanceConstraint , protocols::cyclic_peptide::CreateTorsionConstraint , protocols::cyclic_peptide::DeclareBond , protocols::cyclic_peptide::PeptideCyclizeMover , protocols::denovo_design::movers::DeclareStructureDataCovalentBondMover , protocols::simple_moves::TorsionDOFMover , protocols::toolbox::match_enzdes_util::EnzCstTemplateRes , protocols::toolbox::match_enzdes_util::EnzCstTemplateResAtoms , protocols::topology_broker::claims::JumpClaim
• atom2_angle2_ : protocols::cyclic_peptide::PeptideCyclizeMover
• atom2_angle_ : protocols::cyclic_peptide::PeptideCyclizeMover
• atom2_atom3_distance() : protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder , protocols::toolbox::match_enzdes_util::LigandConformer
• atom2_belongs_in_active_site() : protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder
• atom2_derivs() : core::scoring::lkball::LKB_ResidueInfo
• atom2_dist_ : protocols::cyclic_peptide::PeptideCyclizeMover
• atom2_radius() : protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder
• atom2_torsion_ : protocols::cyclic_peptide::PeptideCyclizeMover
• Atom2ANN_MatrixMap : protocols::sparta::Sparta::SpartaLib
• atom2csa_map_ : core::scoring::methods::ChemicalShiftAnisotropyEnergy
• atom2dc_map_ : core::scoring::methods::DipolarCouplingEnergy
• atom2rdc_map_ : core::scoring::methods::ResidualDipolarCouplingEnergy , protocols::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments
• atom3 : core::id::NamedStubID , core::id::StubID , core::scoring::constraints::AngleConstraint , core::scoring::CSA , core::scoring::lkball::WaterBuilder , protocols::constraint_generator::HydrogenBondingAtom
• atom3_ : core::chemical::AddChi , core::chemical::RedefineChi , core::scoring::constraints::AngleConstraint , core::scoring::constraints::DihedralConstraint , core::scoring::CSA , core::scoring::lkball::WaterBuilder , protocols::constraint_generator::HydrogenBondingAtom , protocols::cyclic_peptide::CreateTorsionConstraint , protocols::simple_moves::TorsionDOFMover , protocols::toolbox::match_enzdes_util::EnzCstTemplateRes , protocols::toolbox::match_enzdes_util::EnzCstTemplateResAtoms
• atom3_belongs_in_active_site() : protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder
• atom3_derivs() : core::scoring::lkball::LKB_ResidueInfo
• atom3_radius() : protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder
• atom3_torsion_ : protocols::cyclic_peptide::PeptideCyclizeMover
• atom4_ : core::chemical::AddChi , core::chemical::RedefineChi , core::scoring::constraints::DihedralConstraint , protocols::cyclic_peptide::CreateTorsionConstraint , protocols::simple_moves::TorsionDOFMover
• atom4_torsion_ : protocols::cyclic_peptide::PeptideCyclizeMover
• atom_ : core::chemical::AddConnectAndTrackingVirt , core::chemical::AddConnectDeleteChildProton , core::chemical::ChangeAncestory , core::chemical::DeleteChildProton , core::chemical::ReplaceProtonWithBromine , core::chemical::ReplaceProtonWithChlorine , core::chemical::ReplaceProtonWithEthyl , core::chemical::ReplaceProtonWithFluorine , core::chemical::ReplaceProtonWithHydroxyl , core::chemical::ReplaceProtonWithIodine , core::chemical::ReplaceProtonWithMethoxy , core::chemical::ReplaceProtonWithMethyl , core::chemical::ReplaceProtonWithTrifluoromethyl , core::chemical::SetICoor , core::id::NamedAtomID , core::io::nmr::AtomSelection
• Atom_() : core::kinematics::tree::Atom_
• atom_ : core::scoring::constraints::CoordinateConstraint , core::scoring::constraints::LocalCoordinateConstraint , core::scoring::PDatom , core::scoring::power_diagram::PDsphere , core::scoring::trie::RotamerDescriptorAtom< AT, CPDAT > , core::scoring::trie::TrieNode< AT, CPDATA > , protocols::constraint_generator::HydrogenBondingAtom , protocols::noesy_assign::EXCN_UnknownResonance , protocols::noesy_assign::Resonance
• atom_2_residue_connection_map_ : core::chemical::ResidueType
• atom_alias() : core::chemical::ResidueTypeBase
• atom_aliases() : core::chemical::ResidueTypeBase
• atom_aliases_ : core::chemical::ResidueTypeBase
• atom_atom_context_derivative() : core::scoring::FACTSPotential
• atom_atom_distance : protocols::ligand_docking::rdf::AtomPairData
• atom_atom_overlap_dist_cutoff_ : protocols::stepwise::screener::ResidueContactScreener
• atom_base() : core::chemical::MutableResidueType , core::chemical::ResidueType , core::conformation::Residue
• atom_base_indices_ : core::chemical::ResidueType
• atom_begin() : core::conformation::Residue
• atom_being_shadowed() : core::chemical::ResidueType
• atom_bin_size_ : core::pose::rna::VDW_Grid , protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• atom_bur_unsat_ : protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator
• atom_center2_ : protocols::cyclic_peptide::PeptideCyclizeMover
• atom_center_ : protocols::cyclic_peptide::CreateAngleConstraint , protocols::cyclic_peptide::PeptideCyclizeMover
• atom_charge() : core::chemical::Adduct , core::chemical::ResidueType
• atom_charge_ : core::chemical::Adduct
• atom_controlled_by_any_chi() : protocols::match::upstream::UpstreamResTypeGeometry
• atom_coordinate_unacceptable() : protocols::match::upstream::ProteinUpstreamBuilder
• atom_counts_ : core::pack::interaction_graph::RotamerDots , core::pack::interaction_graph::RotamerDotsCache
• atom_coverage_ : protocols::vardist_solaccess::VarSolDRotamerDots
• atom_data() : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• atom_delta_sasa_ : core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator
• atom_dependent_calibration_ : protocols::noesy_assign::PeakAssignmentParameters
• atom_depends_on_connection() : core::chemical::ResidueType
• atom_depends_on_connection_ : core::chemical::ResidueType
• atom_depends_on_lower() : core::conformation::Residue
• atom_depends_on_lower_polymeric_connection() : core::chemical::ResidueType
• atom_depends_on_lower_polymeric_connection_ : core::chemical::ResidueType
• atom_depends_on_polymeric_connection() : core::chemical::ResidueType
• atom_depends_on_upper() : core::conformation::Residue
• atom_depends_on_upper_polymeric_connection() : core::chemical::ResidueType
• atom_depends_on_upper_polymeric_connection_ : core::chemical::ResidueType
• atom_derivatives() : core::optimization::CartesianMinimizerMap , core::optimization::MinimizerMap , core::optimization::symmetry::SymMinimizerMap , core::pack::scmin::SCMinMinimizerMap
• atom_derivatives_ : core::optimization::CartesianMinimizerMap , core::optimization::MinimizerMap , core::optimization::symmetry::SymMinimizerMap , core::pack::scmin::SCMinMinimizerMap , core::scoring::nmr::pcs::PCSSingle , core::scoring::nmr::pre::PRESingle , core::scoring::nmr::rdc::RDCSingle
• atom_dont_do_update() : core::kinematics::AtomTree
• atom_end() : core::conformation::Residue
• atom_equiv_ : protocols::comparative_modeling::ThreadingMover
• atom_f1_f2s_ : core::scoring::methods::LK_hack
• atom_feature() : core::scoring::methods::ProQ_Energy
• atom_ff_types_ : core::scoring::saxs::SAXSEnergy
• atom_flags_ : protocols::frag_picker::scores::AtomBasedConstraintsScore
• atom_forms_residue_connection() : core::chemical::ResidueType
• atom_gaussian_value : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• atom_geom_rpes() : protocols::match::downstream::GeometrySecMatchRPE
• atom_geom_rpes_ : protocols::match::downstream::GeometrySecMatchRPE
• atom_gets_derivatives() : core::scoring::disulfides::DisulfideAtomIndices
• atom_gradient() : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• atom_has_exp_chemical_shift_data() : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• atom_has_nonchi_coordinate() : protocols::match::upstream::UpstreamResTypeGeometry
• atom_has_orbital() : core::chemical::AtomType
• atom_has_orbitals_ : core::chemical::AtomType
• atom_has_property() : core::chemical::ResidueType
• atom_hbond_energies_ : core::scoring::hbonds::NPDHBondSet
• atom_hbond_sfxn_wtd_energies_ : core::scoring::hbonds::NPDHBondSet
• atom_hbond_weights_ : core::scoring::hbonds::NPDHBondSet
• atom_hbonds() : core::scoring::hbonds::HBondSet
• atom_Hbonds_ : protocols::simple_pose_metric_calculators::NumberHBondsCalculator
• atom_hbonds_all() : core::scoring::hbonds::HBondSet
• atom_hbonds_to_bridging_water() : protocols::hbnet::HBNet
• atom_hydrophobic_ : protocols::fldsgn::MyAtom
• atom_id() : core::chemical::ICoorAtomID , core::id::DOF_ID , core::kinematics::tree::Atom , core::kinematics::tree::Atom_ , core::optimization::DOF_Node , protocols::cartesian::CartesianAtom
• atom_id_ : core::id::DOF_ID , core::kinematics::tree::Atom_ , protocols::seeded_abinitio::CoordinateCst
• atom_id_1 : protocols::cartesian::MD_Angle , protocols::cartesian::MD_Bond , protocols::cartesian::MD_HarmonicDihedral
• atom_id_2 : protocols::cartesian::MD_Angle , protocols::cartesian::MD_Bond , protocols::cartesian::MD_HarmonicDihedral
• atom_id_3 : protocols::cartesian::MD_Angle , protocols::cartesian::MD_HarmonicDihedral
• atom_id_4 : protocols::cartesian::MD_HarmonicDihedral
• atom_id_domain_map_ : core::pose::copydofs::CopyDofs
• atom_id_map_ : core::kinematics::MoveMap , core::pose::copydofs::CopyDofs
• atom_id_mapper() : core::pose::toolbox::AtomLevelDomainMap
• atom_id_mapper_ : core::pose::toolbox::AtomLevelDomainMap
• atom_id_mapper_to_vanilla_chunk_pose_ : core::import_pose::libraries::ChunkSet
• atom_id_mask_ : core::import_pose::libraries::ChunkSet
• atom_id_to_pcs_xyz_deriv_map_ : protocols::nmr::pcs::PCSEnergy
• atom_id_to_pre_xyz_deriv_map_ : protocols::nmr::pre::PREEnergy
• atom_id_to_rdc_xyz_deriv_map_ : protocols::nmr::rdc::RDCEnergy
• atom_ids_ : core::conformation::UltraLightResidue , core::pack::dunbrack::DunbrackConstraint , core::pack::dunbrack::RotamerConstraint , core::scoring::constraints::BackboneStubConstraint , core::scoring::constraints::BackboneStubLinearConstraint , protocols::pockets::PocketConstraint , protocols::rna::denovo::coarse::CoarseRNA_LoopCloser , protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser , protocols::stepwise::sampler::rna::RNA_KinematicCloser
• atom_ids_for_coordinates_ : protocols::match::downstream::TargetRotamerCoords
• atom_ids_in_res() : core::pose::toolbox::AtomID_Mapper
• atom_ids_in_res_ : core::pose::toolbox::AtomID_Mapper
• atom_index() : core::chemical::MutableResidueType , core::chemical::ResidueType , core::chemical::sdf::MolFileIOMolecule , core::conformation::Residue
• atom_index_ : core::scoring::custom_pair_distance::resatom_and_func_struct
• atom_index_to_relevant_atom_index_ : protocols::features::AtomAtomPairFeatures
• atom_indices_ : core::io::pose_to_sfr::PoseToStructFileRepConverter , core::optimization::CartesianMinimizerMap , protocols::electron_density::BfactorMultifunc
• atom_indices_initialized_ : core::io::pose_to_sfr::PoseToStructFileRepConverter
• atom_inds_for_restype() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• atom_inds_for_restype_ : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• atom_inds_for_restype_begin() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• atom_inds_for_restype_end() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• atom_is_acceptor() : core::scoring::geometric_solvation::OccludedHbondSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody , core::scoring::hbonds::HBond
• atom_is_aro_hydrogen() : core::chemical::ResidueType
• atom_is_backbone() : core::chemical::ResidueType , core::conformation::Residue
• atom_is_backbone_norefold() : core::conformation::Conformation
• atom_is_chitip() : protocols::match::upstream::UpstreamResTypeGeometry
• atom_is_donor_h() : core::scoring::geometric_solvation::OccludedHbondSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody
• atom_is_donorH() : core::scoring::hbonds::HBond
• atom_is_heavy() : core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• atom_is_hydrogen() : core::chemical::ResidueType , core::conformation::Residue
• atom_is_ideal() : protocols::minimization_packing::MinimalRotamer
• atom_is_independent() : core::conformation::symmetry::SymmetryInfo
• atom_is_on_path_from_root() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• atom_is_phosphate() : core::chemical::rna::RNA_Info
• atom_is_polar_hydrogen() : core::chemical::ResidueType , core::conformation::Residue
• atom_is_repulsive_ : core::chemical::AtomType
• atom_is_sidechain() : core::chemical::ResidueType
• atom_is_valid_base() : core::scoring::geometric_solvation::OccludedHbondSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody
• atom_is_virtual() : core::chemical::rna::RNA_Info
• atom_is_virtual_ : core::chemical::AtomType
• atom_it_ : protocols::legacy_sewing::ModelConstIterator< T > , protocols::legacy_sewing::ModelIterator< T >
• atom_iterators() : core::chemical::MutableResidueType
• atom_level_domain_map() : core::import_pose::libraries::RNA_ChunkLibrary , core::import_pose::RNA_JumpMover , protocols::rna::denovo::coarse::CoarseRNA_LoopCloser , protocols::rna::denovo::RNA_FragmentMonteCarlo
• atom_level_domain_map_ : core::import_pose::libraries::RNA_ChunkLibrary , core::import_pose::RNA_JumpMover , protocols::rna::denovo::coarse::CoarseRNA_LoopCloser , protocols::rna::denovo::movers::RNA_FragmentMover , protocols::rna::denovo::movers::RNA_Minimizer , protocols::rna::denovo::RNA_FragmentMonteCarlo , protocols::rna::movers::RNA_LoopCloser , protocols::simple_moves::ConstrainToIdealMover , protocols::stepwise::modeler::StepWiseMinimizer
• atom_level_domain_map_input_ : protocols::rna::denovo::movers::RNA_Minimizer
• atom_limit_ : protocols::ligand_docking::AtomCountFilter
• atom_map_ : core::scoring::hbonds::HBondSet , core::scoring::packstat::MultiProbePerSphereAccumulator , core::scoring::packstat::MultiProbePoseAccumulator , core::scoring::packstat::PerSphereAccumulator , protocols::hybridization::InsertChunkMover , protocols::qsar::qsarMap
• atom_map_from_score_result() : protocols::legacy_sewing::Assembly
• atom_map_init_ : core::scoring::hbonds::HBondSet
• ATOM_MASK : core::scoring::electron_density::ElectronDensity
• ATOM_MASK_PADDING : core::scoring::electron_density::ElectronDensity
• atom_mode() : protocols::simple_filters::BuriedSurfaceAreaFilter
• atom_mode_ : protocols::simple_filters::BuriedSurfaceAreaFilter
• atom_name() : core::chemical::Adduct , core::chemical::MutableResidueType , core::chemical::ResidueType , core::conformation::AtomGraphVertexData , core::conformation::Residue , core::pose::MiniPose , core::pose::UnrecognizedAtomRecord , core::scoring::nmr::VoxelGridPoint , core::scoring::packing::PoseBalls , core::scoring::rna::chemical_shift::ChemicalShiftData , protocols::nmr::pcs::AtomGridPoint , protocols::scoring::methods::pcs::PCS_line_data , protocols::scoring::methods::pcsTs1::PCS_line_data_Ts1 , protocols::scoring::methods::pcsTs2::PCS_line_data_Ts2 , protocols::scoring::methods::pcsTs3::PCS_line_data_Ts3 , protocols::scoring::methods::pcsTs4::PCS_line_data_Ts4
• atom_name1() : core::import_pose::libraries::RNA_PairingTemplate
• atom_name1_ : core::import_pose::libraries::RNA_PairingTemplate , protocols::constraint_generator::DistanceConstraintGenerator
• atom_name2() : core::import_pose::libraries::RNA_PairingTemplate
• atom_name2_ : core::import_pose::libraries::RNA_PairingTemplate , protocols::constraint_generator::DistanceConstraintGenerator
• atom_name_ : core::chemical::AddAtom , core::chemical::Adduct , core::chemical::AppendMainchainAtom , core::chemical::DeleteActCoordAtom , core::chemical::DeleteAtom , core::chemical::DeleteMetalbindingAtom , core::chemical::PrependMainchainAtom , core::chemical::SetAtomicCharge , core::chemical::SetAtomType , core::chemical::SetBackboneHeavyatom , core::chemical::SetDisulfideAtomName , core::chemical::SetFormalCharge , core::chemical::SetMMAtomType , core::chemical::SetNbrAtom , core::chemical::SetPolymerConnectAtom , core::conformation::AtomGraphVertexData , core::pose::UnrecognizedAtomRecord , core::scoring::nmr::VoxelGridPoint , core::scoring::packing::PoseBalls , protocols::helical_bundle::FitSimpleHelixMultiFunc , protocols::nmr::pcs::AtomGridPoint , protocols::qsar::qsarPoint , protocols::scoring::methods::pcs2::PcsInputLine , protocols::scoring::methods::pcs::PCS_line_data , protocols::scoring::methods::pcsTs1::PCS_line_data_Ts1 , protocols::scoring::methods::pcsTs2::PCS_line_data_Ts2 , protocols::scoring::methods::pcsTs3::PCS_line_data_Ts3 , protocols::scoring::methods::pcsTs4::PCS_line_data_Ts4
• atom_name_id_cache_ : core::chemical::ResidueDatabaseIO
• atom_name_to_index_ : core::chemical::ResidueType
• atom_name_to_vd_ : core::chemical::MutableResidueType
• atom_names_ : core::chemical::ResidueType
• atom_names_for_distance_measure_ : core::select::residue_selector::NeighborhoodResidueSelector
• atom_names_list() : core::pose::MiniPose
• atom_names_list_ : core::pose::MiniPose
• atom_names_soft() : core::chemical::ResidueTypeFinder
• atom_names_soft_ : core::chemical::ResidueTypeFinder
• atom_needs_update_from_wide_ : core::scoring::NeighborList
• atom_neighbors() : core::scoring::NeighborList , core::scoring::ResidueNblistData , core::scoring::ResiduePairNeighborList
• atom_neighbors_ : core::scoring::ResidueNblistData , core::scoring::ResiduePairNeighborList
• atom_num() : core::scoring::packing::PoseBalls , core::scoring::packing::PoseBallsLite
• atom_num_ : core::scoring::packing::PoseBalls , core::scoring::packing::PoseBallsLite
• atom_numbers_for_backbone_score_calculations_ : core::scoring::rna::RNA_LowResolutionPotential
• atom_numbers_for_mg_calculation() : core::scoring::rna::RNA_ScoringInfo
• atom_numbers_for_mg_calculation_ : core::scoring::rna::RNA_ScoringInfo
• atom_numbers_for_vdw_calculation() : core::scoring::rna::RNA_ScoringInfo
• atom_numbers_for_vdw_calculation_ : core::scoring::rna::RNA_ScoringInfo
• atom_numbers_sugar_ : core::scoring::rna::data::RNA_DataBackboneEnergy
• atom_numbers_sugar_coarse_ : core::scoring::rna::data::RNA_DataBackboneEnergy
• atom_overlap_is_exposed() : core::pack::interaction_graph::InvRotamerDots
• atom_overlaps_voxel() : core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid
• atom_pair_constraint_contact_map_ : protocols::frag_picker::FragmentPicker
• atom_pair_constraint_energy() : core::scoring::constraints::ConstraintEdge
• atom_pair_constraint_energy_ : core::scoring::constraints::ConstraintEdge
• atom_pair_constraint_weight() : protocols::idealize::IdealizeMover
• atom_pair_constraint_weight_ : protocols::idealize::IdealizeMover
• atom_pair_cutoff() : core::scoring::NeighborList
• atom_pair_energy() : core::scoring::etable::AnalyticEtableEvaluator , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::etable::TableLookupEvaluator , core::scoring::vdwaals::VDW_Energy
• atom_pair_energy_v() : core::scoring::etable::AnalyticEtableEvaluator , core::scoring::etable::EtableEvaluator , core::scoring::etable::TableLookupEvaluator
• atom_pair_func() : protocols::constraint_generator::HydrogenBondConstraintGenerator
• atom_pair_func_ : protocols::constraint_generator::HydrogenBondConstraintGenerator
• atom_pair_lk_energy_and_deriv_v() : core::scoring::etable::AnalyticEtableEvaluator , core::scoring::etable::EtableEvaluator , core::scoring::etable::TableLookupEvaluator
• atom_pair_lk_energy_and_deriv_v_efficient() : core::scoring::etable::AnalyticEtableEvaluator , core::scoring::etable::EtableEvaluator , core::scoring::etable::TableLookupEvaluator
• atom_pair_sd_ : protocols::constraint_generator::HydrogenBondConstraintGenerator
• atom_pair_weight_ : protocols::antibody::design::GeneralAntibodyModeler
• atom_parent_ : core::scoring::packing::PoseBalls
• atom_pointer() : core::kinematics::AtomTree
• atom_pointer_ : core::kinematics::AtomTree
• atom_positions_ : core::pack::rotamers::SingleLigandRotamerLibrary
• atom_properties() : core::chemical::ResidueType
• atom_property_status_ : core::chemical::AtomProperties
• atom_radii_ : protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder , protocols::match::upstream::BuildSet
• atom_radius() : protocols::match::upstream::BuildSet
• atom_radius_squared() : core::conformation::AtomGraphVertexData
• atom_radius_squared_ : core::conformation::AtomGraphVertexData
• atom_required_in_active_site_ : protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder
• atom_res_idx_ : core::scoring::methods::dfire::DFIRE_Potential
• atom_sasa : protocols::constel::FilterBySASA
• atom_sasa_ : core::pack::interaction_graph::RotamerDots , core::pose::metrics::simple_calculators::SasaCalculator2 , core::pose::metrics::simple_calculators::SasaCalculatorLegacy , core::scoring::sasa::SasaCalc , protocols::vardist_solaccess::VarSolDistSasaCalculator
• atom_score() : protocols::qsar::scoring_grid::ChargeGrid , protocols::qsar::scoring_grid::ConstantScoreBase , protocols::qsar::scoring_grid::GridBase , protocols::qsar::scoring_grid::GridSet , protocols::qsar::scoring_grid::HbaGrid , protocols::qsar::scoring_grid::HbdGrid , protocols::qsar::scoring_grid::PCSMultiGrid , protocols::qsar::scoring_grid::PCSSingleGrid , protocols::qsar::scoring_grid::ShapeGrid , protocols::qsar::scoring_grid::SingleGrid , protocols::qsar::scoring_grid::SolvationMetaGrid , protocols::qsar::scoring_grid::VdwGrid
• atom_scores : core::scoring::packing::HolesResult
• atom_semiexpl_score_ : protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator
• atom_set() : core::scoring::etable::Etable
• atom_set_ : core::scoring::etable::Etable
• atom_shadowed_ : core::chemical::MutableResidueType
• atom_shadowed_indices_ : core::chemical::ResidueType
• atom_subset_ : core::scoring::sasa::SasaCalc
• atom_table_ : core::scoring::nmr::NMRDummySpinlabelConformer
• atom_to_measure_ : protocols::simple_filters::ResidueSelectionDistanceFilter
• atom_to_modify : core::enzymes::EnzymeData
• atom_tree() : core::conformation::Conformation , core::pose::Pose
• atom_tree_ : core::conformation::Conformation
• atom_tree_collection_ : core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap
• atom_tree_diff_ : protocols::jd2::AtomTreeDiffJobInputter , protocols::jd2::AtomTreeDiffJobOutputter
• atom_tree_minimizer_ : protocols::stepwise::modeler::StepWiseMinimizer
• atom_tree_representatives_ : core::pack::scmin::ResidueAtomTreeCollection
• atom_tree_torsion() : core::conformation::Conformation
• atom_tree_uptodate_ : core::pack::scmin::ResidueAtomTreeCollection
• atom_two_body_energies_ : core::scoring::SplitUnfoldedTwoBodyPotential
• atom_type() : core::chemical::gasteiger::GasteigerAtomTypeSet , core::chemical::MutableResidueType , core::chemical::ResidueType , core::conformation::Residue , core::scoring::etable::Etable , core::scoring::etable::etrie::EtableAtom , core::scoring::MultipoleParameter , core::scoring::packing::PoseBalls , core::scoring::vdwaals::VDWAtom , protocols::noesy_assign::PeakCalibrator , protocols::pockets::CCluster::Cxyz
• atom_type_ : core::scoring::MultipoleParameter , core::scoring::packing::PoseBalls , core::scoring::vdwaals::VDWAtom
• atom_type_dbio_ : protocols::features::AtomTypesFeatures
• atom_type_index() : core::chemical::Atom , core::chemical::AtomTypeSet , core::chemical::gasteiger::GasteigerAtomTypeSet , core::chemical::MMAtomTypeSet , core::chemical::ResidueType , core::conformation::Residue
• atom_type_index_ : core::chemical::Atom , core::chemical::AtomTypeSet , core::chemical::gasteiger::GasteigerAtomTypeSet , core::chemical::MMAtomTypeSet
• atom_type_is_charged_ : core::scoring::lkball::LK_BallEnergy
• atom_type_label_set_used_ : core::scoring::SplitUnfoldedTwoBodyPotential
• atom_type_name() : core::chemical::Adduct , core::chemical::AtomType , core::chemical::orbitals::OrbitalType , protocols::membrane::scoring::MEnvAtomParams
• atom_type_name_ : core::chemical::AddAtom , core::chemical::Adduct , core::chemical::orbitals::OrbitalType , core::chemical::SetAtomType , protocols::membrane::scoring::MEnvAtomParams
• atom_type_set() : core::chemical::ChemicalManager , core::chemical::PoseResidueTypeSet , core::chemical::ResidueTypeBase , core::chemical::ResidueTypeSet , core::conformation::Residue
• atom_type_set_name() : core::scoring::AtomVDW
• atom_type_set_name_ : core::scoring::AtomVDW , core::scoring::vdwaals::VDW_Energy
• atom_type_set_ptr() : core::chemical::ResidueTypeBase
• atom_type_set_ptr_ : core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy
• atom_type_sets_ : core::chemical::ChemicalManager
• atom_types_ : core::chemical::AcceptorAtomFilter , core::chemical::APolarHydrogenFilter , core::chemical::AromaticAtomFilter , core::chemical::gasteiger::GasteigerAtomTypeSet , core::chemical::HeavyAtomFilter , core::chemical::HeavyAtomWithHydrogensFilter , core::chemical::HeavyAtomWithPolarHydrogensFilter , core::chemical::HydrogenAtomFilter , core::chemical::PolarHydrogenFilter , core::chemical::ResidueTypeBase , core::chemical::ResidueTypeSet , protocols::sewing::hashing::LigandBindingResPlacer , protocols::sewing::requirements::LigandClashRequirement , protocols::sewing::scoring::LigandScorer
• atom_unsat_ : protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator
• atom_vdw_ : core::scoring::AtomVDW , core::scoring::methods::HybridVDW_Energy , core::scoring::ScoringManager , core::scoring::vdwaals::VDW_Energy , protocols::scoring::InterchainPotential
• atom_vdw_atom_type_set_name() : core::scoring::methods::EnergyMethodOptions
• atom_vdw_atom_type_set_name_ : core::scoring::methods::EnergyMethodOptions
• atom_vector_ : protocols::sewing::data_storage::SmartSewingResidue
• atom_vertex() : core::chemical::MutableResidueType
• atom_weight_stored : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• atom_weights() : core::scoring::lkball::LKB_ResidueInfo , core::scoring::lkball::lkbtrie::LKBAtom , core::scoring::lkball::WaterBuilderForRestype
• atom_weights_ : core::scoring::lkball::lkbtrie::LKBAtom , core::scoring::lkball::WaterBuilderForRestype
• atom_xyz_map_ : protocols::nmr::pcs::PCSLigandTransformMover::LMMinPCSDataRef
• atom_z_position() : core::conformation::membrane::MembraneInfo
• atomA1_ : core::scoring::constraints::DihedralPairConstraint , core::scoring::constraints::DistancePairConstraint
• atomA2_ : core::scoring::constraints::DihedralPairConstraint , core::scoring::constraints::DistancePairConstraint
• atomA3_ : core::scoring::constraints::DihedralPairConstraint
• atomA4_ : core::scoring::constraints::DihedralPairConstraint
• AtomAngleSecMatchRPE() : protocols::match::downstream::AtomAngleSecMatchRPE
• AtomAtomPairFeatures() : protocols::features::AtomAtomPairFeatures
• atomB1_ : core::scoring::constraints::DihedralPairConstraint , core::scoring::constraints::DistancePairConstraint
• atomB2_ : core::scoring::constraints::DihedralPairConstraint , core::scoring::constraints::DistancePairConstraint
• atomB3_ : core::scoring::constraints::DihedralPairConstraint
• atomB4_ : core::scoring::constraints::DihedralPairConstraint
• AtomBasedConstraintsScore() : protocols::frag_picker::scores::AtomBasedConstraintsScore
• AtomByResList : protocols::noesy_assign::PeakAssignmentResidueMap
• AtomCoordinateCstMover() : protocols::relax::AtomCoordinateCstMover
• AtomCOP : core::kinematics::AtomTree
• AtomCountFilter() : protocols::ligand_docking::AtomCountFilter
• atomdesg1_ : protocols::simple_filters::AtomicDistanceFilter
• atomdesg2_ : protocols::simple_filters::AtomicDistanceFilter
• atomdesg_ : protocols::protein_interface_design::filters::HbondsToAtomFilter
• AtomDihedralSecMatchRPE() : protocols::match::downstream::AtomDihedralSecMatchRPE
• AtomDistanceSecMatchRPE() : protocols::match::downstream::AtomDistanceSecMatchRPE
• AtomEntries : protocols::sparta::PDB
• atomGDTha() : protocols::loop_grower::LoopGrower
• AtomGeometrySecMatchRPE() : protocols::match::downstream::AtomGeometrySecMatchRPE
• AtomGraphEdgeData() : core::conformation::AtomGraphEdgeData
• AtomGraphVertexData() : core::conformation::AtomGraphVertexData
• AtomGrid() : protocols::nmr::pcs::AtomGrid
• AtomGridPoint() : protocols::nmr::pcs::AtomGridPoint
• AtomHash() : protocols::simple_moves::AtomHash
• atomic_charge() : core::conformation::Residue
• atomic_depth_apo_surface_ : protocols::simple_filters::BuriedUnsatHbondFilter
• atomic_depth_cutoff() : protocols::task_operations::PruneBuriedUnsatsOperation
• atomic_depth_cutoff_ : protocols::task_operations::PruneBuriedUnsats_RotamerSetsOperation , protocols::task_operations::PruneBuriedUnsatsOperation
• atomic_depth_deeper_than_ : protocols::simple_filters::BuriedUnsatHbondFilter
• atomic_depth_poly_leu_ : protocols::simple_filters::BuriedUnsatHbondFilter
• atomic_depth_probe_radius() : protocols::task_operations::PruneBuriedUnsatsOperation
• atomic_depth_probe_radius_ : protocols::simple_filters::BuriedUnsatHbondFilter , protocols::task_operations::PruneBuriedUnsats_RotamerSetsOperation , protocols::task_operations::PruneBuriedUnsatsOperation
• atomic_depth_resolution() : protocols::task_operations::PruneBuriedUnsatsOperation
• atomic_depth_resolution_ : protocols::simple_filters::BuriedUnsatHbondFilter , protocols::task_operations::PruneBuriedUnsats_RotamerSetsOperation , protocols::task_operations::PruneBuriedUnsatsOperation
• atomic_depth_selection_ : protocols::simple_filters::BuriedUnsatHbondFilter
• atomic_interaction_cutoff() : core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty , core::scoring::carbon_hbonds::CarbonHBondEnergy , core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy , core::scoring::dna::DNATorsionEnergy , core::scoring::elec::FA_ElecEnergy , core::scoring::elec::FA_GrpElecEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::geometric_solvation::ContextDependentGeometricSolEnergy , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::geometric_solvation::DatabaseOccSolEne , core::scoring::geometric_solvation::GeometricSolEnergyEvaluator , core::scoring::geometric_solvation::OccludedHbondSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody , core::scoring::hackaro::HackAroEnergy , core::scoring::hbonds::HBondEnergy , core::scoring::hbonds::NPDHBondEnergy , core::scoring::interface_::DDPscore , core::scoring::lkball::LK_BallEnergy , core::scoring::magnesium::MgEnergy , core::scoring::magnesium::RNA_MgPointEnergy , core::scoring::membrane::FaMPEnvSmoothEnergy , core::scoring::membrane::FaMPSolvEnergy , core::scoring::membrane::MPHelicalityEnergy , core::scoring::membrane::MPPairEnergy , core::scoring::membrane::MPResidueLipophilicityEnergy , core::scoring::methods::ArgCationPiEnergy , core::scoring::methods::AspartimidePenaltyEnergy , core::scoring::methods::CartesianBondedEnergy , core::scoring::methods::CenHBEnergy , core::scoring::methods::CenPairEnergy , core::scoring::methods::CenRotPairEnergy , core::scoring::methods::CustomAtomPairEnergy , core::scoring::methods::DNA_BaseEnergy , core::scoring::methods::DNA_ReferenceEnergy , core::scoring::methods::EnvSmoothEnergy , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::methods::FACTSEnergy , core::scoring::methods::GaussianOverlapEnergy , core::scoring::methods::GenericBondedEnergy , core::scoring::methods::GoapEnergy , core::scoring::methods::HybridVDW_Energy , core::scoring::methods::LK_hack , core::scoring::methods::LK_PolarNonPolarEnergy , core::scoring::methods::MembraneCenPairEnergy , core::scoring::methods::MembraneEnvSmoothEnergy , core::scoring::methods::MMBondAngleEnergy , core::scoring::methods::MMBondLengthEnergy , core::scoring::methods::MMLJEnergyInter , core::scoring::methods::MMLJEnergyIntra , core::scoring::methods::MMTorsionEnergy , core::scoring::methods::MotifDockEnergy , core::scoring::methods::PairEnergy , core::scoring::methods::PeptideBondEnergy , core::scoring::methods::PointWaterEnergy , core::scoring::methods::ProClosureEnergy , core::scoring::methods::ProQ_Energy , core::scoring::methods::RamachandranEnergy2B , core::scoring::methods::RamaPreProEnergy , core::scoring::methods::SecondaryStructureEnergy , core::scoring::methods::ShortRangeTwoBodyEnergy , core::scoring::methods::SmoothCenPairEnergy , core::scoring::methods::SuckerEnergy , core::scoring::methods::WaterAdductHBondEnergy , core::scoring::methods::WholeStructureEnergy , core::scoring::orbitals::OrbitalsScore , core::scoring::rna::data::RNA_ChemicalMappingEnergy , core::scoring::rna::data::RNA_DataBackboneEnergy , core::scoring::rna::RNA_FullAtomStackingEnergy , core::scoring::rna::RNA_JR_SuiteEnergy , core::scoring::rna::RNA_LJ_BaseEnergy , core::scoring::rna::RNA_PairwiseLowResolutionEnergy , core::scoring::rna::RNA_SuiteEnergy , core::scoring::rna::RNA_TorsionEnergy , core::scoring::rna::RNA_VDW_Energy , core::scoring::rna::RNP_LowResEnergy , core::scoring::rna::RNP_LowResPairDistEnergy , core::scoring::rna::RNP_LowResStackEnergy , core::scoring::rna::StackElecEnergy , core::scoring::rna::TNA_SuiteEnergy , core::scoring::vdwaals::VDW_Energy , core::scoring::vdwaals::VDWTrieEvaluator , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy , protocols::scoring::methods::InterchainPairEnergy
• atomic_interaction_cutoff_ : core::scoring::geometric_solvation::DatabaseOccSolEne , core::scoring::vdwaals::VDWTrieEvaluator
• atomic_number_ : core::chemical::Element
• atomic_orbitals_nonbinding_ : core::chemical::gasteiger::GasteigerAtomTypeData
• atomic_properties_ : core::chemical::ResidueType
• atomic_radius() : core::scoring::GenBornResidueInfo
• atomic_radius_ : core::scoring::GenBornResidueInfo
• atomicCharge : protocols::ligand_docking::ga_ligand_dock::atmInfo
• AtomicContactCountFilter() : protocols::protein_interface_design::filters::AtomicContactCountFilter
• AtomicContactFilter() : protocols::simple_filters::AtomicContactFilter
• AtomicDepth() : core::scoring::atomic_depth::AtomicDepth
• AtomicDistanceFilter() : protocols::simple_filters::AtomicDistanceFilter
• AtomICoor() : core::chemical::AtomICoor
• AtomicOrbitalTypes : core::chemical::gasteiger::GasteigerAtomTypeData
• AtomicOrbitalTypes_strings() : core::chemical::gasteiger::GasteigerAtomTypeData
• AtomID : core::conformation::Conformation , core::conformation::symmetry::SymmetryInfo , core::id::AtomID , core::kinematics::AtomTree , core::kinematics::MinimizerMapBase , core::kinematics::MoveMap , core::kinematics::tree::Atom , core::optimization::DOF_Node , core::optimization::MinimizerMap , core::pose::Pose , core::scoring::constraints::Constraint , core::scoring::constraints::Constraints , core::scoring::constraints::ConstraintSet , core::scoring::Energies , core::scoring::func::FourPointsFunc , core::scoring::func::XYZ_Func , core::scoring::hbonds::HBondSet , core::scoring::hbonds::NPDHBondSet
• atomid() : protocols::ligand_docking::ga_ligand_dock::ConstraintInfo
• AtomID : protocols::match::downstream::DownstreamBuilder , protocols::match::output::DownstreamRMSEvaluator , protocols::rna::movers::ErraserMinimizerMover
• atomid_ : core::kinematics::AtomWithDOFChange
• atomID_ : protocols::normalmode::NormalMode
• AtomID_Map() : core::id::AtomID_Map< T >
• AtomID_Mapper() : core::pose::toolbox::AtomID_Mapper
• AtomID_Mask : core::conformation::Conformation , core::kinematics::AtomTree , core::kinematics::MoveMap , core::kinematics::tree::Atom , core::scoring::Energies
• AtomID_to_atomnbr_ : core::scoring::fiber_diffraction::FiberDiffractionEnergy , core::scoring::fiber_diffraction::FiberDiffractionEnergyDens
• atomid_to_csts_ : core::scoring::constraints::MultiConstraint
• AtomIDs : core::conformation::symmetry::SymmetryInfo , core::kinematics::AtomTree , core::optimization::DOF_Node
• atomids() : core::scoring::packing::PoseBalls
• atomIDs : protocols::chemically_conjugated_docking::UBQ_GTPaseMover
• AtomIDs : protocols::denovo_design::movers::RotateSegmentMover
• AtomIndices : core::conformation::Residue
• AtomIndsForRestypeMap : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• AtomInfo() : core::scoring::hbonds::graph::AtomInfo
• AtomInformation() : core::io::AtomInformation
• AtomInResidueAtomInResiduePairFeatures() : protocols::features::AtomInResidueAtomInResiduePairFeatures
• AtomLevelDomainMap() : core::pose::toolbox::AtomLevelDomainMap
• AtomList : core::fragment::DownJumpSRFD , core::id::NamedStubID , core::scoring::rna::RNA_AtomVDW , protocols::jumping::DisulfTemplate , protocols::jumping::PairingTemplate , protocols::noesy_assign::MethylNames , protocols::noesy_assign::PeakAssignmentResidueMap
• atomlist_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• AtomMap : core::id::AtomID_Map< T > , core::id::DOF_ID_Map< T > , core::id::NamedAtomID_Map< T >
• atomname() : protocols::contact_map::ContactPartner
• atomName : protocols::sparta::PDB_Entry
• atomname_ : protocols::contact_map::ContactPartner
• AtomNameList : protocols::forge::build::ConnectRight , protocols::sparta::Sparta::SpartaLib
• AtomNameMap : protocols::constraint_generator::HydrogenBondInfo
• atomnames_ : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• AtomNameSet : protocols::constraint_generator::HydrogenBondConstraintGenerator
• AtomNeighbor() : core::scoring::AtomNeighbor
• atomno() : core::chemical::ICoorAtomID , core::chemical::ResidueConnection , core::id::AtomID , core::id::DOF_ID , core::optimization::DOF_Node , core::scoring::AtomNeighbor , protocols::legacy_sewing::HashValue , protocols::sewing::hashing::HashValue
• atomNo : protocols::sparta::RingData
• atomno1() : core::scoring::SmallAtNb
• atomno1_ : core::scoring::SmallAtNb
• atomno2() : core::scoring::SmallAtNb
• atomno2_ : core::scoring::SmallAtNb
• atomno_ : core::chemical::ICoorAtomID , core::chemical::ResidueConnection , core::id::AtomID , core::scoring::AtomNeighbor , protocols::legacy_sewing::SewAtom , protocols::scoring::ImplicitFastClashCheck
• atomNum : protocols::sparta::PDB_Entry
• AtomOP : core::kinematics::AtomTree
• AtomPack() : protocols::abinitio::abscript::AtomPack
• atompair_scale() : core::scoring::FACTSPotential
• AtomPairConstraint() : core::scoring::constraints::AtomPairConstraint
• AtomPairConstraintCreator() : core::scoring::constraints::AtomPairConstraintCreator
• AtomPairConstraintGenerator() : protocols::constraint_generator::AtomPairConstraintGenerator
• AtomPairConstraintList : protocols::abinitio::Template
• AtomPairConstraintOP : core::scoring::constraints::Obsolet_NamedAtomPairConstraint
• AtomPairConstraintsData() : protocols::frag_picker::scores::AtomPairConstraintsData
• AtomPairConstraintsScore() : protocols::frag_picker::scores::AtomPairConstraintsScore
• AtomPairData() : protocols::ligand_docking::rdf::AtomPairData
• AtomPairFuncList() : core::scoring::custom_pair_distance::AtomPairFuncList
• AtomProperties() : core::chemical::AtomProperties , protocols::ligand_docking::ga_ligand_dock::AtomProperties
• AtomPropertiesManager() : core::chemical::AtomPropertiesManager
• AtomRadiusMap() : core::scoring::packstat::AtomRadiusMap
• atomRec : core::pose::PDBInfo::ResidueRecord
• AtomRecord() : core::pose::PDBInfo::AtomRecord
• AtomRecords : core::pose::PDBInfo
• AtomRenamingMap : core::chemical::MergeBehaviorManager
• atoms() : core::chemical::Metapatch , core::conformation::Residue , core::io::ResidueInformation
• Atoms : core::kinematics::tree::Atom
• atoms() : core::optimization::DOF_Node
• Atoms : core::scoring::constraints::AmbiguousNMRDistanceConstraint
• atoms() : core::scoring::packstat::SimplePDB , core::scoring::PDinter , core::scoring::power_diagram::PDinter , core::scoring::sc::MolecularSurfaceCalculator , core::scoring::trie::RotamerTrie< AT, CPDATA > , protocols::constraint_generator::HydrogenBondInfo
• Atoms : protocols::denovo_design::movers::RotateSegmentMover
• atoms() : protocols::environment::claims::JumpClaim , protocols::environment::EnvClaimBroker::BrokeredJumpData
• ATOMS : protocols::sparta::PDB
• atoms : protocols::sparta::RingData
• atoms1() : core::scoring::constraints::AmbiguousNMRDistanceConstraint
• atoms1_ : core::scoring::constraints::AmbiguousNMRDistanceConstraint , protocols::constraint_generator::HydrogenBondConstraintGenerator
• atoms2() : core::scoring::constraints::AmbiguousNMRDistanceConstraint
• atoms2_ : core::scoring::constraints::AmbiguousNMRDistanceConstraint , protocols::constraint_generator::HydrogenBondConstraintGenerator
• atoms_ : core::chemical::AtomTypeSet , core::chemical::MMAtomTypeSet , core::chemical::Selector_HAS_ATOMS , core::conformation::Residue , core::io::ResidueInformation , core::kinematics::tree::Atom_ , core::optimization::DOF_Node , core::scoring::packstat::SimplePDB , core::scoring::PDinter , core::scoring::power_diagram::PDinter , core::scoring::trie::RotamerDescriptor< AT, CPDAT > , protocols::constraint_generator::HydrogenBondInfo , protocols::denovo_design::movers::RotateSegmentMover , protocols::environment::claims::JumpClaim , protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber , protocols::noesy_assign::PeakAssignmentResidueMap , protocols::stepwise::sampler::rna::RNA_KinematicCloser
• atoms_123_ : protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder , protocols::toolbox::match_enzdes_util::LigandConformer
• atoms_are_bonded() : core::chemical::MutableResidueType , core::chemical::ResidueType , core::conformation::Conformation
• atoms_are_equiv() : protocols::comparative_modeling::ThreadingMover
• atoms_begin() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• Atoms_ConstIterator : core::kinematics::tree::Atom
• atoms_downstream_ : protocols::jumping::DisulfTemplate , protocols::jumping::PairingTemplate
• atoms_end() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• atoms_in_patches_ : protocols::pose_metric_calculators::HPatchCalculator
• Atoms_Iterator : core::kinematics::tree::Atom
• atoms_last_controlled_by_chi() : core::chemical::ResidueType
• atoms_last_controlled_by_chi_ : core::chemical::ResidueType
• atoms_representing_chis_ : core::pack::scmin::AtomTreeSCMinMinimizerMap
• atoms_representing_ds_ : core::pack::scmin::AtomTreeSCMinMinimizerMap
• atoms_representing_thetas_ : core::pack::scmin::AtomTreeSCMinMinimizerMap
• atoms_to_atoms_ : protocols::task_operations::CrystalContactsOperation
• atoms_to_compare_ : protocols::match::output::DownstreamRMSEvaluator
• atoms_to_constrain() : protocols::constraint_generator::AtomPairConstraintGenerator
• atoms_to_dofid_ : core::pack::scmin::CartSCMinMinimizerMap
• atoms_to_superimpose_on_ : protocols::enzdes::EnzdesBaseProtocol
• atoms_to_update_ : core::scoring::NeighborList
• atoms_upstream_ : protocols::jumping::DisulfTemplate , protocols::jumping::PairingTemplate
• atoms_with_orb_index() : core::chemical::ResidueType , core::conformation::Residue
• atoms_with_orb_index_ : core::chemical::ResidueType
• atoms_within_one_bond_of_a_residue_connection() : core::chemical::ResidueType
• atoms_within_one_bond_of_a_residue_connection_ : core::chemical::ResidueType
• atoms_within_two_bonds_of_a_residue_connection() : core::chemical::ResidueType
• atoms_within_two_bonds_of_a_residue_connection_ : core::chemical::ResidueType
• AtomSelection() : core::io::nmr::AtomSelection
• AtomsMap : protocols::sparta::PDB
• AtomSurfaceFullList : protocols::sparta::PDB
• AtomSurfacePartList : protocols::sparta::PDB
• AtomTree : core::conformation::Conformation , core::kinematics::AtomTree
• AtomTreeCollection() : core::pack::scmin::AtomTreeCollection
• AtomTreeDiff() : core::import_pose::atom_tree_diffs::AtomTreeDiff
• AtomTreeDiffJobDistributor() : protocols::jobdist::AtomTreeDiffJobDistributor
• AtomTreeDiffJobInputter() : protocols::jd2::AtomTreeDiffJobInputter
• AtomTreeDiffJobOutputter() : protocols::jd2::AtomTreeDiffJobOutputter
• AtomTreeMinimizer() : core::optimization::AtomTreeMinimizer
• AtomTreeMultifunc() : core::optimization::AtomTreeMultifunc
• AtomTreeOP : core::conformation::Conformation
• AtomTreeSCMinMinimizerMap() : core::pack::scmin::AtomTreeSCMinMinimizerMap
• AtomType() : core::chemical::AtomType , core::conformation::Residue
• AtomTypeDatabaseIO() : core::chemical::AtomTypeDatabaseIO
• AtomTypeSet() : core::chemical::AtomTypeSet
• AtomTypeSets : core::chemical::ChemicalManager
• AtomTypesFeatures() : protocols::features::AtomTypesFeatures
• AtomVDW() : core::scoring::AtomVDW
• atomWaters : protocols::ligand_docking::ga_ligand_dock::atmInfo
• AtomWithDOFChange() : core::kinematics::AtomWithDOFChange
• atr : protocols::ligand_docking::Ligand_info
• atr_cutoff_ : protocols::stepwise::modeler::protein::checker::ProteinAtrRepChecker , protocols::stepwise::screener::PartitionContactScreener
• atr_radius_ : protocols::qsar::scoring_grid::ClassicGrid , protocols::qsar::scoring_grid::SiteGrid
• atr_rep_checker_ : protocols::stepwise::legacy::screener::ProteinAtrRepScreener , protocols::stepwise::legacy::screener::RNA_AtrRepScreener , protocols::stepwise::screener::BulgeApplier
• atr_rep_checker_with_instantiated_sugar_ : protocols::stepwise::screener::AnchorSugarScreener
• atr_rep_checkers_for_anchor_sugar_models_ : protocols::stepwise::screener::AnchorSugarScreener
• atr_rep_screen() : protocols::stepwise::options::StepWiseBasicOptions
• atr_rep_screen_ : protocols::stepwise::options::StepWiseBasicOptions
• atr_rep_screen_for_docking() : protocols::stepwise::options::StepWiseBasicOptions
• atr_rep_screen_for_docking_ : protocols::stepwise::options::StepWiseBasicOptions
• atr_rep_screening_scorefxn_ : protocols::stepwise::modeler::protein::checker::ProteinAtrRepChecker , protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker
• atr_weight() : core::scoring::etable::EtableEvaluator
• atr_weight_ : core::scoring::etable::EtableEvaluator , protocols::qsar::scoring_grid::ClassicGrid , protocols::qsar::scoring_grid::SiteGrid
• AtrGrid() : protocols::qsar::scoring_grid::AtrGrid
• ats123_reqd_in_active_site_ : protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder
• ats_n_func_list() : core::scoring::custom_pair_distance::AtomPairFuncList
• attach() : core::pose::datacache::ObserverCache , protocols::moves::PyMOLObserver , protocols::network::UIObserver
• attach_annotation() : protocols::environment::ProtectedConformation
• attach_boinc_ghost_observer() : protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter , protocols::generalized_kinematic_closure::GeneralizedKIC , protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• attach_boinc_ghost_observer_ : protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter , protocols::generalized_kinematic_closure::GeneralizedKIC , protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• attach_conformation_obs() : core::pose::Pose
• attach_connection_obs() : core::conformation::Conformation
• attach_destruction_obs() : core::chemical::ResidueType , core::pose::Pose
• attach_energy_obs() : core::pose::Pose
• attach_general_obs() : core::conformation::Conformation , core::pose::Pose
• attach_identity_obs() : core::conformation::Conformation
• attach_impl() : core::conformation::carbohydrates::GlycanTreeSetObserver , core::pose::datacache::CacheableObserver , core::pose::datacache::LengthEventCollector , core::pose::datacache::SpecialSegmentsObserver , protocols::denovo_design::components::StructureDataObserver , protocols::moves::PyMOLObserver , protocols::network::UIObserver , protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver
• attach_length_obs() : core::conformation::Conformation
• attach_ligand() : protocols::sewing::data_storage::LigandSegment
• attach_next_part() : protocols::pose_creation::MakeJunctionsMover
• attach_observer() : protocols::denovo_design::components::StructureDataFactory
• attach_observer_to_last_accepted_conformation() : protocols::moves::MonteCarlo
• attach_observer_to_last_accepted_pose() : protocols::moves::MonteCarlo
• attach_observer_to_lowest_score_conformation() : protocols::moves::MonteCarlo
• attach_observer_to_lowest_score_pose() : protocols::moves::MonteCarlo
• attach_pose_ : protocols::pose_creation::MergePDBatOverlapMover
• attach_rotamer_clouds_to_pose_and_rotset() : protocols::simple_moves::ExplicitWaterMover
• attach_secondary_structure_pools() : protocols::frag_picker::quota::QuotaCollector
• attach_to() : core::conformation::carbohydrates::GlycanTreeSetObserver , core::pose::datacache::CacheableObserver , core::pose::metrics::PoseMetricContainer , core::pose::PDBInfo , protocols::boinc::BoincCurrentPoseObserver , protocols::forge::build::BuildInstruction , protocols::viewer::SilentObserver
• attach_to_conformation() : core::scoring::constraints::ConstraintSet
• attach_topological_observer() : core::kinematics::AtomTree
• attach_unowned_ligand() : protocols::sewing::data_storage::LigandSegment
• attach_xyz_obs() : core::conformation::Conformation
• attached_ : core::pose::datacache::ObserverCache
• attached_H_begin() : core::chemical::ResidueType , core::conformation::Residue
• attached_H_begin_ : core::chemical::ResidueType
• attached_H_end() : core::chemical::ResidueType , core::conformation::Residue
• attached_H_end_ : core::chemical::ResidueType
• attached_res() : protocols::stepwise::monte_carlo::mover::Attachment , protocols::stepwise::monte_carlo::mover::StepWiseMove
• attached_res_ : protocols::stepwise::monte_carlo::mover::Attachment
• attaches_to_residue_type() : core::pack::rotamer_set::WaterAnchorInfo
• Attachment() : protocols::stepwise::monte_carlo::mover::Attachment
• attachment_chain_ : protocols::pose_creation::MergePDBatOverlapMover
• attachment_termini_ : protocols::pose_creation::MergePDBatOverlapMover
• attachment_type() : protocols::stepwise::monte_carlo::mover::Attachment , protocols::stepwise::monte_carlo::mover::StepWiseMove
• attachment_type_ : protocols::stepwise::monte_carlo::mover::Attachment
• attachments() : protocols::stepwise::monte_carlo::mover::StepWiseMove
• attachments_ : protocols::stepwise::monte_carlo::mover::StepWiseMove
• attempt_ccd() : protocols::abinitio::abscript::AbscriptLoopCloserCM
• attempt_closure_cutoff_ : protocols::rna::movers::RNA_LoopCloser
• attempt_idealize() : protocols::abinitio::abscript::AbscriptLoopCloserCM
• attempt_insert() : protocols::mean_field::ResHashMap
• attempt_loop_move() : protocols::loop_modeling::LoopProtocol
• attempt_pyrimidine_flip_ : protocols::rna::movers::ErraserMinimizerMover
• attempt_readin() : core::chemical::GlobalResidueTypeSet
• atten : core::scoring::sc::Atom
• attractive : core::scoring::etable::AtomPairEnergy
• attributes() : protocols::calc_taskop_filters::Operator , protocols::calc_taskop_filters::RelativePoseFilter , protocols::calc_taskop_filters::Sigmoid
• attributes_for_append_assembly_mover() : protocols::sewing::movers::AppendAssemblyMover
• attributes_for_hbnet() : protocols::hbnet::HBNet
• attributes_for_parse_center_normal_from_tag() : protocols::membrane::AddMembraneMover
• attributes_for_parse_my_tag() : protocols::denovo_design::architects::CompoundArchitect , protocols::denovo_design::architects::StructureArchitect , protocols::denovo_design::connection::ConnectionArchitect
• attributes_for_remodel_constraint_generator() : protocols::forge::remodel::RemodelConstraintGenerator
• attributes_for_report_to_db() : protocols::features::ReportToDB
• attributes_for_sheet_constraint_generator() : protocols::fldsgn::SheetConstraintGenerator
• attributes_for_tempering_base() : protocols::canonical_sampling::TemperingBase
• attributes_for_trajectory_recorder() : protocols::canonical_sampling::TrajectoryRecorder
• atype2holes_ : core::scoring::packing::HolesParams
• atypes_list_ : protocols::membrane::scoring::FaWaterToBilayerEnergy
• auction_ : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• auction_results() : protocols::protein_interface_design::movers::PlacementAuctionMover
• auction_results_ : protocols::protein_interface_design::movers::PlacementAuctionMover
• author_in_progress() : core::io::HeaderInformation
• author_in_progress_ : core::io::HeaderInformation
• authors() : core::io::HeaderInformation
• Authors : core::io::HeaderInformation
• authors_ : core::io::HeaderInformation
• auto_adjust_factorA_ : protocols::simple_moves::BBGaussianMover
• auto_assign_nu_atoms() : core::chemical::ResidueType
• auto_choose_cutpoint() : protocols::loops::Loop
• auto_choose_cutpoints() : protocols::loops::Loops
• auto_clash() : core::scoring::motif::ResPairMotifQuery
• auto_clash_ : core::scoring::motif::ResPairMotifQuery
• auto_cut() : protocols::environment::Environment
• auto_cuts : protocols::environment::EnvClaimBroker::BrokerResult
• auto_cuts_ : protocols::environment::AutoCutData
• auto_design : protocols::forge::remodel::RemodelData
• auto_detect_contacts : protocols::sewing::data_storage::LigandDescription
• auto_detect_glycan_connections() : core::io::StructFileRepOptions
• auto_detect_glycan_connections_ : core::io::StructFileRepOptions
• auto_detect_symmetry() : protocols::cyclic_peptide::SymmetricCycpepAlign
• auto_detect_symmetry_ : protocols::cyclic_peptide::SymmetricCycpepAlign
• auto_frag_insertion_weight() : protocols::hybridization::FoldTreeHybridize
• auto_frag_insertion_weight_ : protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol
• auto_generate_kink_constraint() : protocols::antibody::snugdock::SnugDockProtocol
• auto_generate_kink_constraint_ : protocols::antibody::snugdock::SnugDockProtocol
• auto_h3_constraint_ : protocols::antibody::AntibodyModelerProtocol
• auto_mm_ : protocols::seeded_abinitio::SegmentHybridizer
• auto_range_ : protocols::matdes::SymDofMover
• auto_stop_ : protocols::loop_grower::FragmentExtension , protocols::loop_grower::LoopGrower
• auto_tune_ : protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• auto_update_ : core::scoring::NeighborList
• autoAdjustPercentile : protocols::cluster::calibur::Clustering
• autocorrelate() : protocols::electron_density::DensitySymmInfo
• AutoCutData() : protocols::environment::AutoCutData
• autodetermine_chi_bonds() : core::chemical::MutableResidueType
• autoexpanding_pocket_eval() : protocols::pockets::PocketGrid
• autofill() : protocols::hotspot_hashing::HotspotStubSet
• autofilter() : core::import_pose::options::RNA_FragmentMonteCarloOptions
• autofilter_ : core::import_pose::options::RNA_FragmentMonteCarloOptions
• autofilter_score_quantile() : core::import_pose::options::RNA_FragmentMonteCarloOptions
• autofilter_score_quantile_ : core::import_pose::options::RNA_FragmentMonteCarloOptions
• autofoldtree_ : protocols::docking::DockingInitialPerturbation , protocols::docking::DockingProtocol , protocols::docking::EllipsoidalRandomizationMover , protocols::docking::TemperedDocking , protocols::symmetric_docking::SymDockProtocol
• autogenerate_constseq_frags() : protocols::anchored_design::AnchorMoversData
• autogenerate_design_frags() : protocols::anchored_design::AnchorMoversData
• autogenerate_frags() : protocols::anchored_design::AnchorMoversData
• autoinitialize_ : protocols::anchored_design::AnchoredDesignMover
• automatic_ : protocols::forge::remodel::RemodelMover::instruction_flags
• automatic_connection_ : protocols::protein_interface_design::movers::TryRotamers
• automatic_distance_cutoff() : protocols::protein_interface_design::movers::AddChainBreak
• automatic_distance_cutoff_ : protocols::protein_interface_design::movers::AddChainBreak
• automatic_repacking_definition_ : protocols::calc_taskop_movers::DesignRepackMover
• AutomaticSheetConstraintGenerator() : protocols::fold_from_loops::constraint_generator::AutomaticSheetConstraintGenerator
• automode() : protocols::hybridization::FragmentBiasAssigner
• automode_scorecut_ : protocols::hybridization::CartesianSampler
• automode_scores() : protocols::hybridization::FragmentBiasAssigner
• AutomorphismIterator() : core::chemical::AutomorphismIterator
• AutoRBMover() : protocols::rbsegment_relax::AutoRBMover
• autoset_wt_ : protocols::cryst::SetCrystWeightMover
• autotemp_ : protocols::moves::MonteCarlo
• autotemp_accept() : protocols::moves::MonteCarlo
• autotemp_reject() : protocols::moves::MonteCarlo
• auxClustering() : protocols::cluster::calibur::Clustering
• auxiliary_clusters_ : protocols::cluster::calibur::Clustering
• available_ : protocols::moves::SwitchMover
• available_AAs_file() : protocols::evolution::AlignmentAAFinder , protocols::evolution::AlignmentGapInserter
• available_AAs_file_ : protocols::evolution::AlignmentAAFinder , protocols::evolution::AlignmentGapInserter
• available_lower_termini() : protocols::denovo_design::components::StructureData , protocols::denovo_design::connection::ConnectionArchitect
• available_moves_ : protocols::simple_moves::oop::OopRandomPuckMover
• available_nodes_ : protocols::legacy_sewing::Assembly
• available_seg_list_ : protocols::simple_moves::BBGaussianMover
• available_upper_termini() : protocols::denovo_design::components::StructureData , protocols::denovo_design::connection::ConnectionArchitect
• Avd_ : core::chemical::orbitals::AssignOrbitals
• ave_abs_diff() : protocols::mean_field::AAMatrix
• ave_type_ : core::scoring::nmr::pcs::PCSSingleSet , core::scoring::nmr::pre::PREMultiSet , core::scoring::nmr::rdc::RDCMultiSet
• average() : protocols::ddg::ddGMover
• average_change_in_rama_score_ : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• average_change_in_rama_score_over_range() : protocols::loops::loop_closure::ccd::RamaCheckBase
• average_change_in_torsion_angle_ : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• average_dist() : protocols::noesy_assign::FragsToAtomDist::DistanceRecord
• average_dist6() : protocols::noesy_assign::FragsToAtomDist::DistanceRecord
• average_pairwise_distance() : protocols::rna::setup::RNA_CSA_JobDistributor
• average_residue_hASA() : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::interaction_graph::SurfacePotential
• average_score() : protocols::qsar::scoring_grid::GridSet
• average_score_components() : protocols::ddg::ddGMover
• average_shortest_path_length() : protocols::toolbox::ResidueNetwork
• AverageDegreeFilter() : protocols::protein_interface_design::filters::AverageDegreeFilter
• AveragePathLengthFilter() : protocols::simple_filters::AveragePathLengthFilter
• avg : protocols::make_rot_lib::running_average_pair
• avg_dg_span_multi_ : core::scoring::membrane::MPSpanInsertionEnergy
• avg_dg_span_single_ : core::scoring::membrane::MPSpanInsertionEnergy
• avg_rank_as_energy() : core::scoring::methods::NMerSVMEnergy
• avg_rank_as_energy_ : core::scoring::methods::NMerSVMEnergy
• avg_rho_obs : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• avoid_building_any_rotamers_dueto_native_ : protocols::match::upstream::ProteinUpstreamBuilder
• avoid_negative_zero() : protocols::peptide_deriver::PeptideDeriverOutputter
• avoid_sc_hbonds() : core::scoring::hbonds::hbtrie::HBCPData
• avoid_sc_hbonds_ : core::scoring::hbonds::hbtrie::HBCPData
• ax_ : core::scoring::nmr::NMRTensor , protocols::scoring::methods::pcs2::PcsTensor , protocols::scoring::methods::pcs::PCS_tensor , protocols::scoring::methods::pcsTs1::PCS_tensor_Ts1 , protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2 , protocols::scoring::methods::pcsTs3::PCS_tensor_Ts3 , protocols::scoring::methods::pcsTs4::PCS_tensor_Ts4
• ax_init() : core::optimization::MinimizerOptions
• ax_init_ : core::optimization::MinimizerOptions
• ax_rh_from_eigenvalues() : core::scoring::nmr::pcs::PCSTensor
• ax_rh_to_eigenvalues() : core::scoring::nmr::pcs::PCSTensor
• axis() : protocols::matdes::GetRBDOFValues
• axis_ : protocols::matdes::GetRBDOFValues , protocols::membrane::FlipMover , protocols::rigid::RollMover , protocols::rigid::WholeBodyRotationMover , protocols::simple_moves::UniformRotationMover
• axis_bin_width_ : core::scoring::rna::RNA_LowResolutionPotential
• axis_num_bins_ : core::scoring::rna::RNA_LowResolutionPotential
• axis_origin_ : core::conformation::symmetry::VirtualCoordinate
• axis_primary : protocols::electron_density::DensitySymmInfo
• axis_secondary : protocols::electron_density::DensitySymmInfo
• axis_x_ : core::conformation::symmetry::VirtualCoordinate
• axis_y_ : core::conformation::symmetry::VirtualCoordinate
• axs : protocols::kinmatch::KRSQuery
• azmiuth_max : protocols::hotspot_hashing::SphericalRotationSearchPattern
• azmiuth_min : protocols::hotspot_hashing::SphericalRotationSearchPattern
• azmiuth_rotation_sampling : protocols::hotspot_hashing::SphericalRotationSearchPattern