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ubi_e2c_modeler() : protocols::ub_e2c::ubi_e2c_modeler
UDPSocketClient() : protocols::moves::UDPSocketClient
unaligned() : protocols::star::Extender
unassigned() : protocols::loops::ResidueIndexDescription
unbind() : protocols::protein_interface_design::filters::BindingStrainFilter , protocols::protein_interface_design::filters::FilterScanFilter , protocols::simple_filters::DeltaFilter , protocols::simple_moves::ddG
unbound() : protocols::protein_interface_design::filters::FilterScanFilter , protocols::simple_filters::DeltaFilter , protocols::simple_filters::RelativePoseFilter , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_filters::TaskAwareScoreTypeFilter
unbound_score() : protocols::dna::DnaInterfacePacker
unbound_struct() : protocols::optimize_weights::DGBindOptEData
UnconstrainedTorsionsMover() : protocols::ligand_docking::UnconstrainedTorsionsMover
undefined_positions() : protocols::forge::build::Bridge , protocols::forge::build::BuildInstruction , protocols::forge::build::BuildManager , protocols::forge::build::ConnectRight , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap
unfinished_batches() : protocols::jd2::archive::ArchiveManager
unfolded_energy_emap_vector() : protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData
UnfoldedStateEnergyCalculatorJobDistributor() : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorJobDistributor
UnfoldedStateEnergyCalculatorMover() : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover
UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor() : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor
unfreeze() : protocols::rigid::RigidBodyMover
uniform_modeler() : protocols::stepwise::sampler::MC_StepWiseSampler
uniform_translate_ligand() : protocols::ligand_docking::Translate
UniformPolicy() : protocols::nonlocal::UniformPolicy
UniformRigidBodyCM() : protocols::rigid::UniformRigidBodyCM
UniformRigidBodyMover() : protocols::rigid::UniformRigidBodyMover
UniformRotationMover() : protocols::simple_moves::UniformRotationMover
UniformSphereTransMover() : protocols::rigid::UniformSphereTransMover
UniformTranslationMover() : protocols::simple_moves::UniformTranslationMover
union_of_intervals_containing_undefined_positions() : protocols::forge::build::BuildManager
UnionEdge() : protocols::pockets::UnionEdge
unique_id() : protocols::motifs::IRCollection
unknown_tag() : protocols::topology_broker::TopologyClaimer
unlock_file() : protocols::jd2::archive::ArchiveManager , protocols::jd2::archive::BaseArchiveManager
unlock_semaphore() : protocols::boinc::Boinc
unpack() : protocols::rpc::JSON_RPC
UnrecognizedAtomFeatures() : protocols::features::UnrecognizedAtomFeatures
UnrecognizedAtomFeaturesCreator() : protocols::features::UnrecognizedAtomFeaturesCreator
up_coll_filt() : protocols::match::output::MatchProcessor
up_down_filt() : protocols::match::output::MatchProcessor
update() : protocols::canonical_sampling::BiasEnergy , protocols::hybridization::HybridizeFoldtreeDynamic , protocols::stepwise::sampler::MC_Comb , protocols::stepwise::sampler::MC_OneTorsion , protocols::stepwise::sampler::MC_StepWiseSampler , protocols::stepwise::sampler::rna::RNA_MC_Sugar , protocols::toolbox::GreedyKCenter , protocols::toolbox::KCluster , protocols::toolbox::KMedoid , protocols::trajectory::DbTrajectoryWriter , protocols::viewer::triangle
update_a_ik() : protocols::cluster::APCluster
update_after_boltzmann() : protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::TrajectoryRecorder , protocols::simple_moves::DOFHistogramRecorder
update_allow_insert() : protocols::farna::RNA_ChunkLibrary
update_allow_insert_with_extra_minimize_res() : protocols::farna::RNA_Minimizer
update_allow_sc_vectors() : protocols::loops::loop_mover::refine::LoopMover_Refine_KIC
update_assignment_list() : protocols::noesy_assign::CrossPeakList
update_bank() : protocols::stepwise::setup::StepWiseCSA_JobDistributor
update_base_bin_map() : protocols::stepwise::screener::BaseBinMapUpdater
update_base_stub_list() : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
update_base_stub_list_and_check_centroid_interaction() : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
update_base_stub_list_and_check_that_terminal_res_are_unstacked() : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
update_bond_connections() : protocols::noesy_assign::ResonanceList
update_calc_rms_atom_id_map() : protocols::stepwise::modeler::align::StepWisePoseAligner
update_center() : protocols::pockets::SmallMol
update_chemshiftscore() : protocols::noesy_assign::CrossPeakList
update_chemshiftscore_from_peak() : protocols::noesy_assign::PeakAssignment
update_chunks() : protocols::rigid::RigidBodyMotionMover
update_com() : protocols::environment::CoMTrackerCM
update_comm() : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
update_counting_last_PDR() : protocols::simple_moves::BBGaussianMover
update_decoy_compatibility_score() : protocols::noesy_assign::CrossPeakList
update_denovo_scorefxn_weights() : protocols::farna::RNA_DeNovoProtocol
update_domain_rot_trans_mag() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol
update_energy() : protocols::moves::PyMolMover
update_entity_history() : protocols::pack_daemon::MultistateFitnessFunction , protocols::pack_daemon::TopEntitySet
update_fold_tree_at_virtual_sugars() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
update_frag_size() : protocols::farna::RNA_DeNovoProtocol
update_fragment_library_pointers() : protocols::hybridization::CartesianSampler
update_full_model_info_and_switch_focus_to_new_pose() : protocols::stepwise::monte_carlo::mover::FromScratchMover
update_grids() : protocols::qsar::scoring_grid::GridManager
update_hydrogens() : protocols::simple_moves::oop::OopMover
update_hydrogens_() : protocols::simple_moves::oop::OopMover
update_indices() : protocols::fldsgn::topology::BB_Pos
update_inertia_tensor() : protocols::normalmode::NormalMode
update_insert_map() : protocols::farna::RNA_FragmentMover , protocols::simple_moves::FragmentMover
update_internal_energy_sums() : protocols::flexpack::interaction_graph::FlexbbNode
update_internal_energy_totals() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
update_internal_vectors() : protocols::flexpack::interaction_graph::FlexbbNode
update_interval() : protocols::moves::PyMolMover
update_library_NSGAII() : protocols::mpi_refinement::MPI_Refinement , protocols::mpi_refinement::MultiObjective
update_matrix_A() : 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
update_matrix_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
update_matrix_A_all_for_cstyle() : protocols::scoring::methods::pcs2::PcsDataCenter
update_matrix_A_all_for_svd() : protocols::scoring::methods::pcs2::PcsDataCenter
update_matrix_A_cstyle() : protocols::scoring::methods::pcs2::PcsDataCenter
update_max_seq_sep() : protocols::abinitio::abscript::AbscriptStageMover
update_movemap() : protocols::docking::SidechainMinMover , protocols::symmetric_docking::SymSidechainMinMover
update_movemap_vectors() : protocols::loops::loop_mover::refine::LoopMover_Refine_KIC
update_moves() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::MembraneAbinitio
update_my_A_matrix() : 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
update_my_A_matrix_for_cstyle() : protocols::scoring::methods::pcs2::PcsDataLanthanide
update_my_A_matrix_for_svd() : protocols::scoring::methods::pcs2::PcsDataLanthanide
update_noesy_filter_files() : protocols::abinitio::IterativeBase , protocols::abinitio::IterativeCentroid
update_offset_data() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
update_one_body_energy() : protocols::flexpack::interaction_graph::FlexbbNode
update_original_weights() : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
update_packer_task() : protocols::simple_moves::MSDMover
update_pct_complete() : protocols::boinc::Boinc
update_pdb_numbering() : protocols::cyclic_peptide::PeptideStubMover
update_pdb_remarks() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
update_pdb_remarks_for_backbone_params() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
update_pdblist_file() : protocols::docking::DockingEnsemble
update_peak_volumina() : protocols::noesy_assign::CrossPeakList
update_pose_constraints() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::RNA_DeNovoProtocol
update_pose_list() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection
update_r_ik() : protocols::cluster::APCluster
update_range() : protocols::optimize_weights::OptEPositionData
update_ranks() : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD
update_reference_pose_local() : protocols::stepwise::modeler::align::StepWisePoseAligner
update_residue_map() : protocols::noesy_assign::ResonanceList
update_resonances_from_peak() : protocols::noesy_assign::PeakAssignment
update_restraint() : protocols::md::CartesianMD
update_rhos_() : protocols::pockets::PlaidFingerprint
update_rot_trans_mag() : protocols::farna::MultipleDomainMover
update_rotamer_ids() : protocols::stepwise::sampler::StepWiseSamplerSizedComb
update_sampler_weights() : protocols::hybridization::WeightedFragmentSmoothTrialMover , protocols::hybridization::WeightedFragmentTrialMover
update_segments() : protocols::backrub::BackrubSidechainMover
update_sequence() : protocols::antibody_legacy::Antibody , protocols::loops::loop_closure::kinematic_closure::KinematicMover
update_superimpose_atom_id_map() : protocols::stepwise::modeler::align::StepWisePoseAligner
update_symmetry_score() : protocols::noesy_assign::CrossPeakList
update_task_and_neighbors() : protocols::enzdes::PackRotamersMoverPartGreedy
update_tracking_residue() : protocols::environment::CoMTrackerCM
update_type() : protocols::backrub::BackrubMover , protocols::backrub::BackrubSidechainMover , protocols::simple_moves::sidechain_moves::SidechainMover
update_upperdistance_score() : protocols::noesy_assign::CrossPeakList , protocols::noesy_assign::PeakAssignment
update_value_from_list() : protocols::optimize_weights::OptEVariableExpression
update_VDW_screen_bin() : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
update_weighted_total() : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
update_weights() : protocols::moves::RampingMover
update_working_moving_suite() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
update_working_sequence() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
update_X_Y_Z_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
updateChains() : protocols::flexpep_docking::FlexPepDockingFlags
updateChainsAndAnchors_fromParamsFile() : protocols::flexpep_docking::FlexPepDockingFlags
UpdateEnzdesHeaderMover() : protocols::enzdes::UpdateEnzdesHeaderMover
UpdateSolventMover() : protocols::cryst::UpdateSolventMover
updateWithDsspAssignment() : protocols::forge::remodel::RemodelData
upper() : protocols::protein_interface_design::filters::Torsion , protocols::simple_filters::DeltaFilter
upper_chain() : protocols::toolbox::task_operations::RestrictToInterfaceVectorOperation
upper_threshold() : protocols::matdes::InterfacePackingFilter , protocols::matdes::SymUnsatHbondFilter , protocols::protein_interface_design::filters::DesignableResiduesFilter
upper_value() : protocols::helical_bundle::PerturbBundleOptions
upstream_builder() : protocols::match::Matcher
upstream_conf_id() : protocols::match::Hit , protocols::match::upstream_hit
upstream_conformation_for_hit() : protocols::match::output::UpstreamHitCacher
upstream_downstream_atom_collision_tolerance() : protocols::match::MatcherTask
upstream_downstream_residue_collision_score_cutoff() : protocols::match::MatcherTask
upstream_downstream_residue_collision_Wfa_atr() : protocols::match::MatcherTask
upstream_downstream_residue_collision_Wfa_rep() : protocols::match::MatcherTask
upstream_downstream_residue_collision_Wfa_sol() : protocols::match::MatcherTask
upstream_hit() : protocols::match::upstream_hit
upstream_only() : protocols::match::downstream::ClassicMatchAlgorithm , protocols::match::downstream::DownstreamAlgorithm , protocols::match::downstream::SecondaryMatcherToDownstreamResidue , protocols::match::downstream::SecondaryMatcherToUpstreamResidue , protocols::match::output::WriteUpstreamCoordinateKinemage
upstream_only_geom_cst() : protocols::match::MatcherTask
upstream_pose() : protocols::match::Matcher , protocols::match::MatcherTask
upstream_pose_build_resids_for_geometric_constraint() : protocols::match::MatcherTask
upstream_pose_name() : protocols::match::MatcherTask
upstream_res() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
upstream_resids_and_radii_defining_active_site() : protocols::match::MatcherTask
upstream_residue_collision_score_cutoff() : protocols::match::MatcherTask
upstream_residue_collision_tolerance() : protocols::match::MatcherTask
upstream_residue_collision_Wfa_atr() : protocols::match::MatcherTask
upstream_residue_collision_Wfa_rep() : protocols::match::MatcherTask
upstream_residue_collision_Wfa_sol() : protocols::match::MatcherTask
upstream_restypes() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList
UpstreamCollisionFilter() : protocols::match::output::UpstreamCollisionFilter
UpstreamDownstreamCollisionFilter() : protocols::match::output::UpstreamDownstreamCollisionFilter
UpstreamHitCacher() : protocols::match::output::UpstreamHitCacher
UpstreamResTypeGeometry() : protocols::match::upstream::UpstreamResTypeGeometry
use_abego_bias() : protocols::fldsgn::BluePrintBDR
use_all_blocks() : protocols::forge::remodel::RemodelEnzdesCstModule
use_backbone_only_blocks() : protocols::forge::remodel::RemodelEnzdesCstModule
use_cartesian() : protocols::loop_modeling::refiners::MinimizationRefiner
use_coarse_vdw() : protocols::relax::ClassicRelax
use_coordinate_constraints() : protocols::farna::RNA_Minimizer , protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer
use_current_pose() : protocols::toolbox::task_operations::JointSequenceOperation
use_custom_task() : protocols::simple_filters::DdgFilter , protocols::simple_moves::ddG
use_cutpoints() : protocols::seeded_abinitio::CloseFold , protocols::seeded_abinitio::DefineMovableLoops
use_default_movemap() : protocols::grafting::AnchoredGraftMover
use_defaults() : protocols::helical_bundle::PerturbBundleOptions
use_different_build_points_for_each_geometric_constraint() : protocols::match::MatcherTask
use_distance_cst() : protocols::simple_moves::AddConstraintsToCurrentConformationMover
use_fragments() : protocols::loop_modeling::LoopBuilder
use_fullmer() : protocols::fldsgn::BluePrintBDR , protocols::forge::components::BDR , protocols::forge::components::VarLengthBuild
use_green_packer() : protocols::stepwise::modeler::options::StepWiseBasicModelerOptions
use_hierarchical_clustering() : protocols::canonical_sampling::CanonicalSamplingMover
use_input_for_ref() : protocols::jd2::AtomTreeDiffJobOutputter
use_input_sc() : protocols::match::MatcherTask
use_interface() : protocols::dna::DnaInterfaceMinMover
use_job_pose() : protocols::topology_broker::TopologyBroker
use_late_scoring_for_zeros() : protocols::frag_picker::scores::FragmentScoreManager
use_loops_from_observer_cache() : protocols::loops::loop_mover::LoopMover
use_loops_from_threading_job() : protocols::topology_broker::RigidChunkClaimer
use_mean() : protocols::ddg::ddGMover
use_min() : protocols::ddg::ddGMover
use_mover_status() : protocols::moves::SequenceMover
use_MPI_bcast() : protocols::canonical_sampling::CanonicalSamplingMover
use_MPI_sync_pools() : protocols::canonical_sampling::CanonicalSamplingMover
use_natro() : protocols::toolbox::task_operations::JointSequenceOperation
use_nobias() : protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy
use_numbers() : protocols::toolbox::pose_metric_calculators::ResidueDecompositionByChainCalculator
use_only_calpha() : protocols::fldsgn::NcontactsCalculator
use_original_seq() : protocols::flxbb::LayerDesignOperation
use_original_weights() : protocols::toolbox::pose_metric_calculators::EnergiesData
use_origseq_for_not_dsgned_layer() : protocols::flxbb::FlxbbDesign
use_packer_instead_of_rotamer_trials() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
use_phenix_geo() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
use_pose_sequence_as_native() : protocols::antibody::design::ConservativeDesignOperation
use_precomputed_library() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
use_prefiltering() : protocols::loophash::LoopHashSampler
use_preset_task() : protocols::simple_moves::DesignRepackMover
use_rama_2B() : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
use_random_conformer() : protocols::docking::ConformerSwitchMover
use_rattle() : protocols::md::CartesianMD
use_rt() : protocols::forge::build::ConnectRight
use_sequence_bias() : protocols::fldsgn::BluePrintBDR , protocols::forge::components::BDR
use_sidechain_neighbors() : protocols::toolbox::SelectResiduesByLayer
use_ss_length_screen() : protocols::simple_moves::SmoothFragmentMover
user_inputted_VDW_screen_pose() : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
user_options() : protocols::jd2::archive::Batch
user_provided_movers_apply_cycle() : protocols::forge::remodel::RemodelLoopMover
using_parser() : protocols::jd2::JobDistributor