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

- p -

• p : protocols::environment::claims::CutBiasElement , protocols::environment::claims::CutElement , protocols::forge::build::CountFromLeft , protocols::sic_dock::Rose
• p0() : protocols::features::helixAssembly::HelicalFragment
• p0_ : protocols::features::helixAssembly::HelicalFragment
• P0_ : protocols::simple_moves::PeriodicBoxMover
• p0_E_ : core::scoring::P_AA_ss
• p0_H_ : core::scoring::P_AA_ss
• p0_L_ : core::scoring::P_AA_ss
• p1 : protocols::environment::claims::JumpElement , protocols::features::helixAssembly::HelicalFragment
• p1_ : protocols::features::helixAssembly::HelicalFragment
• p1_cosine_deriv() : core::scoring::constraints::DihedralConstraint
• p1_deriv() : core::scoring::constraints::AngleConstraint
• p1_theta_deriv() : core::scoring::constraints::AngleConstraint
• p2 : protocols::environment::claims::JumpElement
• p2_cosine_deriv() : core::scoring::constraints::DihedralConstraint
• p2_deriv() : core::scoring::constraints::AngleConstraint
• p_ : core::optimization::Particle , core::scoring::fiber_diffraction::FiberDiffractionEnergy , core::scoring::fiber_diffraction::FiberDiffractionEnergyDens
• P_AA() : core::scoring::P_AA
• P_aa1 : core::scoring::motif::RPM_FilterStats
• P_aa2 : core::scoring::motif::RPM_FilterStats
• p_aa_ : core::scoring::methods::P_AA_Energy , core::scoring::methods::P_AA_pp_Energy
• P_AA_ : core::scoring::P_AA
• p_aa_ : core::scoring::ScoringManager
• P_AA_Energy() : core::scoring::methods::P_AA_Energy
• P_AA_energy() : core::scoring::P_AA
• P_AA_initialize() : core::scoring::P_AA
• P_AA_n_ : core::scoring::P_AA
• P_AA_pp_ : core::scoring::P_AA
• P_AA_pp_Energy() : core::scoring::methods::P_AA_pp_Energy
• P_AA_pp_energy() : core::scoring::P_AA
• P_AA_pp_energy_splines_ : core::scoring::P_AA
• P_AA_ss() : core::scoring::P_AA_ss
• P_AA_ss_ : core::scoring::methods::P_AA_ss_Energy
• p_aa_ss_ : core::scoring::ScoringManager
• P_AA_SS_burial_ : protocols::simple_moves::StructProfileMover
• P_AA_ss_Energy() : core::scoring::methods::P_AA_ss_Energy
• P_AA_ss_energy() : core::scoring::P_AA_ss
• p_atom_index() : core::chemical::rna::RNA_ResidueType
• p_atom_index_ : core::chemical::rna::RNA_ResidueType
• p_cond_ : protocols::moves::WhileMover
• P_coorderr : core::scoring::motif::RPM_FilterStats
• p_DMS_ : core::scoring::rna::data::RNA_DMS_Potential
• P_dssp1 : core::scoring::motif::RPM_FilterStats
• P_dssp2 : core::scoring::motif::RPM_FilterStats
• p_E_ : core::scoring::P_AA_ss
• P_faatr : core::scoring::motif::RPM_FilterStats
• P_faatr_or_hb : core::scoring::motif::RPM_FilterStats
• P_faatr_or_hbbb : core::scoring::motif::RPM_FilterStats
• p_H_ : core::scoring::P_AA_ss
• P_hb_bb : core::scoring::motif::RPM_FilterStats
• P_hb_bb_sc : core::scoring::motif::RPM_FilterStats
• P_hb_sc : core::scoring::motif::RPM_FilterStats
• p_i_given_iplus1() : core::scoring::bin_transitions::BinTransitionCalculator
• p_iplus1_given_i() : core::scoring::bin_transitions::BinTransitionCalculator
• p_L_ : core::scoring::P_AA_ss
• P_lig : core::scoring::motif::RPM_FilterStats
• p_max_ : core::optimization::ParticleSwarmMinimizer
• P_max_seqsep : core::scoring::motif::RPM_FilterStats
• P_maxdist2 : core::scoring::motif::RPM_FilterStats
• p_min_ : core::optimization::ParticleSwarmMinimizer
• P_mindist2 : core::scoring::motif::RPM_FilterStats
• p_model_ : core::scoring::rna::data::RNA_DMS_Potential
• P_no_hb_bb : core::scoring::motif::RPM_FilterStats
• P_nodisulf : core::scoring::motif::RPM_FilterStats
• P_noloops : core::scoring::motif::RPM_FilterStats
• P_not_restype : core::scoring::motif::RPM_FilterStats
• P_not_restype_one : core::scoring::motif::RPM_FilterStats
• P_occupancy : core::scoring::motif::RPM_FilterStats
• P_oneloop : core::scoring::motif::RPM_FilterStats
• P_pdb : core::scoring::motif::RPM_FilterStats
• p_range_ : core::optimization::ParticleSwarmMinimizer
• P_restype : core::scoring::motif::RPM_FilterStats
• P_restype1 : core::scoring::motif::RPM_FilterStats
• P_restype2 : core::scoring::motif::RPM_FilterStats
• P_restype_one : core::scoring::motif::RPM_FilterStats
• P_score : core::scoring::motif::RPM_FilterStats
• P_seqsep : core::scoring::motif::RPM_FilterStats
• P_ss1 : core::scoring::motif::RPM_FilterStats
• P_ss2 : core::scoring::motif::RPM_FilterStats
• P_type_BB_BB : core::scoring::motif::RPM_FilterStats
• P_type_BB_PH : core::scoring::motif::RPM_FilterStats
• P_type_BB_PO : core::scoring::motif::RPM_FilterStats
• P_type_PH_PO : core::scoring::motif::RPM_FilterStats
• P_type_SC_BB : core::scoring::motif::RPM_FilterStats
• P_type_SC_PH : core::scoring::motif::RPM_FilterStats
• P_type_SC_PO : core::scoring::motif::RPM_FilterStats
• P_type_SC_SC : core::scoring::motif::RPM_FilterStats
• P_uniformfrag : core::scoring::motif::RPM_FilterStats
• p_value() : protocols::frag_picker::scores::AdaptiveScoreHistogram
• pack_ : protocols::residue_optimization::MetapatchEnumeration
• pack_all_side_chains() : protocols::stepwise::modeler::packer::StepWisePacker
• pack_all_side_chains_ : protocols::stepwise::modeler::packer::StepWisePacker
• pack_cst_scorefxn_ : protocols::ub_e2c::ubi_e2c_modeler
• pack_full_repack_ : protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionSampler , protocols::relax::ClassicRelax
• pack_glycans_ : protocols::carbohydrates::GlycanRelaxMover
• pack_input_ : protocols::analysis::InterfaceAnalyzerMover
• pack_interface_repack_ : protocols::symmetric_docking::SymDockingHiRes
• pack_mg_water_hydrogens_in_pose() : protocols::magnesium::MgWaterHydrogenPacker
• pack_missing_sidechains() : core::import_pose::ImportPoseOptions , protocols::hybridization::MRMover
• pack_missing_sidechains_ : core::import_pose::ImportPoseOptions
• pack_neighbors_ : protocols::simple_moves::SimpleThreadingMover
• pack_o2prime_hydrogens() : protocols::stepwise::modeler::packer::StepWisePacker
• pack_o2prime_hydrogens_ : protocols::stepwise::modeler::packer::StepWisePacker
• pack_operations_ : protocols::docking::DockingEnsemble , protocols::docking::DockingEnsemblePrepackProtocol , protocols::docking::DockingPrepackProtocol
• pack_phosphate_penalty() : core::scoring::methods::FreeDOF_Options
• pack_phosphate_penalty_ : core::scoring::methods::FreeDOF_Options
• pack_region_ala_pose_ : protocols::enzdes::EnzdesFlexBBProtocol
• pack_residue() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• pack_residue_ : core::pack::task::PackerTask_
• pack_rotamers_ : protocols::abinitio::ClassicAbinitio
• pack_rotamers_fullatom_ : protocols::surface_docking::SurfaceDockingProtocol
• pack_rottrial_ : protocols::relax::ClassicRelax , protocols::symmetric_docking::SymDockingHiRes
• pack_rounds_ : protocols::simple_moves::SimpleThreadingMover
• pack_scorefxn_ : protocols::antibody::AntibodyModelerProtocol , protocols::antibody::LHRepulsiveRamp , protocols::antibody::LHRepulsiveRampLegacy , protocols::antibody::RefineBetaBarrel , protocols::stepwise::modeler::StepWiseModeler , protocols::ub_e2c::ubi_e2c_modeler
• pack_scrfxn_ : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover
• pack_separated_ : protocols::analysis::InterfaceAnalyzerMover , protocols::features::InterfaceFeatures
• pack_sfxn_ : protocols::relax::LocalRelax
• pack_shell_ : protocols::antibody::design::MutateFrameworkForCluster
• pack_task_ : protocols::stepwise::modeler::packer::StepWisePacker
• pack_together_ : protocols::features::InterfaceFeatures
• pack_virtual_o2prime_hydrogen_ : protocols::stepwise::modeler::rna::o2prime::O2PrimePacker
• pack_weights() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• pack_weights_ : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• PACKABLE : protocols::flxbb::LayerDesignOperation
• packable() : protocols::protein_interface_design::filters::DesignableResiduesFilter , protocols::simple_filters::MutationsFilter , protocols::simple_filters::ResidueCountFilter
• packable_ : protocols::protein_interface_design::filters::DesignableResiduesFilter , protocols::simple_filters::MutationsFilter , protocols::simple_filters::ResidueCountFilter
• PackDaemon() : protocols::pack_daemon::PackDaemon
• packed_residues() : protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• packed_residues_ : protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• packed_rotamer_2_regular_rotamer() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::rotamers::RotamericSingleResiduePeptoidLibrary< T, N >
• packed_rotno() : core::pack::dunbrack::PackedDunbrackRotamer< S, N, P >
• packed_rotno_ : core::pack::dunbrack::BBDepNRChiSample< P > , core::pack::dunbrack::PackedDunbrackRotamer< S, N, P >
• packed_rotno_2_rotno_ : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::rotamers::SingleResiduePeptoidLibrary
• packed_rotno_2_rotwell() : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::rotamers::SingleResiduePeptoidLibrary
• packed_rotno_2_rotwell_ : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::rotamers::SingleResiduePeptoidLibrary
• packed_rotno_2_sorted_rotno() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::rotamers::RotamericSingleResiduePeptoidLibrary< T, N >
• packed_rotno_2_sorted_rotno_ : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >
• packed_rotno_conversion_data_current_ : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::rotamers::SingleResiduePeptoidLibrary
• PackedDunbrackRotamer() : core::pack::dunbrack::PackedDunbrackRotamer< S, N, P >
• packer() : protocols::stepwise::modeler::packer::StepWiseMasterPacker
• packer_ : protocols::antibody_legacy::GraftMover , protocols::stepwise::modeler::packer::StepWiseMasterPacker
• packer_neighbor_graph_ : core::optimization::SingleResidueMultifunc
• packer_pose_ : protocols::stepwise::modeler::packer::StepWiseMasterPacker
• packer_task() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• packer_task_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::task::residue_selector::ClashBasedRepackShellSelector , protocols::simple_moves::CoupledMover
• PackerEnergy : protocols::flexpack::annealer::FlexbbSimAnnealer , protocols::flexpack::interaction_graph::FlexbbEdge , protocols::flexpack::interaction_graph::FlexbbInteractionGraph , protocols::flexpack::interaction_graph::FlexbbNode , protocols::flexpack::interaction_graph::OTFFlexbbNode , protocols::flexpack::rotamer_set::FlexbbRotamerSets
• PackerEnergyAdd() : core::pack::rotamer_set::symmetry::SymmetricRotamerSet_
• PackerEnergyMultiply() : core::pack::rotamer_set::symmetry::SymmetricRotamerSet_
• PackerEnergySubtract() : core::pack::rotamer_set::symmetry::SymmetricRotamerSet_
• PackerNeighborGraphFilter() : protocols::simple_filters::PackerNeighborGraphFilter
• PackerTask : core::pack::task::operation::NoRepackDisulfides , core::pack::task::operation::OptCysHG , core::pack::task::operation::OptH , protocols::dna::RestrictDesignToProteinDNAInterface , protocols::dna::WatsonCrickRotamerCouplings , protocols::enzdes::AddLigandMotifRotamers , protocols::enzdes::AddRigidBodyLigandConfs , protocols::enzdes::DetectProteinLigandInterface , protocols::enzdes::ProteinLigandInterfaceUpweighter , protocols::enzdes::SetCatalyticResPackBehavior
• packertask() : protocols::flxbb::DesignTask
• PackerTask : protocols::flxbb::LayerDesignOperation , protocols::forge::remodel::RemodelAccumulator , protocols::forge::remodel::RemodelDesignMover , protocols::forge::remodel::RemodelGlobalFrame , protocols::forge::remodel::RemodelRotamerLinks , protocols::motifs::LigandMotifSearch , protocols::pack_daemon::DaemonSet , protocols::pack_daemon::PackDaemon , protocols::simple_moves::BoltzmannRotamerMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::RotamerTrialsMinMover , protocols::simple_moves::RotamerTrialsMover , protocols::toolbox::task_operations::ImportUnboundRotamersOperation , protocols::toolbox::task_operations::JointSequenceOperation , protocols::toolbox::task_operations::LimitAromaChi2_RotamerSetOperation , protocols::toolbox::task_operations::LimitAromaChi2Operation , protocols::toolbox::task_operations::LinkResidues , protocols::toolbox::task_operations::RestrictNativeResiduesOperation , protocols::toolbox::task_operations::SeqprofConsensusOperation
• PackerTask_() : core::pack::task::PackerTask_
• PackerTaskCOP : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubsets , core::pack::rotamer_set::symmetry::SymmetricRotamerSets , protocols::dna::DnaInterfaceMultiStateDesign , protocols::dna::PDBOutput , protocols::flexpack::rotamer_set::FlexbbRotamerSets , protocols::flxbb::FlxbbDesignPack , protocols::pack_daemon::PackDaemon , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover , protocols::simple_moves::BoltzmannRotamerMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::MinPackMover , protocols::simple_moves::PackRotamersMover , protocols::simple_moves::RotamerizeMover , protocols::simple_moves::RotamerTrialsMinMover , protocols::simple_moves::RotamerTrialsMover , protocols::toolbox::task_operations::LimitAromaChi2_RotamerSetOperation
• PackerTaskOP : protocols::enzdes::PackRotamersMoverPartGreedy , protocols::flxbb::DesignTask , protocols::flxbb::DesignTask_Layer , protocols::flxbb::DesignTask_Normal , protocols::forge::remodel::RemodelAccumulator , protocols::forge::remodel::RemodelDesignMover , protocols::forge::remodel::RemodelGlobalFrame , protocols::pack_daemon::DaemonSet , protocols::pack_daemon::PackDaemon , protocols::pack_daemon::QuickRepacker , protocols::scoring::Interface , protocols::simple_moves::BoltzmannRotamerMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::GreenPacker , protocols::simple_moves::RotamerizeMover , protocols::simple_moves::RotamerTrialsMinMover , protocols::simple_moves::RotamerTrialsMover
• packing_angle_degrees_ : protocols::sewing::Model
• packing_angle_enum_to_string() : protocols::antibody::AntibodyEnumManager
• packing_angle_numbering_ : protocols::antibody::AntibodyInfo
• packing_angle_residues_ : protocols::antibody::AntibodyInfo
• packing_angle_string_to_enum() : protocols::antibody::AntibodyEnumManager
• packing_angle_to_enum_ : protocols::antibody::AntibodyEnumManager
• packing_angle_to_string_ : protocols::antibody::AntibodyEnumManager
• packing_interaction_cutoff() : core::scoring::methods::FACTSEnergy , core::scoring::methods::GenBornEnergy , core::scoring::methods::MultipoleElecEnergy , core::scoring::methods::VdWTinkerEnergy
• packing_isolated_to_active_loops_ : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• packing_range_ : protocols::sewing::NodeConstraint
• packing_shell() : protocols::simple_filters::RelativePoseFilter
• packing_shell_ : protocols::simple_filters::RelativePoseFilter
• PackingScore() : core::scoring::packstat::PackingScore
• PackingScoreResData() : core::scoring::packstat::PackingScoreResData
• PackingState() : protocols::multistate_design::PackingState
• packonly_after_graft_ : protocols::antibody::AntibodyModelerProtocol , protocols::antibody::GraftCDRLoopsProtocol
• PackRotamersMover() : protocols::simple_moves::PackRotamersMover
• packrotamersmover_ : protocols::backrub::BackrubProtocol
• PackRotamersMoverLazy() : protocols::simple_moves::PackRotamersMoverLazy
• PackRotamersMoverPartGreedy() : protocols::enzdes::PackRotamersMoverPartGreedy
• PackScreener() : protocols::stepwise::screener::PackScreener
• packstat : protocols::analysis::InterfaceData
• packstat_pdb_ : protocols::analysis::PackStatMover
• PackstatCalculator() : protocols::toolbox::pose_metric_calculators::PackstatCalculator
• PackStatEnergy() : core::scoring::methods::PackStatEnergy
• PackStatFilter() : protocols::simple_filters::PackStatFilter
• PackStatMover() : protocols::analysis::PackStatMover
• packtask_ : protocols::seeded_abinitio::SeedSetupMover
• Page : core::fragment::picking_old::concepts::Book< Pages > , core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library > , core::fragment::picking_old::vall::VallResidues
• PageConstIterator : core::fragment::picking_old::concepts::Book< Pages > , core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library > , core::fragment::picking_old::vall::eval::ABEGOEval , core::fragment::picking_old::vall::eval::EnergyEval , core::fragment::picking_old::vall::eval::IdentityEval , core::fragment::picking_old::vall::eval::VallFragmentEval , core::fragment::picking_old::vall::scores::VallFragmentScore , core::fragment::picking_old::vall::VallLibrarian , core::fragment::picking_old::vall::VallSection
• PageIterator : core::fragment::picking_old::concepts::Book< Pages > , core::fragment::picking_old::concepts::Extent< PageIterator > , core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library > , core::fragment::picking_old::vall::gen::LengthGen , core::fragment::picking_old::vall::gen::SecStructGen , core::fragment::picking_old::vall::gen::VallFragmentGen , core::fragment::picking_old::vall::VallLibrarian , core::fragment::picking_old::vall::VallSection
• pages() : core::fragment::picking_old::concepts::Book< Pages >
• pages_ : core::fragment::picking_old::concepts::Book< Pages >
• pair_ : core::scoring::SmoothEnvPairPotential
• pair_allowed() : protocols::denovo_design::connection::Connection
• pair_and_func_map_ : core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy
• pair_bin_lower_bounds_ : core::scoring::dna::DNA_EnvPairPotential
• pair_corr_ : core::scoring::PairEPotential
• pair_dis_ : protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD
• pair_dp() : core::scoring::SecondaryStructurePotential , protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential
• pair_energy_H() : core::scoring::etable::AnalyticEtableEvaluator , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::etable::TableLookupEvaluator
• pair_energy_H_v() : core::scoring::etable::AnalyticEtableEvaluator , core::scoring::etable::EtableEvaluator , core::scoring::etable::TableLookupEvaluator
• pair_has_linkage_statistics() : core::chemical::carbohydrates::CarbohydrateInfoManager
• pair_list() : protocols::scoring::Interface
• pair_list_ : protocols::scoring::Interface
• pair_log_ : core::scoring::EnvPairPotential
• pair_overlap_tolerance() : protocols::match::BumpGrid
• pair_permit_overlap_ : protocols::match::BumpGrid
• pair_score_bin_base_ : core::scoring::PairEPotential
• pair_score_bin_range_ : core::scoring::PairEPotential
• pair_score_cb_thresh_ : core::scoring::PairEPotential
• pair_score_min_sep_ : core::scoring::PairEPotential
• pair_set_ : core::scoring::dssp::Dssp
• pair_sets_with_positions() : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• pair_stats_ : core::scoring::dna::DNA_EnvPairPotential
• pair_term_energy() : core::scoring::PairEPotential
• pair_term_energy_and_deriv() : core::scoring::PairEPotential
• pair_term_energy_exists() : core::scoring::PairEPotential
• pair_vector_ : protocols::toolbox::task_operations::RestrictInterGroupVectorOperation
• pair_with_scaffold() : protocols::hotspot_hashing::HotspotStub , protocols::hotspot_hashing::HotspotStubSet
• paircover : core::scoring::motif::MotifHits
• pairE_potential_ : core::scoring::ScoringManager
• paired() : core::scoring::dssp::Dssp , core::scoring::dssp::StrandPairing , core::scoring::dssp::StrandPairingSet , protocols::dna::DnaPosition
• paired_ : protocols::dna::DnaPosition
• PairEnergy() : core::scoring::methods::PairEnergy
• PairEPotential() : core::scoring::PairEPotential
• PairFeatures() : protocols::features::PairFeatures
• PairFeaturesCreator() : protocols::features::PairFeaturesCreator
• PairFuncMap : core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy
• Pairing() : core::scoring::dssp::Pairing
• pairing() : protocols::abinitio::PairingStatEntry
• pairing1 : core::scoring::dssp::StrandPairing
• pairing2 : core::scoring::dssp::StrandPairing
• pairing_dists_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• PairingLibrary() : protocols::jumping::PairingLibrary
• Pairings : protocols::abinitio::AlternativePairings
• pairings() : protocols::abinitio::Templates
• pairings_ : core::scoring::dssp::StrandPairingSet , protocols::abinitio::AlternativePairings , protocols::abinitio::Templates , protocols::jumping::DisulfPairingLibrary , protocols::jumping::MembraneJump , protocols::jumping::PairingLibrary , protocols::jumping::SheetBuilder , protocols::topology_broker::TemplateJumpClaimer
• pairings_file_ : protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol
• pairings_size() : protocols::jumping::MembraneJump
• pairings_size_ : protocols::jumping::MembraneJump
• PairingStatEntry() : protocols::abinitio::PairingStatEntry
• PairingStatistics() : protocols::abinitio::PairingStatistics
• PairingTemplate() : protocols::jumping::PairingTemplate
• PairingTemplateList : protocols::jumping::PairingLibrary
• PairingTemplateMap : protocols::jumping::PairingLibrary
• PairList : protocols::sparta::PDB
• pairs() : core::sequence::PairScoringScheme
• pairs_ : core::sequence::PairScoringScheme
• PairScoringScheme() : core::sequence::PairScoringScheme
• pairsplines_ : core::scoring::CenRotEnvPairPotential
• PalesEvaluator() : protocols::simple_filters::PalesEvaluator
• PalesEvaluatorCreator() : protocols::simple_filters::PalesEvaluatorCreator
• PARALLEL : core::scoring::dssp::Pairing
• parallel() : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator
• parallel_ : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator
• parallel_weight_ : core::scoring::SecondaryStructureWeights
• ParallelBetaPairingPreferenceFilter() : protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter
• ParallelTempering() : protocols::canonical_sampling::ParallelTempering
• param() : core::scoring::packing::HolesParamsRes
• param1() : protocols::branch_angle::BranchAngleOptimizer , protocols::relax::RelaxScriptCommand
• param2() : protocols::branch_angle::BranchAngleOptimizer , protocols::relax::RelaxScriptCommand
• param3 : protocols::relax::RelaxScriptCommand
• param4 : protocols::relax::RelaxScriptCommand
• param_cache() : protocols::toolbox::match_enzdes_util::EnzdesCstCache
• param_cache_ : protocols::toolbox::match_enzdes_util::EnzdesCstCache
• param_index() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• param_index_ : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• param_set_ : core::scoring::methods::MMBondAngleEnergy
• Param_TA : core::scoring::GenBornPotential
• Param_TB : core::scoring::GenBornPotential
• Param_TC : core::scoring::GenBornPotential
• Param_TD : core::scoring::GenBornPotential
• Param_TDD : core::scoring::GenBornPotential
• param_type_ : protocols::simple_filters::RepeatParameterFilter
• ParamB : core::scoring::GenBornPotential
• ParamD : core::scoring::GenBornPotential
• parameter_set4final() : protocols::hybridization::TMalign
• parameter_set4scale() : protocols::hybridization::TMalign
• parameter_set4search() : protocols::hybridization::TMalign
• parameter_tag_ : protocols::qsar::scoring_grid::LigandPropertyScore
• parameter_values_as_res_lists_ : core::pose::full_model_info::FullModelParameters
• parameter_values_at_res_ : core::pose::full_model_info::FullModelParameters
• Parameters : core::conformation::Conformation , core::conformation::parametric::Parameters
• parameters() : core::conformation::parametric::ParametersSet
• Parameters : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters , protocols::helical_bundle::parameters::BundleParametersSet , protocols::helical_bundle::PerturbBundle , protocols::helical_bundle::PerturbBundleHelix
• parameters_ : core::conformation::parametric::ParametersSet
• parameters_for_restype() : core::scoring::methods::IdealParametersDatabase
• parameters_index() : protocols::helical_bundle::PerturbBundleHelix
• parameters_index_ : protocols::helical_bundle::PerturbBundleHelix
• parameters_set() : core::conformation::Conformation
• parameters_set_ : core::conformation::Conformation
• parameters_set_index() : protocols::helical_bundle::PerturbBundleHelix
• parameters_set_index_ : protocols::helical_bundle::PerturbBundleHelix
• ParametersCOP : core::conformation::Conformation
• ParametersOP : core::conformation::Conformation , protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters , protocols::helical_bundle::parameters::BundleParametersSet , protocols::helical_bundle::PerturbBundle , protocols::helical_bundle::PerturbBundleHelix
• ParametersSet : core::conformation::Conformation , core::conformation::parametric::ParametersSet , protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters , protocols::helical_bundle::parameters::BundleParametersSet , protocols::helical_bundle::PerturbBundle , protocols::helical_bundle::PerturbBundleHelix
• ParametersSetCOP : core::conformation::Conformation
• ParametersSetOP : core::conformation::Conformation , protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters , protocols::helical_bundle::parameters::BundleParametersSet , protocols::helical_bundle::PerturbBundle , protocols::helical_bundle::PerturbBundleHelix
• ParamG : core::scoring::GenBornPotential
• Params : core::scoring::dna::DNA_BasePotential
• ParamS : core::scoring::GenBornPotential
• params_ : core::scoring::disulfides::FullatomDisulfidePotential , core::scoring::packing::HolesEnergyRes , core::scoring::packing::HolesParamsRes , protocols::mpi_refinement::Scheduler
• params_database_tag() : core::scoring::hbonds::HBondOptions
• params_database_tag_ : core::scoring::hbonds::HBondDatabase , core::scoring::hbonds::HBondOptions
• params_derivs_to_vars() : protocols::helical_bundle::FitSimpleHelixMultiFunc
• params_file : protocols::flexpep_docking::FlexPepDockingFlags
• params_vec : protocols::relax::RelaxScriptCommand
• paratope : protocols::antibody::ParatopeMetric< T >
• paratope_cdrs_ : protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover , protocols::antibody::design::AntibodyDesignMover
• paratope_charge_ : protocols::antibody::AntibodyFeatures
• paratope_cst_mover_ : protocols::antibody::design::AntibodyDesignMover
• paratope_epitope_cst_mover_ : protocols::antibody::design::AntibodyDesignMover
• paratope_heavy : protocols::antibody::ParatopeMetric< T >
• paratope_light : protocols::antibody::ParatopeMetric< T >
• paratope_residues_ : protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover , protocols::antibody::constraints::ParatopeSiteConstraintMover
• paratope_residues_from_cdrs() : protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover
• paratope_sasa_ : protocols::antibody::AntibodyFeatures
• ParatopeEpitopeSiteConstraintMover() : protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover
• ParatopeMetric() : protocols::antibody::ParatopeMetric< T >
• ParatopeSiteConstraintMover() : protocols::antibody::constraints::ParatopeSiteConstraintMover
• parent : core::chemical::rotamers::RotamerLibrarySpecificationRegistrator< T > , core::conformation::RotamerSetBase
• Parent : core::environment::EXCN_Env_Exception , core::environment::EXCN_FTSketchGraph , core::fragment::AnnotatedFragData , core::fragment::BBTorsionAndAnglesSRFD , core::fragment::BBTorsionSRFD , core::fragment::ConstantLengthFragSet , core::fragment::DownJumpSRFD , core::fragment::FragCache< T > , core::fragment::FragSetCollection , core::fragment::FragStore< T > , core::fragment::MinimalFragSet , core::fragment::NonContinuousFrame , core::fragment::OrderedFragSet , core::fragment::SecstructSRFD , core::fragment::UpJumpSRFD
• parent : core::graph::DS_Node , core::graph::Graph
• Parent : core::io::silent::BinarySilentStruct , core::io::silent::ProteinSilentStruct_Template< T >
• parent : core::io::silent::SilentStructRegistrator< T >
• Parent : core::kinematics::EXCN_InvalidFoldTree
• parent : core::kinematics::Node , core::kinematics::tree::Atom , core::kinematics::tree::Atom_ , core::optimization::DOF_Node , core::optimization::MinimizerMap , core::optimization::Multifunc , core::optimization::NumDerivCheckData , core::optimization::NumericalDerivCheckResult , core::optimization::SingleResidueMultifunc , core::pack::annealer::FASTERAnnealer , core::pack::dunbrack::BBDepSemiRotamericData< T, N > , core::pack::dunbrack::BBIndSemiRotamericData< T, N > , core::pack::dunbrack::cenrot::CenRotDunEnergy , core::pack::dunbrack::DunbrackEnergy , core::pack::dunbrack::DunbrackRotamer< S, N, P > , core::pack::dunbrack::PackedDunbrackRotamer< S, N, P > , core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N > , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::FASTERNode , 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::HPatchEnergy , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G > , core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceEdge< V, E, G > , core::pack::interaction_graph::SurfaceEnergy , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::rotamer_set::ContinuousRotamerSet , core::pack::rotamer_set::FixbbRotamerSets , core::pack::rotamer_set::RotamerSet , core::pack::rotamers::RotamericSingleResiduePeptoidLibrary< T, N > , core::pack::rotamers::SingleResidueRotamerLibraryRegistrator< T > , core::pack::task::operation::AddBehaviorRLT , core::pack::task::operation::AllResFilter , core::pack::task::operation::AnyResFilter , core::pack::task::operation::AppendResidueRotamerSet , core::pack::task::operation::AppendRotamer , core::pack::task::operation::AppendRotamerSet , core::pack::task::operation::ChainIs , core::pack::task::operation::ChainIsnt , core::pack::task::operation::DisallowIfNonnative , core::pack::task::operation::DisallowIfNonnativeRLT , 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::IncludeCurrent , core::pack::task::operation::IncludeCurrentRLT , core::pack::task::operation::InitializeExtraRotsFromCommandline , core::pack::task::operation::InitializeFromCommandline , core::pack::task::operation::NoResFilter , core::pack::task::operation::OperateOnCertainResidues , core::pack::task::operation::OperateOnResidueSubset , core::pack::task::operation::PreserveCBeta , core::pack::task::operation::PreserveCBetaRLT , core::pack::task::operation::PreventRepacking , core::pack::task::operation::PreventRepackingRLT , core::pack::task::operation::ReadResfile , core::pack::task::operation::ReadResfileAndObeyLengthEvents , core::pack::task::operation::ReplicateTask , core::pack::task::operation::ResFilterComposition , core::pack::task::operation::ResFilterRegistrator< T > , core::pack::task::operation::ResidueHasProperty , core::pack::task::operation::ResidueIndexIs , core::pack::task::operation::ResidueIndexIsnt , core::pack::task::operation::ResidueLacksProperty , core::pack::task::operation::ResidueName3Is , core::pack::task::operation::ResidueName3Isnt , core::pack::task::operation::ResiduePDBIndexIs , core::pack::task::operation::ResiduePDBIndexIsnt , core::pack::task::operation::ResiduePDBInfoHasLabel , core::pack::task::operation::ResiduePDBInfoLacksLabel , core::pack::task::operation::ResidueTypeFilter , core::pack::task::operation::ResLvlTaskOperationRegistrator< T > , core::pack::task::operation::RestrictAbsentCanonicalAAS , core::pack::task::operation::RestrictAbsentCanonicalAASRLT , core::pack::task::operation::RestrictResidueToRepacking , core::pack::task::operation::RestrictToRepacking , core::pack::task::operation::RestrictToRepackingRLT , core::pack::task::operation::RestrictYSDesign , core::pack::task::operation::RotamerExplosion , core::pack::task::operation::SetRotamerCouplings , core::pack::task::operation::SetRotamerLinks , core::pack::task::operation::TaskOperationRegistrator< T > , core::pack::task::TaskFactory
• Parent : core::pose::datacache::SpecialSegmentsObserver
• parent : core::scoring::constraints::ConstraintEdge , core::scoring::constraints::ConstraintGraph , core::scoring::constraints::ConstraintNode , core::scoring::constraints::ConstraintRegistrator< T > , core::scoring::constraints::OffsetPeriodicBoundFunc , core::scoring::constraints::PeriodicBoundFunc , core::scoring::ContextGraph , core::scoring::disulfides::FullatomDisulfidePotential , core::scoring::dna::DNAChiEnergy , core::scoring::dna::DNATorsionEnergy , core::scoring::DockingScoreFunction , core::scoring::elec::ElecAtom , core::scoring::elec::FA_ElecEnergyAroAll , core::scoring::elec::FA_ElecEnergyAroAro , core::scoring::elec::RNA_FA_ElecEnergy , core::scoring::EnergyEdge , core::scoring::EnergyGraph , core::scoring::EnergyNode , core::scoring::etable::AnalyticEtableEnergy , core::scoring::etable::BB_BB_EnergyInvoker< Evaluator > , core::scoring::etable::count_pair::CountPair1B< CrossoverBehavior > , core::scoring::etable::count_pair::CountPair2B< CrossoverBehavior > , core::scoring::etable::count_pair::CountPairAll , core::scoring::etable::count_pair::CountPairCrossover34 , core::scoring::etable::count_pair::CountPairCrossover3 , core::scoring::etable::count_pair::CountPairCrossover4 , core::scoring::etable::count_pair::CountPairGeneric , core::scoring::etable::count_pair::CountPairIntraRes< CrossoverBehavior > , core::scoring::etable::count_pair::CountPairNone , core::scoring::etable::etrie::EtableAtom , core::scoring::etable::SC_BB_EnergyInvoker< Evaluator > , core::scoring::etable::SC_SC_EnergyInvoker< Evaluator > , core::scoring::etable::SC_Whole_EnergyInvoker< Evaluator > , core::scoring::etable::TableLookupEtableEnergy , core::scoring::etable::WholeWholeEnergyInvoker< Evaluator > , core::scoring::func::FourPointsFunc , core::scoring::membrane::FaMPEnvEnergy , core::scoring::membrane::FaMPEnvSmoothEnergy , core::scoring::membrane::FaMPSolvEnergy , core::scoring::membrane::MPCbetaEnergy , core::scoring::membrane::MPEnvEnergy , core::scoring::membrane::MPLipoEnergy , core::scoring::membrane::MPNonHelixPenalty , core::scoring::membrane::MPPairEnergy , core::scoring::membrane::MPTerminiPenalty , core::scoring::membrane::MPTMProjPenalty , core::scoring::methods::CartesianBondedEnergy , core::scoring::methods::CenHBEnergy , core::scoring::methods::CenPairEnergy , core::scoring::methods::CenPairMotifDegreeEnergy , core::scoring::methods::CenPairMotifEnergy , core::scoring::methods::CenRotEnvEnergy , core::scoring::methods::CenRotPairEnergy , core::scoring::methods::ChainbreakEnergy , core::scoring::methods::ChemicalShiftAnisotropyEnergy , core::scoring::methods::ContactOrderEnergy , core::scoring::methods::ContextDependentLRTwoBodyEnergy , core::scoring::methods::ContextDependentOneBodyEnergy , core::scoring::methods::ContextDependentTwoBodyEnergy , core::scoring::methods::ContextIndependentLRTwoBodyEnergy , core::scoring::methods::ContextIndependentOneBodyEnergy , core::scoring::methods::ContextIndependentTwoBodyEnergy , core::scoring::methods::CustomAtomPairEnergy , core::scoring::methods::D2H_SA_Energy , core::scoring::methods::dfire::DFIRE_Energy , core::scoring::methods::DipolarCouplingEnergy , core::scoring::methods::DirectReadoutEnergy , core::scoring::methods::DistanceChainbreakEnergy , core::scoring::methods::DNA_BaseEnergy , core::scoring::methods::DNA_DihedralEnergy , core::scoring::methods::DNA_EnvPairEnergy , core::scoring::methods::DNA_ReferenceEnergy , core::scoring::methods::EnergyMethod , core::scoring::methods::EnergyMethodRegistrator< T > , core::scoring::methods::EnvEnergy , core::scoring::methods::EnvSmoothEnergy , core::scoring::methods::Fa_MbenvEnergy , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::methods::FACTSEnergy , core::scoring::methods::FreeDOF_Energy , core::scoring::methods::GaussianOverlapEnergy , core::scoring::methods::GenBornEnergy , core::scoring::methods::GoapEnergy , core::scoring::methods::HybridVDW_Energy , core::scoring::methods::LinearChainbreakEnergy , core::scoring::methods::LK_hack , core::scoring::methods::LK_PolarNonPolarEnergy , core::scoring::methods::LongRangeTwoBodyEnergy , core::scoring::methods::MembraneCbetaEnergy , core::scoring::methods::MembraneCenPairEnergy , core::scoring::methods::MembraneEnvEnergy , core::scoring::methods::MembraneEnvPenalties , core::scoring::methods::MembraneEnvSmoothEnergy , core::scoring::methods::MembraneLipo , core::scoring::methods::MMBondAngleEnergy , core::scoring::methods::MMBondLengthEnergy , core::scoring::methods::MMLJEnergyInter , core::scoring::methods::MMLJEnergyIntra , core::scoring::methods::MMTorsionEnergy , core::scoring::methods::MultipoleElecEnergy , core::scoring::methods::NMerPSSMEnergy , core::scoring::methods::NMerRefEnergy , core::scoring::methods::NMerSVMEnergy , core::scoring::methods::OmegaTetherEnergy , core::scoring::methods::OneBodyEnergy , core::scoring::methods::OtherPoseEnergy , core::scoring::methods::P_AA_Energy , core::scoring::methods::P_AA_pp_Energy , core::scoring::methods::P_AA_ss_Energy , core::scoring::methods::PackStatEnergy , core::scoring::methods::PairEnergy , core::scoring::methods::PeptideBondEnergy , core::scoring::methods::pHEnergy , core::scoring::methods::PoissonBoltzmannEnergy , core::scoring::methods::ProClosureEnergy , core::scoring::methods::ProQ_Energy , core::scoring::methods::RamachandranEnergy2B , core::scoring::methods::RamachandranEnergy , core::scoring::methods::RamaPreProEnergy , core::scoring::methods::ReferenceEnergy , core::scoring::methods::ReferenceEnergyNoncanonical , core::scoring::methods::ResidualDipolarCouplingEnergy , core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl , core::scoring::methods::RG_Energy_Fast , core::scoring::methods::RingClosureEnergy , core::scoring::methods::RMS_Energy , core::scoring::methods::SA_Energy , core::scoring::methods::SecondaryStructureEnergy , core::scoring::methods::SequenceDependentRefEnergy , core::scoring::methods::ShortRangeTwoBodyEnergy , core::scoring::methods::SmoothCenPairEnergy , core::scoring::methods::SmoothEnvEnergy , core::scoring::methods::SplitUnfoldedTwoBodyEnergy , core::scoring::methods::SSElementMotifContactEnergy , core::scoring::methods::SuckerEnergy , core::scoring::methods::SymmetricLigandEnergy , core::scoring::methods::TwoBodyEnergy , core::scoring::methods::UnfoldedStateEnergy , core::scoring::methods::VdWTinkerEnergy , core::scoring::methods::WaterAdductHBondEnergy , core::scoring::methods::WaterAdductIntraEnergy , core::scoring::methods::WholeStructureEnergy , core::scoring::methods::YHHPlanarityEnergy , core::scoring::MinimizationEdge , core::scoring::MinimizationGraph , core::scoring::MinimizationNode , core::scoring::MinScoreScoreFunction , core::scoring::mm::mmtrie::MMEnergyTableAtom , core::scoring::ResidueNblistData , core::scoring::ResiduePairNeighborList , core::scoring::rna::RNA_BulgeEnergy , core::scoring::rna::RNA_FullAtomVDW_BasePhosphate , core::scoring::rna::RNA_SugarCloseEnergy , core::scoring::solid_surface::SurfaceEnergies , core::scoring::symmetry::SymmetricScoreFunction , core::scoring::TenANeighborEdge , core::scoring::TenANeighborGraph , core::scoring::TenANeighborNode , core::scoring::TwelveANeighborEdge , core::scoring::TwelveANeighborGraph , core::scoring::TwelveANeighborNode , core::select::residue_selector::ResidueSelectorRegistrator< T > , core::sequence::SequenceRegistrator< T >
• Parent : protocols::abinitio::abscript::AbscriptLoopCloserCM , protocols::abinitio::abscript::ConstraintPreparer , protocols::abinitio::abscript::FragmentCM , protocols::abinitio::abscript::FragmentJumpCM , protocols::abinitio::abscript::JumpSampleData , protocols::abinitio::abscript::RigidChunkCM , protocols::abinitio::abscript::StructPerturberCM , protocols::abinitio::ClassicAbinitio , protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints , protocols::abinitio::FragmentSampler , protocols::abinitio::HedgeArchive , protocols::abinitio::IterativeAbrelax , protocols::abinitio::IterativeBase , protocols::abinitio::IterativeCentroid , protocols::abinitio::IterativeFullatom , protocols::abinitio::JumpingFoldConstraintsWrapper , protocols::abinitio::KinematicAbinitio , protocols::abinitio::MembraneAbinitio , protocols::canonical_sampling::AsyncMPITemperingBase , protocols::canonical_sampling::BiasedMonteCarlo , protocols::canonical_sampling::BiasEnergy::Histogram< T > , protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::ParallelTempering , protocols::canonical_sampling::PDBTrajectoryRecorder , protocols::canonical_sampling::SidechainMetropolisHastingsMover , protocols::canonical_sampling::SilentTrajectoryRecorder , protocols::canonical_sampling::SimulatedTempering , protocols::canonical_sampling::TemperingBase , protocols::canonical_sampling::WTEBiasEnergy , protocols::constraints_additional::MaxSeqSepConstraintSet
• parent : protocols::dna::RestrictDesignToProteinDNAInterface
• Parent : protocols::environment::AutoCutData , protocols::environment::claims::ClaimStrength , protocols::environment::claims::CutBiasClaim , protocols::environment::claims::JumpClaim , protocols::environment::claims::TorsionClaim , protocols::environment::claims::VirtResClaim , protocols::environment::claims::XYZClaim , protocols::environment::Environment , protocols::environment::EXCN_Env_Passport , protocols::environment::EXCN_Env_Security_Exception , protocols::environment::ProtectedConformation
• parent : protocols::enzdes::ApplyRandomStoredRBConf , protocols::enzdes::DiversifyStoredRBConfs , protocols::enzdes::EnzdesJobOutputter , protocols::enzdes::GenerateStoredRBConfs , protocols::enzdes::MinimizeStoredRBConfs , protocols::enzdes::ModifyStoredRBConfs , protocols::evaluation::EvaluatorRegistrator< T >
• Parent : protocols::evaluation::MetaPoseEvaluator
• parent : protocols::features::DatabaseJobOutputter , protocols::features::FeaturesReporterRegistrator< T > , protocols::filters::ContingentFilter , protocols::filters::FilterRegistrator< T > , protocols::fldsgn::potentials::AACompositionEnergy , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy
• Parent : protocols::fldsgn::topology::Helix , protocols::fldsgn::topology::Loop , protocols::fldsgn::topology::Strand
• parent : protocols::flexpack::annealer::FlexbbSimAnnealer , protocols::flexpack::interaction_graph::FlexbbEdge , protocols::flexpack::interaction_graph::FlexbbInteractionGraph , protocols::flexpack::interaction_graph::FlexbbNode , protocols::flexpack::interaction_graph::FlexbbSparseMatrixIndex , protocols::flexpack::interaction_graph::MinimalistFlexbbEdge , protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph , protocols::flexpack::interaction_graph::MinimalistFlexbbNode , protocols::flexpack::interaction_graph::OTFFlexbbEdge , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::flexpack::interaction_graph::OTFFlexbbNode , protocols::flexpack::OtherContextScoreFunction , protocols::flexpack::rotamer_set::FlexbbRotamerSet , protocols::flxbb::LayerDesignOperation , protocols::genetic_algorithm::EntityElement , protocols::genetic_algorithm::EntityElementRegistrator< T > , protocols::genetic_algorithm::Mutate1Randomizer , protocols::hotspot_hashing::SearchPatternRotSetOp
• Parent : protocols::jd2::archive::ArchiveManager , protocols::jd2::archive::EvaluatedArchive , protocols::jd2::archive::MPIArchiveJobDistributor , protocols::jd2::archive::NormalizedEvaluatedArchive , protocols::jd2::archive::VarianceStatisticsArchive
• parent : protocols::jd2::FileJobOutputter , protocols::jd2::JobInputterRegistrator< T > , protocols::jd2::JobOutputterRegistrator< T >
• Parent : protocols::jd2::MPIFileBufJobDistributor , protocols::jd2::MPIMultiCommJobDistributor
• parent : protocols::jd2::parser::DataLoaderRegistrator< T >
• Parent : protocols::jd2::parser::FragmentReader
• parent : protocols::jd2::PDBJobOutputter , protocols::jd2::SilentFileJobOutputter , protocols::jobdist::AtomTreeDiffJobDistributor , protocols::jobdist::PlainPdbJobDistributor , protocols::jobdist::PlainRawJobDistributor , protocols::jobdist::PlainSilentFileJobDistributor , protocols::ligand_docking::rdf::RDFFunctionRegistrator< T >
• Parent : protocols::loops::EXCN_Loop_not_closed , protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure , protocols::loops::loop_closure::ccd::RamaCheckBase , protocols::loops::loop_closure::ccd::ShortLoopClosure , protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure
• parent : protocols::loops::loop_closure::kinematic_closure::BaseTabooPerturber , protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::NeighborDependentTorsionSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TabooSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::VicinitySamplingKinematicPerturber
• Parent : protocols::loops::loop_mover::LoopCM
• parent : protocols::loops::loops_definers::LoopsDefinerRegistrator< T > , protocols::match::BumpGrid , protocols::match::downstream::ActiveSiteGrid , protocols::match::downstream::ClassicMatchAlgorithm , protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder , protocols::match::downstream::SecondaryMatcherToDownstreamResidue , protocols::match::downstream::SecondaryMatcherToUpstreamResidue , protocols::match::downstream::SecondaryMatchUpstreamResProcessor , protocols::match::output::CloudPDBWriter
• Parent : protocols::match::output::PDBWriter
• parent : protocols::match::output::PoseMatchOutputWriter , protocols::match::output::SameSequenceAndDSPositionGrouper , protocols::match::output::UpstreamCollisionFilter , protocols::match::output::UpstreamDownstreamCollisionFilter , protocols::match::upstream::BuildSet , protocols::match::upstream::OriginalBackboneBuildPoint , protocols::match::upstream::ProteinBackboneBuildPoint , protocols::matdes::InterfacePackingFilter , protocols::md::MDBase
• Parent : protocols::moves::MoveMapMover , protocols::moves::MoverApplyingMover
• parent : protocols::moves::MoverRegistrator< T >
• Parent : protocols::moves::ReplicaExchangeMC
• parent : protocols::multistate_design::PosType
• Parent : protocols::noesy_assign::EXCN_NoesyAssign , protocols::noesy_assign::FloatingResonance , protocols::noesy_assign::LabelResonance , protocols::noesy_assign::ProtonResonance
• parent : protocols::optimize_weights::PSSMOptEPositionData , protocols::optimize_weights::ScaleAnnealerTemperatureOperation , protocols::pack_daemon::BasicSimAnnealerRepacker , protocols::pack_daemon::DenseIGRepacker , protocols::pack_daemon::DoubleDenseIGRepacker , protocols::pack_daemon::DynamicAggregateFunction , protocols::pack_daemon::EntityCorrespondence , protocols::pack_daemon::EntityFunc , protocols::pack_daemon::EntityFuncExpressionCreator , protocols::pack_daemon::ExpExpression , protocols::pack_daemon::FASTER_IG_Repacker , protocols::pack_daemon::InSetExpression , protocols::pack_daemon::IterativeVectorExpression , protocols::pack_daemon::LnExpression , protocols::pack_daemon::Mean , protocols::pack_daemon::MultistateAggregateFunction , protocols::pack_daemon::MultistateFitnessFunction , protocols::pack_daemon::PowExpression , protocols::pack_daemon::QuickRepacker , protocols::pack_daemon::RotamerSubsetRepacker , protocols::pack_daemon::SurrogateVariableExpression , protocols::pack_daemon::VariableVectorExpression , protocols::pack_daemon::VectorExpression , protocols::pack_daemon::VectorExpressionCreator , protocols::pack_daemon::VectorFunction2 , protocols::pack_daemon::VectorFunction , protocols::pack_daemon::VMax , protocols::pack_daemon::VMaxBy , protocols::pack_daemon::VMin , protocols::pack_daemon::VMinBy , protocols::pockets::SmallMol , protocols::protein_interface_design::filters::AverageDegreeFilter , protocols::protein_interface_design::filters::BindingStrainFilter , protocols::protein_interface_design::filters::BoltzmannFilter , protocols::protein_interface_design::filters::DesignableResiduesFilter , protocols::protein_interface_design::filters::DisulfideFilter , protocols::protein_interface_design::filters::FilterScanFilter , protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter , protocols::protein_interface_design::filters::StubScoreFilter
• Parent : protocols::protein_interface_design::filters::StubScoreLoopsFilter
• parent : protocols::protein_interface_design::filters::Torsion , protocols::protein_interface_design::movers::CoordinateConstraintStack , protocols::protein_interface_design::movers::DisulfideMover , protocols::protein_interface_design::movers::DockWithHotspotMover , protocols::qsar::scoring_grid::GridRegistrator< T > , protocols::relax::AtomCoordinateCstMover , protocols::relax::ClassicRelax , protocols::relax::MiniRelax , protocols::relax::RelaxProtocolBase , 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::RigidBodyMover , protocols::rigid::RigidBodyPerturbMover
• Parent : protocols::rigid::RigidBodyPerturbNoCenterMover
• parent : protocols::rigid::RigidBodyRandomizeMover , protocols::rigid::RigidBodySpinMover , protocols::rigid::RigidBodyTiltMover , protocols::rigid::RigidBodyTransMover , protocols::rigid::UniformSphereTransMover , protocols::rosetta_scripts::PosePropertyReporterRegistrator< T > , protocols::rosetta_scripts::PoseSelectorRegistrator< T > , protocols::rotamer_recovery::RotamerRecoveryRegistrator< T > , protocols::scoring::methods::EnsembleEnergy , protocols::scoring::methods::InterchainEnvEnergy , protocols::scoring::methods::InterchainPairEnergy , protocols::scoring::methods::pcs2::PcsEnergy , protocols::scoring::methods::pcs::PCS_Energy , protocols::scoring::methods::pcsTs1::PCS_Energy_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_Ts4 , protocols::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments , protocols::scoring::methods::SpecialRotamerEnergy , protocols::sewing::AppendAssemblyMover , protocols::sewing::EnumerateAssemblyMover , protocols::sewing::GivenPathAssemblyMover , protocols::sewing::GreedyAssemblyMover , protocols::sewing::MonteCarloAssemblyMover , protocols::sewing::NodeConstraintAssemblyMover , protocols::sewing::ReadNativeRotamersFile , protocols::sewing::ReadRepeatNativeRotamersFile , protocols::sewing::RepeatAssemblyMover , protocols::sewing::sampling::requirements::RequirementRegistrator< T > , protocols::simple_filters::AtomicContactFilter , protocols::simple_filters::AtomicDistanceFilter , protocols::simple_filters::ConservedPosMutationFilter , protocols::simple_filters::ConstraintScoreCutoffFilter , protocols::simple_filters::DeltaFilter , protocols::simple_filters::MutationsFilter , protocols::simple_filters::PoseInfoFilter , protocols::simple_filters::RelativePoseFilter , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_filters::SavePoseConstraintToFileFilter , protocols::simple_filters::ScoreCutoffFilter , protocols::simple_filters::TaskAwareScoreTypeFilter
• Parent : protocols::simple_moves::FragmentMover , protocols::simple_moves::LoggedFragmentMover
• parent : protocols::simple_moves::MembraneTopology
• Parent : protocols::simple_moves::MinMover
• parent : protocols::simple_moves::MutateResidue
• Parent : protocols::simple_moves::ResTypeFragmentMover
• parent : protocols::simple_moves::SetTorsion
• Parent : protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover , protocols::simple_moves::sidechain_moves::PerturbChiSidechainMover , protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover
• parent : protocols::simple_moves::sidechain_moves::SetChiMover
• Parent : protocols::simple_moves::SmoothFragmentMover
• parent : protocols::simple_moves::StorePoseSnapshot
• Parent : protocols::simple_moves::WobbleMover
• parent : protocols::toolbox::match_enzdes_util::ExternalGeomSampler , protocols::toolbox::match_enzdes_util::LigandConformer , protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculator , protocols::toolbox::pose_metric_calculators::NeighborhoodByDistanceCalculator , protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator , protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers , protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO , protocols::toolbox::rotamer_set_operations::RigidBodyMoveRSO , protocols::toolbox::rotamer_set_operations::SpecialRotamerRSO , protocols::toolbox::task_operations::AlignedThreadOperation , protocols::toolbox::task_operations::DatabaseThread , protocols::toolbox::task_operations::DesignAroundOperation , protocols::toolbox::task_operations::DockingNoRepack1 , protocols::toolbox::task_operations::DockingNoRepack2 , protocols::toolbox::task_operations::DsspDesignOperation , protocols::toolbox::task_operations::ImportUnboundRotamersOperation , protocols::toolbox::task_operations::InteractingRotamerExplosion , protocols::toolbox::task_operations::InterfaceTaskOperation , protocols::toolbox::task_operations::JointSequenceOperation , protocols::toolbox::task_operations::LimitAromaChi2Operation , protocols::toolbox::task_operations::LinkResidues , protocols::toolbox::task_operations::PreventChainFromRepackingOperation , protocols::toolbox::task_operations::PreventResiduesFromRepackingOperation , protocols::toolbox::task_operations::ProteinInterfaceDesignOperation , protocols::toolbox::task_operations::ReadResfileFromDB , protocols::toolbox::task_operations::RestrictByCalculatorsOperation , protocols::toolbox::task_operations::RestrictChainToRepackingOperation
• Parent : protocols::toolbox::task_operations::RestrictConservedLowDdgOperation
• parent : protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation , protocols::toolbox::task_operations::RestrictInterGroupVectorOperation , protocols::toolbox::task_operations::RestrictNativeResiduesOperation , protocols::toolbox::task_operations::RestrictOperationsBase , protocols::toolbox::task_operations::RestrictResiduesToRepackingOperation , protocols::toolbox::task_operations::RestrictToAlignedSegmentsOperation , protocols::toolbox::task_operations::RestrictToCDRH3Loop , protocols::toolbox::task_operations::RestrictToInterface , protocols::toolbox::task_operations::RestrictToInterfaceOperation , protocols::toolbox::task_operations::RestrictToInterfaceVectorOperation , protocols::toolbox::task_operations::RestrictToLoops , protocols::toolbox::task_operations::RestrictToLoopsAndNeighbors , protocols::toolbox::task_operations::RestrictToMoveMapChiOperation , protocols::toolbox::task_operations::RestrictToNeighborhoodOperation , protocols::toolbox::task_operations::SelectResiduesWithinChainOperation , protocols::toolbox::task_operations::SeqprofConsensusOperation , protocols::toolbox::task_operations::ThreadSequenceOperation
• Parent : protocols::topology_broker::AsymFoldandDockClaimer , protocols::topology_broker::BasicJumpClaimer , protocols::topology_broker::claims::SequenceClaim , protocols::topology_broker::ConstraintClaimer , protocols::topology_broker::CoordConstraintClaimer , protocols::topology_broker::DisulfJumpClaimer , protocols::topology_broker::EXCN_FailedBroking , protocols::topology_broker::EXCN_FilterFailed , protocols::topology_broker::EXCN_Input , protocols::topology_broker::EXCN_TopologyBroker , protocols::topology_broker::FibrilModelingClaimer , protocols::topology_broker::FoldandDockClaimer , protocols::topology_broker::FragmentClaimer , protocols::topology_broker::FragmentJumpClaimer , 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::RigidChunkClaimer , protocols::topology_broker::SequenceClaimer , protocols::topology_broker::SymmetryClaimer , protocols::topology_broker::TMHTopologySamplerClaimer
• parent1 : core::scoring::aa_composition_energy::AACompositionEnergy
• parent2 : core::scoring::aa_composition_energy::AACompositionEnergy , core::scoring::aa_repeat_energy::AARepeatEnergy
• parent_ : core::environment::FoldTreeSketch::Node , core::kinematics::tree::Atom_ , core::optimization::DOF_Node , core::scoring::PolymerBondedNeighborConstIterator , core::scoring::PolymerBondedNeighborIterator , protocols::protein_interface_design::movers::CoordinateConstraintStack
• parent_atom_ : core::chemical::AddConnect
• parent_entities_ : protocols::genetic_algorithm::GeneticAlgorithmBase
• parent_full_model_parameters() : core::pose::full_model_info::FullModelParameters
• parent_full_model_parameters_ : core::pose::full_model_info::FullModelParameters
• parent_id() : core::optimization::DOF_DataPoint , protocols::denovo_design::components::NamedMover
• parent_id_ : core::optimization::DOF_DataPoint , protocols::denovo_design::components::NamedMover
• parent_name_ : protocols::loop_modeling::LoopMover
• parent_node() : protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase
• parent_node_ : protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase
• parent_pose_ : protocols::simple_moves::MergePDBMover
• parent_remarks_map_ : core::io::silent::SilentStruct
• parent_tags_map_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• ParentOP : protocols::abinitio::abscript::JumpSampleData , protocols::environment::AutoCutData
• parin_favorite_output() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• parin_favorite_output_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• parse() : core::chemical::mmCIF::mmCIFParser , core::chemical::sdf::CtabParserBase , core::chemical::sdf::CtabV2000Parser , core::chemical::sdf::CtabV3000Parser , core::chemical::sdf::SDFParser
• parse_a_penalty_definition() : core::scoring::aa_composition_energy::AACompositionEnergySetup
• parse_atom_line() : core::chemical::sdf::CtabV2000Parser , core::chemical::sdf::CtabV3000Parser
• parse_atom_pair_constraint() : core::scoring::constraints::ConstraintIO
• parse_batch_description_tag_item() : protocols::features::ReportToDB
• parse_batch_id_tag_item() : protocols::features::ReportToDB
• parse_batch_name_tag_item() : protocols::features::ReportToDB
• parse_body_line() : core::pack::task::ResfileContents
• parse_bond_line() : core::chemical::sdf::CtabV2000Parser , core::chemical::sdf::CtabV3000Parser
• parse_cache_size_tag_item() : protocols::features::ReportToDB
• parse_cdr_design_option() : protocols::antibody::design::CDRSeqDesignOptionsParser
• parse_cdr_general_option() : protocols::antibody::design::CDRGraftDesignOptionsParser , protocols::antibody::design::CDRSeqDesignOptionsParser
• parse_cdr_graft_option() : protocols::antibody::design::CDRGraftDesignOptionsParser
• parse_cdr_option() : protocols::antibody::CDRSetOptionsParser , protocols::antibody::design::CDRGraftDesignOptionsParser , protocols::antibody::design::CDRSeqDesignOptionsParser
• parse_cdr_set_option() : protocols::antibody::CDRSetOptionsParser
• parse_chain_endings() : core::io::silent::BinarySilentStruct , core::io::silent::ProteinSilentStruct_Template< T >
• parse_chi_and_bb() : protocols::simple_moves::MinMover
• parse_command_line() : protocols::frag_picker::FragmentPicker
• parse_configuration_options() : protocols::loops::JSONFormattedLoopsFileReader
• parse_coordinate_constraint() : core::scoring::constraints::ConstraintIO
• parse_ctrl_str() : protocols::environment::claims::EnvClaim
• parse_default_and_user_options() : protocols::antibody::CDRSetOptionsParser , protocols::antibody::design::CDRGraftDesignOptionsParser , protocols::antibody::design::CDRSeqDesignOptionsParser
• parse_disulf_file() : core::io::raw_data::DisulfideFile
• parse_dna_geometry_log() : core::scoring::dna::DNA_DihedralPotential
• parse_dof_task_type() : protocols::simple_moves::MinMover
• parse_dof_tasks() : protocols::simple_moves::MinMover
• parse_energies() : core::io::silent::SilentStruct
• parse_error_ : protocols::metal_interface::ZincSiteFinder
• parse_excluded_properites() : core::scoring::aa_composition_energy::AACompositionPropertiesSet
• parse_excluded_types() : core::scoring::aa_composition_energy::AACompositionPropertiesSet
• parse_file() : core::chemical::sdf::MolFileIOReader
• parse_files() : core::scoring::orbitals::OrbitalsLookup
• parse_global_requirements() : protocols::sewing::AssemblyMover
• parse_header_line() : core::pack::task::ResfileContents
• parse_in_progress() : core::io::HeaderInformation
• parse_included_properites() : core::scoring::aa_composition_energy::AACompositionPropertiesSet
• parse_included_types() : core::scoring::aa_composition_energy::AACompositionPropertiesSet
• parse_intra_segment_requirements() : protocols::sewing::AssemblyMover
• parse_job_tag() : protocols::jd2::JD2ResourceManagerJobInputter
• parse_jobs_table_tag() : protocols::jd2::JD2ResourceManagerJobInputter
• parse_jobs_tags() : protocols::jd2::JD2ResourceManagerJobInputter
• parse_json_formatted_data() : protocols::loops::JSONFormattedLoopsFileReader
• parse_json_residue_info() : protocols::loops::JSONFormattedLoopsFileReader
• parse_jump_def() : protocols::abinitio::LoopJumpFoldCst
• parse_layer_secstruct_tag() : protocols::flxbb::LayerDesignOperation
• parse_layer_tag() : protocols::flxbb::LayerDesignOperation
• parse_line() : core::scoring::aa_repeat_energy::AARepeatEnergy
• parse_loop_tag() : protocols::loops::loops_definers::LoopsExplicitDefiner
• parse_lsm_spec() : protocols::hotspot_hashing::LSMSearchPattern
• parse_mainchain_torsions() : core::scoring::bin_transitions::BinTransitionCalculator
• parse_motif() : protocols::denovo_design::connection::Connection
• parse_motifs() : protocols::denovo_design::connection::Connection
• parse_movemap() : protocols::md::CartesianMD
• parse_my_string_arguments_and_cast_to_globalPrivateSpaceVariables() : protocols::motif_grafting::movers::MotifGraftMover
• parse_my_tag() : core::chemical::ResidueLoaderOptions , core::conformation::symmetry::SymmDataOptions , core::import_pose::ImportPoseOptions , core::io::silent::SilentFileOptions , core::io::StructFileReaderOptions , core::io::StructFileRepOptions , core::pack::task::residue_selector::ClashBasedRepackShellSelector , core::scoring::electron_density::ElectronDensityOptions , core::scoring::etable::EtableOptions , core::scoring::fiber_diffraction::FiberDiffractionOptions , core::scoring::hbonds::HBondOptions , core::select::residue_selector::AndResidueSelector , core::select::residue_selector::ChainSelector , 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::ResidueIndexSelector , core::select::residue_selector::ResidueNameSelector , core::select::residue_selector::ResiduePDBInfoHasLabelSelector , core::select::residue_selector::ResidueSelector , core::select::residue_selector::SecondaryStructureSelector , core::select::residue_selector::TrueResidueSelector , protocols::aa_composition::AddCompositionConstraintMover , protocols::aa_composition::ClearCompositionConstraintsMover , protocols::abinitio::abscript::AbscriptLoopCloserCM , protocols::abinitio::abscript::AbscriptMover , protocols::abinitio::abscript::ConstraintPreparer , protocols::abinitio::abscript::FragmentCM , protocols::abinitio::abscript::FragmentJumpCM , protocols::abinitio::abscript::RigidChunkCM , protocols::abinitio::abscript::StructPerturberCM , protocols::abinitio::DomainAssembly , protocols::analysis::InterfaceAnalyzerMover , protocols::analysis::PeptideDeriverFilter , protocols::antibody::AntibodyCDRGrafter , protocols::antibody::AntibodyFeatures , protocols::antibody::clusters::CDRClusterFeatures , protocols::antibody::constraints::CDRDihedralConstraintMover , protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover , protocols::antibody::constraints::ParatopeSiteConstraintMover , protocols::antibody::design::AntibodyDesignMover , protocols::antibody::design::AntibodyDesignProtocol , protocols::antibody::design::MutateFrameworkForCluster , protocols::backrub::BackrubMover , protocols::backrub::BackrubSidechainMover , protocols::canonical_sampling::BiasEnergy , protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::MetropolisHastingsMover , protocols::canonical_sampling::ParallelTempering , protocols::canonical_sampling::PDBTrajectoryRecorder , protocols::canonical_sampling::SidechainMetropolisHastingsMover , protocols::canonical_sampling::SilentTrajectoryRecorder , protocols::canonical_sampling::SimulatedTempering , protocols::canonical_sampling::TemperingBase , protocols::canonical_sampling::TrajectoryRecorder , protocols::canonical_sampling::TrialCounterObserver , protocols::carbohydrates::GlycanRelaxMover , protocols::carbohydrates::LinkageConformerMover , protocols::carbohydrates::SimpleGlycosylateMover , protocols::comparative_modeling::LoopRelaxMover , protocols::comparative_modeling::PartialThreadingMover , protocols::contact_map::ContactMap , 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::cyclic_peptide::CreateAngleConstraint , protocols::cyclic_peptide::CreateDistanceConstraint , protocols::cyclic_peptide::CreateTorsionConstraint , protocols::cyclic_peptide::DeclareBond , protocols::cyclic_peptide::PeptideStubMover , protocols::cyclic_peptide::TryDisulfPermutations , protocols::denovo_design::components::NamedMover , protocols::denovo_design::connection::BridgeChains , protocols::denovo_design::connection::BridgeTomponents , protocols::denovo_design::connection::Connection , protocols::denovo_design::connection::ConnectTerminiWithDisulfide , protocols::denovo_design::connection::ExtendChain , protocols::denovo_design::connection::StapleChains , protocols::denovo_design::constraints::CoordinateConstraintGenerator , protocols::denovo_design::constraints::FileConstraintGenerator , protocols::denovo_design::DisulfidizeMover , protocols::denovo_design::filters::ExposedHydrophobicsFilter , protocols::denovo_design::filters::PreProlineFilter , protocols::denovo_design::filters::SSPredictionFilter , protocols::design_opt::GreedyOptMutationMover , protocols::dna::DesignProteinBackboneAroundDNA , protocols::dna::DnaInterfaceMinMover , protocols::dna::DnaInterfaceMultiStateDesign , protocols::dna::DnaInterfacePacker , protocols::dna::SeparateDnaFromNonDna , protocols::docking::DockingInitialPerturbation , protocols::docking::DockingProtocol , protocols::docking::DockSetupMover , protocols::docking::membrane::MPDockingMover , protocols::docking::membrane::MPDockingSetupMover , protocols::docking::membrane::MPFindInterfaceMover , protocols::docking::membrane::QuickRelaxPartnersSeparately , protocols::docking::TemperedDocking , protocols::electron_density::BfactorFittingMover , 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::AddOrRemoveMatchCsts , protocols::enzdes::BackboneSampler , protocols::enzdes::DiffAtomSasaFilter , protocols::enzdes::EnzdesScorefileFilter , protocols::enzdes::EnzRepackMinimize , protocols::enzdes::EnzScoreFilter , protocols::enzdes::LigBurialFilter , protocols::enzdes::LigDSasaFilter , protocols::enzdes::LigInterfaceEnergyFilter , protocols::enzdes::PackRotamersMoverPartGreedy , protocols::enzdes::PredesignPerturbMover , protocols::enzdes::RemoveLigandFilter , protocols::enzdes::RepackWithoutLigandFilter , protocols::enzdes::ResidueConformerFilter , protocols::farna::options::RNA_BasicOptions , protocols::farna::options::RNA_DeNovoProtocolOptions , protocols::farna::options::RNA_FragmentMonteCarloOptions , protocols::farna::options::RNA_MinimizerOptions , protocols::features::AtomAtomPairFeatures , protocols::features::DdGFeatures , protocols::features::FeaturesReporter , protocols::features::HBondFeatures , protocols::features::HBondParameterFeatures , protocols::features::helixAssembly::HelixBundleFeatures , protocols::features::HelixCapFeatures , protocols::features::InterfaceFeatures , protocols::features::LoopAnchorFeatures , protocols::features::ModelFeatures , protocols::features::ProteinRMSDFeatures , protocols::features::ProteinRMSDNoSuperpositionFeatures , protocols::features::ReportToDB , protocols::features::ResidueGridScoresFeatures , protocols::features::ResidueScoresFeatures , protocols::features::ResidueTotalScoresFeatures , protocols::features::RotamerBoltzmannWeightFeatures , protocols::features::RotamerRecoveryFeatures , protocols::features::ScoreFunctionFeatures , protocols::features::ScreeningFeatures , protocols::features::SecondaryStructureSegmentFeatures , protocols::features::SmotifFeatures , protocols::features::strand_assembly::SandwichFeatures , protocols::features::StructureScoresFeatures , protocols::features::TaskOperationFeatures , protocols::features::TotalScoreFeatures , protocols::features::TrajectoryReportToDB , protocols::features::UnrecognizedAtomFeatures , protocols::features::WaterFeatures , protocols::filters::CalculatorFilter , protocols::filters::CombinedFilter , protocols::filters::CompoundFilter , protocols::filters::ContingentFilter , protocols::filters::Filter , protocols::filters::IfThenFilter , protocols::filters::MoveBeforeFilter , protocols::filters::ReplicateFilter , protocols::filters::StochasticFilter , protocols::filters::TimeFilter , protocols::fldsgn::BluePrintBDR , protocols::fldsgn::CircularPermutation , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::filters::FragQualFilter , 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::MatchResidues , protocols::fldsgn::MatchResiduesMover , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::fldsgn::SheetConstraintGenerator , protocols::flexpep_docking::FlexPepDockingProtocol , protocols::flxbb::FlxbbDesign , protocols::flxbb::InterlockAroma , protocols::forge::constraints::InverseRotamersRCG , protocols::forge::constraints::InvrotTreeRCG , protocols::forge::constraints::NtoCConstraintGenerator , protocols::forge::constraints::RemoveConstraints , protocols::forge::remodel::RemodelConstraintGenerator , protocols::forge::remodel::RemodelMover , protocols::forge::remodel::ResidueVicinityRCG , protocols::frag_picker::frag_movers::FragSetFromH5Mover , protocols::frag_picker::frag_movers::MergeFragSetMover , protocols::frag_picker::frag_movers::ReduceFragLengthMover , protocols::generalized_kinematic_closure::GeneralizedKIC , protocols::grafting::AnchoredGraftMover , protocols::grafting::simple_movers::DeleteRegionMover , protocols::grafting::simple_movers::InsertPoseIntoPoseMover , protocols::grafting::simple_movers::KeepRegionMover , protocols::grafting::simple_movers::ReplaceRegionMover , protocols::helical_bundle::BackboneGridSampler , protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::BundleReporterFilter , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::PerturbBundle , protocols::hotspot_hashing::movers::PlaceSurfaceProbe , protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionSampler , protocols::hybridization::CartesianSampler , protocols::hybridization::HybridizeProtocol , protocols::idealize::IdealizeMover , protocols::indexed_structure_store::filters::FragmentLookupFilter , 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::GrowLigand , protocols::ligand_docking::HBondAcceptorFilter , protocols::ligand_docking::HBondDonorFilter , protocols::ligand_docking::HeavyAtomFilter , protocols::ligand_docking::HighResDocker , protocols::ligand_docking::InterfaceBuilder , protocols::ligand_docking::InterfaceScoreCalculator , protocols::ligand_docking::LigandArea , protocols::ligand_docking::LigandDesign , protocols::ligand_docking::MinimizeBackbone , protocols::ligand_docking::MolarMassFilter , protocols::ligand_docking::MolecularMassFilter , protocols::ligand_docking::MoveMapBuilder , protocols::ligand_docking::RandomConformers , protocols::ligand_docking::rdf::RDFBase , protocols::ligand_docking::rdf::RDFBinaryHbondFunction , protocols::ligand_docking::rdf::RDFBinaryOrbitalFunction , protocols::ligand_docking::rdf::RDFChargeFunction , protocols::ligand_docking::rdf::RDFElecFunction , protocols::ligand_docking::rdf::RDFEtableFunction , protocols::ligand_docking::rdf::RDFHbondFunction , protocols::ligand_docking::rdf::RDFOrbitalFunction , protocols::ligand_docking::Rotate , protocols::ligand_docking::Rotates , protocols::ligand_docking::SlideTogether , protocols::ligand_docking::StartFrom , protocols::ligand_docking::Transform , protocols::ligand_docking::Translate , protocols::ligand_docking::WriteLigandMolFile , protocols::loop_build::LoopmodelWrapper , protocols::loop_modeling::LoopBuilder , protocols::loop_modeling::LoopModeler , protocols::loop_modeling::LoopMover , protocols::loop_modeling::LoopProtocol , protocols::loop_modeling::refiners::MinimizationRefiner , protocols::loop_modeling::refiners::RepackingRefiner , protocols::loop_modeling::refiners::RotamerTrialsRefiner , protocols::loop_modeling::utilities::PrepareForFullatom , protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashLibraryOptions , protocols::loophash::LoopHashMoverWrapper , protocols::loops::FoldTreeFromLoops , protocols::loops::loop_closure::ccd::CCDLoopClosureMover , protocols::loops::loop_closure::ccd::RamaCheckBase , protocols::loops::loop_mover::LoopCM , protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::loops::loops_definers::LoopsDatabaseDefiner , protocols::loops::loops_definers::LoopsDefiner , protocols::loops::loops_definers::LoopsExplicitDefiner , protocols::loops::loops_definers::LoopsFileDefiner , protocols::loops::LoopsFileOptions , protocols::match::MatcherMover , 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::membrane::AddMembraneMover , protocols::membrane::AddMPLigandMover , protocols::membrane::benchmark::MakeCanonicalHelix , protocols::membrane::benchmark::SampleTiltAngles , protocols::membrane::FlipMover , protocols::membrane::MembranePositionFromTopologyMover , protocols::membrane::MPMutateRelaxMover , protocols::membrane::MPQuickRelaxMover , protocols::membrane::OptimizeMembranePositionMover , protocols::membrane::OptimizeProteinEmbeddingMover , protocols::membrane::RotationMover , protocols::membrane::SetMembraneCenterMover , protocols::membrane::SetMembraneNormalMover , protocols::membrane::SetMembranePositionMover , protocols::membrane::SpinAroundPartnerMover , protocols::membrane::symmetry::SymmetricAddMembraneMover , protocols::membrane::TiltMover , protocols::membrane::TransformIntoMembraneMover , protocols::membrane::TranslationMover , protocols::membrane::TranslationRotationMover , protocols::membrane::visualize::VisualizeMembraneMover , protocols::motif_grafting::movers::MotifGraftMover , protocols::moves::ConstraintGenerator , protocols::moves::DsspMover , protocols::moves::IfMover , protocols::moves::IteratedConvergenceMover , protocols::moves::MonteCarloUtil , protocols::moves::Mover , protocols::moves::PyMolMover , protocols::moves::RampingMover , protocols::moves::RandomMover , protocols::moves::StructureRestrictor , protocols::moves::TrialMover , protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopCreatorMover , protocols::ncbb::oop::OopDockDesignProtocol , protocols::ncbb::SecStructFinder , protocols::ncbb::SecStructMinimizeMover , protocols::nonlocal::SingleFragmentMover , protocols::normalmode::NormalModeMinimizer , protocols::pb_potential::SetupPoissonBoltzmannPotential , protocols::pose_length_moves::FixAllLoopsMover , protocols::pose_length_moves::InsertResMover , protocols::pose_length_moves::NearNativeLoopCloser , protocols::pose_reporters::EnergyReporter , protocols::pose_reporters::FilterReporter , protocols::pose_reporters::RMSDReporter , protocols::pose_selectors::ClusterPoseSelector , protocols::pose_selectors::Filter , protocols::pose_selectors::LogicalSelector , protocols::pose_selectors::TopNByProperty , 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::StubScoreLoopsFilter , 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::qsar::qsarMover , protocols::qsar::RenderGridsToKinemage , protocols::qsar::scoring_grid::AtrGrid , protocols::qsar::scoring_grid::ChargeGrid , protocols::qsar::scoring_grid::ClassicGrid , protocols::qsar::scoring_grid::ConstantScoreBase , protocols::qsar::scoring_grid::GridBase , protocols::qsar::scoring_grid::GridInitMover , protocols::qsar::scoring_grid::HbaGrid , protocols::qsar::scoring_grid::HbdGrid , protocols::qsar::scoring_grid::LigandPropertyScore , protocols::qsar::scoring_grid::RepGrid , protocols::qsar::scoring_grid::ShapeGrid , protocols::qsar::scoring_grid::SingleGrid , protocols::qsar::scoring_grid::SolvationGrid , protocols::qsar::scoring_grid::SolvationMetaGrid , protocols::qsar::scoring_grid::VdwGrid , protocols::rbsegment_relax::IdealizeHelicesMover , protocols::rbsegment_relax::MakeStarTopologyMover , protocols::rbsegment_relax::OptimizeThreadingMover , protocols::relax::AtomCoordinateCstMover , protocols::relax::FastRelax , protocols::relax::LocalRelax , protocols::relax::membrane::MPFastRelaxMover , protocols::relax::membrane::MPRangeRelaxMover , protocols::residue_selectors::TaskSelector , protocols::rigid::RigidBodyPerturbNoCenterMover , protocols::rigid::RigidBodyTiltMover , protocols::rigid::RigidBodyTransMover , protocols::rigid::RollMover , protocols::rigid::UniformRigidBodyCM , protocols::rigid::UniformRigidBodyMover , protocols::rosetta_scripts::AdditionalOutputWrapper , protocols::rosetta_scripts::MultipleOutputWrapper , protocols::rosetta_scripts::MultiplePoseMover , protocols::rosetta_scripts::ParsedProtocol , protocols::rosetta_scripts::PosePropertyReporter , protocols::rosetta_scripts::PoseSelector , protocols::rosetta_scripts::SavePoseMover , protocols::rotamer_recovery::RotamerRecoveryMover , 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::AddStartnodeFragments , protocols::sewing::AppendAssemblyMover , protocols::sewing::AssemblyConstraintsMover , protocols::sewing::AssemblyMover , protocols::sewing::EnumerateAssemblyMover , protocols::sewing::GivenPathAssemblyMover , protocols::sewing::GreedyAssemblyMover , protocols::sewing::LoophashAssemblyMover , protocols::sewing::MonteCarloAssemblyMover , protocols::sewing::RehashAssemblyMover , protocols::sewing::RepeatAssemblyMover , protocols::sewing::sampling::requirements::GlobalLengthRequirement , protocols::sewing::sampling::requirements::GlobalRequirement , protocols::sewing::sampling::requirements::IntraSegmentRequirement , protocols::sewing::sampling::requirements::ResidueRetentionRequirement , protocols::sewing::sampling::requirements::SegmentDsspRequirement , protocols::sewing::sampling::requirements::SegmentLengthRequirement , protocols::simple_filters::AlaScan , protocols::simple_filters::AngleToVector , protocols::simple_filters::AtomicContactFilter , protocols::simple_filters::AtomicDistanceFilter , protocols::simple_filters::AveragePathLengthFilter , protocols::simple_filters::BuriedUnsatHbondFilter , protocols::simple_filters::ConservedPosMutationFilter , protocols::simple_filters::ConstraintScoreCutoffFilter , protocols::simple_filters::DdgFilter , protocols::simple_filters::DdGScan , protocols::simple_filters::DeltaFilter , protocols::simple_filters::DisulfideEntropyFilter , protocols::simple_filters::DomainInterfaceFilter , protocols::simple_filters::EnergyPerResidueFilter , protocols::simple_filters::ExpiryFilter , protocols::simple_filters::FileExistFilter , protocols::simple_filters::FileRemoveFilter , protocols::simple_filters::GeometryFilter , protocols::simple_filters::HolesFilter , protocols::simple_filters::InterfaceBindingEnergyDensityFilter , protocols::simple_filters::InterfaceSasaFilter , protocols::simple_filters::InterRepeatContactFilter , protocols::simple_filters::IntraRepeatContactFilter , protocols::simple_filters::LeastNativeLike9merFilter , protocols::simple_filters::MotifScoreFilter , protocols::simple_filters::MultipleSigmoids , 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::Operator , protocols::simple_filters::PackStatFilter , protocols::simple_filters::PoseComment , protocols::simple_filters::PoseInfoFilter , protocols::simple_filters::RangeFilter , protocols::simple_filters::RelativePoseFilter , protocols::simple_filters::RepeatParameterFilter , protocols::simple_filters::ReportFilter , protocols::simple_filters::ResidueBurialFilter , protocols::simple_filters::ResidueCountFilter , protocols::simple_filters::ResidueDistanceFilter , protocols::simple_filters::ResidueIEFilter , protocols::simple_filters::ResidueSetChainEnergyFilter , protocols::simple_filters::ResiduesInInterfaceFilter , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_filters::SavePoseConstraintToFileFilter , protocols::simple_filters::SaveResfileToDiskFilter , protocols::simple_filters::ScoreCutoffFilter , protocols::simple_filters::ScoreTypeFilter , protocols::simple_filters::ShapeComplementarityFilter , protocols::simple_filters::SidechainRmsdFilter , protocols::simple_filters::Sigmoid , protocols::simple_filters::SSElementMotifContactFilter , protocols::simple_filters::SSMotifFinder , protocols::simple_filters::StemFinder , protocols::simple_filters::SymmetricMotifFilter , protocols::simple_filters::TaskAwareSASAFilter , protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::simple_filters::TerminusDistanceFilter , protocols::simple_filters::TotalSasaFilter , protocols::simple_moves::AddChainMover , protocols::simple_moves::AddConstraintsToCurrentConformationMover , protocols::simple_moves::AddJobPairData , protocols::simple_moves::AlignChainMover , protocols::simple_moves::BackboneMover , protocols::simple_moves::BBDihedralSamplerMover , protocols::simple_moves::BBGaussianMover , protocols::simple_moves::bin_transitions::InitializeByBins , protocols::simple_moves::bin_transitions::PerturbByBins , protocols::simple_moves::BoltzmannRotamerMover , protocols::simple_moves::ClearConstraintsMover , protocols::simple_moves::ConsensusDesignMover , protocols::simple_moves::ConstraintSetMover , protocols::simple_moves::ContingentAcceptMover , protocols::simple_moves::CoupledMover , protocols::simple_moves::CutChainMover , protocols::simple_moves::ddG , protocols::simple_moves::DeleteChainMover , protocols::simple_moves::DeleteChainsMover , protocols::simple_moves::DesignRepackMover , protocols::simple_moves::DisulfideInsertionMover , protocols::simple_moves::DumpPdb , protocols::simple_moves::ExtendedPoseMover , protocols::simple_moves::FavorSequenceProfile , protocols::simple_moves::FavorSymmetricSequence , protocols::simple_moves::FindConsensusSequence , protocols::simple_moves::ForceDisulfidesMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::LoadPDBMover , protocols::simple_moves::LoadUnboundRotMover , protocols::simple_moves::MakePolyXMover , protocols::simple_moves::MembraneTopology , protocols::simple_moves::MergePDBMover , protocols::simple_moves::MinMover , protocols::simple_moves::MinPackMover , protocols::simple_moves::ModifyVariantTypeMover , protocols::simple_moves::MonteCarloRecover , protocols::simple_moves::MonteCarloReset , protocols::simple_moves::MonteCarloTest , protocols::simple_moves::MSDMover , protocols::simple_moves::MutateResidue , protocols::simple_moves::PackRotamersMover , protocols::simple_moves::PackRotamersMoverLazy , protocols::simple_moves::PDBReloadMover , protocols::simple_moves::PeriodicBoxMover , protocols::simple_moves::PSSM2BfactorMover , protocols::simple_moves::RandomOmegaFlipMover , protocols::simple_moves::RandomTorsionMover , protocols::simple_moves::RepackSidechainsMover , protocols::simple_moves::RepeatPropagationMover , protocols::simple_moves::ReportEffectivePKA , protocols::simple_moves::ResetBaselineMover , protocols::simple_moves::ResidueTypeConstraintMover , protocols::simple_moves::RingConformationMover , protocols::simple_moves::RotamerTrialsMinMover , protocols::simple_moves::RotamerTrialsMover , protocols::simple_moves::ScoreMover , protocols::simple_moves::SequenceProfileMover , protocols::simple_moves::SetTorsion , protocols::simple_moves::ShortBackrubMover , protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover , protocols::simple_moves::sidechain_moves::PerturbChiSidechainMover , protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover , 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::symmetry::DetectSymmetry , protocols::simple_moves::symmetry::ExtractAsymmetricPoseMover , protocols::simple_moves::symmetry::ExtractAsymmetricUnitMover , protocols::simple_moves::symmetry::SetupForSymmetryMover , protocols::simple_moves::symmetry::SetupNCSMover , protocols::simple_moves::symmetry::SymMinMover , protocols::simple_moves::symmetry::SymPackRotamersMover , protocols::simple_moves::symmetry::SymRotamerTrialsMover , protocols::simple_moves::symmetry::TaskAwareSymMinMover , protocols::simple_moves::TaskAwareMinMover , protocols::simple_moves::Tumble , protocols::simple_moves::VirtualRootMover , protocols::stepwise::modeler::options::StepWiseBasicModelerOptions , protocols::stepwise::modeler::options::StepWiseModelerOptions , protocols::stepwise::modeler::options::StepWiseProteinModelerOptions , protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions , protocols::stepwise::options::StepWiseBasicOptions , protocols::surface_docking::SurfaceVectorOptions , protocols::symmetric_docking::membrane::MPSymDockMover , protocols::symmetric_docking::SymDockProtocol , protocols::symmetric_docking::SymFoldandDockMoveRbJumpMover , protocols::symmetric_docking::SymFoldandDockRbTrialMover , protocols::symmetric_docking::SymFoldandDockSlideTrialMover , protocols::toolbox::pose_metric_calculators::FragQualCalculator , protocols::toolbox::task_operations::StoreCombinedStoredTasksMover , protocols::toolbox::task_operations::StoreCompoundTaskMover , protocols::toolbox::task_operations::StoreTaskMover
• parse_ncaa_list() : protocols::flxbb::LayerDesignOperation
• parse_optional_data() : core::chemical::sdf::SDFParser
• parse_options() : protocols::analysis::PeptideDeriverFilter , protocols::antibody::CDRSetOptionsParser , protocols::antibody::design::CDRGraftDesignOptionsParser , protocols::antibody::design::CDRSeqDesignOptionsParser
• parse_options_name_and_value() : protocols::jd2::JD2ResourceManagerJobInputter
• parse_opts() : protocols::md::CartesianMD , protocols::simple_moves::MinMover
• parse_or_properties() : core::scoring::aa_composition_energy::AACompositionPropertiesSet
• parse_output_mode() : protocols::hotspot_hashing::movers::PlaceProbeMover
• parse_pdb_file() : protocols::ligand_docking::StartFrom
• parse_PDBnum_icode() : core::pack::task::ResfileContents
• parse_penalty_definitions() : core::scoring::aa_composition_energy::AACompositionEnergySetup
• parse_place_probe_tag() : protocols::hotspot_hashing::movers::PlaceProbeMover
• parse_property() : core::scoring::aa_composition_energy::AACompositionPropertiesSet
• parse_property_line() : core::chemical::sdf::CtabV2000Parser
• parse_protocol_id_tag_item() : protocols::features::ReportToDB
• parse_protocol_tag() : protocols::rosetta_scripts::RosettaScriptsParser
• parse_psipred_horiz_output() : core::io::external::PsiPredInterface
• parse_psipred_output() : core::io::external::PsiPredInterface
• parse_quota_command_line() : protocols::frag_picker::FragmentPicker
• parse_region_string() : protocols::contact_map::ContactMap
• parse_relevant_residues_mode_tag_item() : protocols::features::ReportToDB
• parse_remarks() : protocols::denovo_design::components::StructureData
• parse_remove_xray_virt_tag_item() : protocols::features::ReportToDB
• parse_report_format_string() : protocols::analysis::PeptideDeriverFilter
• parse_requirements() : protocols::sewing::AssemblyMover
• parse_resfile() : protocols::simple_moves::FindConsensusSequence , protocols::simple_moves::MSDMover
• parse_resfiles() : protocols::simple_moves::FindConsensusSequence , protocols::simple_moves::MSDMover
• parse_resid() : core::pack::task::ResfileContents
• parse_residue() : core::scoring::constraints::ConstraintIO
• parse_schfile() : protocols::md::MDBase
• parse_score_function() : protocols::simple_moves::MinPackMover , protocols::simple_moves::PackRotamersMover , protocols::simple_moves::RepackSidechainsMover
• parse_stage_id() : protocols::abinitio::abscript::AbscriptMover
• parse_startfrom_file() : protocols::ligand_docking::StartFrom
• parse_stride_tag_item() : protocols::features::TrajectoryReportToDB
• parse_sub_filters_tag() : core::pack::task::operation::ResFilterComposition
• parse_subtag() : protocols::denovo_design::connection::Connection , protocols::environment::EnvMover
• parse_subtags() : protocols::abinitio::abscript::AbscriptMover
• parse_tag() : core::pack::task::operation::AddBehaviorRLT , core::pack::task::operation::ChainIs , core::pack::task::operation::DisallowIfNonnative , core::pack::task::operation::DisallowIfNonnativeRLT , 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::InitializeFromCommandline , core::pack::task::operation::OperateOnCertainResidues , core::pack::task::operation::OperateOnResidueSubset , core::pack::task::operation::PreventRepacking , core::pack::task::operation::ReadResfile , core::pack::task::operation::ReadResfileAndObeyLengthEvents , core::pack::task::operation::ReplicateTask , core::pack::task::operation::ResFilter , core::pack::task::operation::ResFilterComposition , core::pack::task::operation::ResidueHasProperty , core::pack::task::operation::ResidueIndexIs , core::pack::task::operation::ResidueName3Is , core::pack::task::operation::ResiduePDBIndexIs , core::pack::task::operation::ResiduePDBInfoHasLabel , core::pack::task::operation::ResidueTypeFilter , core::pack::task::operation::ResLvlTaskOperation , core::pack::task::operation::RestrictAbsentCanonicalAAS , core::pack::task::operation::RestrictAbsentCanonicalAASRLT , core::pack::task::operation::RestrictResidueToRepacking , core::pack::task::operation::RestrictToRepacking , core::pack::task::operation::RotamerExplosion , core::pack::task::operation::TaskOperation , 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::denovo_design::components::Segment , protocols::denovo_design::task_operations::ConsensusLoopDesignOperation , protocols::dna::RestrictDesignToProteinDNAInterface , protocols::dna::WatsonCrickRotamerCouplings , protocols::enzdes::AddLigandMotifRotamers , protocols::enzdes::AddRigidBodyLigandConfs , protocols::enzdes::DetectProteinLigandInterface , protocols::enzdes::ProteinLigandInterfaceUpweighter , protocols::enzdes::SetCatalyticResPackBehavior , protocols::flxbb::LayerDesignOperation , protocols::forge::remodel::RemodelRotamerLinks , protocols::hotspot_hashing::AddSearchPatternRotSetOp , protocols::jd2::parser::FragmentReader , protocols::matdes::BuildingBlockInterfaceOperation , protocols::sewing::ReadNativeRotamersFile , protocols::toolbox::task_operations::AlignedThreadOperation , protocols::toolbox::task_operations::CrystalContactsOperation , protocols::toolbox::task_operations::DatabaseThread , protocols::toolbox::task_operations::DesignAroundOperation , protocols::toolbox::task_operations::DsspDesignOperation , protocols::toolbox::task_operations::ImportUnboundRotamersOperation , protocols::toolbox::task_operations::InteractingRotamerExplosion , protocols::toolbox::task_operations::JointSequenceOperation , protocols::toolbox::task_operations::LimitAromaChi2Operation , protocols::toolbox::task_operations::LinkResidues , protocols::toolbox::task_operations::ModifyAnnealer , protocols::toolbox::task_operations::PreventChainFromRepackingOperation , protocols::toolbox::task_operations::PreventResiduesFromRepackingOperation , protocols::toolbox::task_operations::ProteinCore , protocols::toolbox::task_operations::ProteinInterfaceDesignOperation , protocols::toolbox::task_operations::ReadResfileFromDB , protocols::toolbox::task_operations::RestrictChainToRepackingOperation , protocols::toolbox::task_operations::RestrictConservedLowDdgOperation , protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation , protocols::toolbox::task_operations::RestrictIdentitiesOperation , protocols::toolbox::task_operations::RestrictNativeResiduesOperation , protocols::toolbox::task_operations::RestrictNonSurfaceToRepackingOperation , protocols::toolbox::task_operations::RestrictResiduesToRepackingOperation , protocols::toolbox::task_operations::RestrictToAlignedSegmentsOperation , protocols::toolbox::task_operations::RestrictToInterface , protocols::toolbox::task_operations::RestrictToInterfaceVectorOperation , protocols::toolbox::task_operations::RestrictToLoops , protocols::toolbox::task_operations::RestrictToLoopsAndNeighbors , protocols::toolbox::task_operations::RestrictToTerminiOperation , protocols::toolbox::task_operations::RetrieveStoredTaskOperation , protocols::toolbox::task_operations::SelectByDeltaScoreOperation , protocols::toolbox::task_operations::SelectByDensityFitOperation , protocols::toolbox::task_operations::SelectBySASAOperation , protocols::toolbox::task_operations::SelectResiduesWithinChainOperation , protocols::toolbox::task_operations::SeqprofConsensusOperation , protocols::toolbox::task_operations::SetIGTypeOperation , protocols::toolbox::task_operations::ThreadSequenceOperation
• parse_task_operations() : protocols::simple_moves::AddConstraintsToCurrentConformationMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::MinPackMover , protocols::simple_moves::PackRotamersMover , protocols::simple_moves::TaskAwareMinMover
• parse_use_transactions_tag_item() : protocols::features::ReportToDB
• parsed_json_ : protocols::rpc::JSON_RPC
• parsed_position_ : protocols::simple_moves::SimpleThreadingMover
• parsed_positions_ : protocols::carbohydrates::GlycanRelaxMover , protocols::carbohydrates::SimpleGlycosylateMover
• parsed_string_for_resfile : protocols::forge::remodel::RemodelData
• ParsedProtocol() : protocols::rosetta_scripts::ParsedProtocol
• ParsedProtocolOP : protocols::simple_moves::GenericMonteCarloMover
• parser() : protocols::jd2::JobDistributor
• parser_ : protocols::jd2::JobDistributor
• ParserJobInputter() : protocols::protein_interface_design::ParserJobInputter
• partial_assign_relaxed_state() : core::pack::interaction_graph::FASTERNode
• partial_assign_state() : core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode
• partial_assign_state_with_lowest_one_body_energy() : core::pack::interaction_graph::FASTERNode
• partial_charge() : core::chemical::sdf::MolFileIOAtom
• partial_charge_ : core::chemical::sdf::MolFileIOAtom
• partial_state_assignment() : protocols::flexpack::interaction_graph::FlexbbNode
• partial_state_assignment_ : core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmMinimalistEdge
• partially_assign_state() : protocols::flexpack::interaction_graph::MinimalistFlexbbNode
• PartialSecondarySimilarity() : protocols::frag_picker::scores::PartialSecondarySimilarity
• PartialThreadingMover() : protocols::comparative_modeling::PartialThreadingMover
• Particle() : core::optimization::Particle
• ParticleSwarmMinimizer() : core::optimization::ParticleSwarmMinimizer
• partition() : protocols::toolbox::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator
• partition_ : protocols::hotspot_hashing::PartitionedSearchPattern
• partition_by_jump() : core::kinematics::FoldTree
• partition_by_residue() : core::kinematics::FoldTree
• partition_coloring() : core::kinematics::FoldTree
• partition_definition() : protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• partition_definition_ : protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::stepwise::modeler::rna::o2prime::O2PrimePacker , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• partition_into_coordinates() : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD
• partition_splits_an_input_domain() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• PartitionAggregateFunction() : protocols::multistate_design::PartitionAggregateFunction< T >
• PartitionContactScreener() : protocols::stepwise::screener::PartitionContactScreener
• PartitionedSearchPattern() : protocols::hotspot_hashing::PartitionedSearchPattern
• partitions_split_a_submotif() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• partner() : protocols::docking::DockingEnsemble
• partner1() : protocols::contact_map::Contact
• partner1_ : protocols::contact_map::Contact
• partner2() : protocols::contact_map::Contact
• partner2_ : protocols::contact_map::Contact
• partner_ : core::scoring::dna::BasePartner , protocols::docking::DockingEnsemble , protocols::farna::MultipleDomainMover , protocols::rigid::RigidBodyPerturbMover , protocols::rigid::RigidBodyRandomizeMover , protocols::scoring::Interface
• partner_ids_ : protocols::noesy_assign::FloatingResonance
• partner_pose_ : protocols::sewing::AppendAssemblyMover , protocols::sewing::Assembly
• PartnerMotifScorer() : protocols::sewing::scoring::PartnerMotifScorer
• partners() : protocols::docking::DockingHighRes , protocols::docking::DockingProtocol , protocols::docking::DockSetupMover , protocols::docking::TemperedDocking , protocols::protein_interface_design::filters::HbondsToResidueFilter
• partners_ : protocols::dna::DNAParameters , protocols::docking::DockingHighRes , protocols::docking::DockingProtocol , protocols::docking::DockSetupMover , protocols::docking::EllipsoidalRandomizationMover , protocols::docking::membrane::MPFindInterfaceMover , protocols::docking::membrane::QuickRelaxPartnersSeparately , protocols::docking::TemperedDocking , protocols::protein_interface_design::filters::HbondsToAtomFilter , protocols::protein_interface_design::filters::HbondsToResidueFilter
• pass_ : protocols::environment::DofUnlock , protocols::environment::EXCN_Env_Security_Exception
• pass_1_merge_residues_as_necessary() : core::io::pose_from_sfr::PoseFromSFRBuilder
• pass_2_resolve_residue_types() : core::io::pose_from_sfr::PoseFromSFRBuilder
• pass_3_verify_sufficient_backbone_atoms() : core::io::pose_from_sfr::PoseFromSFRBuilder
• pass_4_redo_termini() : core::io::pose_from_sfr::PoseFromSFRBuilder
• pass_5_note_discarded_atoms() : core::io::pose_from_sfr::PoseFromSFRBuilder
• pass_all_filters() : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• pass_all_pose_screens() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer
• pass_base_centroid_screen : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• pass_clash_check() : protocols::stepwise::modeler::rna::phosphate::PhosphateMover
• pass_count() : protocols::stepwise::screener::AlignRMSD_Screener
• pass_count_ : protocols::stepwise::screener::AlignRMSD_Screener
• pass_FARFAR_no_auto_bulge_filter() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• pass_metropolis() : core::pack::annealer::SimAnnealerBase , protocols::canonical_sampling::SidechainMetropolisHastingsMover , protocols::simple_moves::sidechain_moves::SidechainMCMover
• pass_metropolis_multiple_nodes_changing() : protocols::flexpack::annealer::FlexbbSimAnnealer
• pass_screen_struct_pair_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• pass_start_pose() : protocols::antibody::H3RefineCCD , protocols::antibody::RefineOneCDRLoop
• pass_the_loop() : protocols::antibody::H3PerturbCCD
• passed_automorphism() : protocols::motifs::MotifHit
• passed_automorphism_ : protocols::motifs::MotifHit
• passed_centroid_filter_ : protocols::ub_e2c::ubi_e2c_modeler
• passed_fullatom_filter_ : protocols::ub_e2c::ubi_e2c_modeler
• passed_highres_filter_ : protocols::symmetric_docking::SymDockProtocol
• passed_lowres_filter_ : protocols::symmetric_docking::SymDockProtocol
• passes_com_vector_criterion() : protocols::match::NumNeighborsMPM
• passes_etable_filter() : protocols::match::output::UpstreamDownstreamCollisionFilter
• passes_fast_scan() : protocols::farna::movers::RNA_LoopCloser
• passes_filter() : protocols::match::output::LimitHitsPerRotamerFilter , protocols::match::output::MatchCollisionFilter , protocols::match::output::MatchFilter , protocols::match::output::StateAccumulatingMatchFilter , protocols::match::output::UpstreamCollisionFilter , protocols::match::output::UpstreamDownstreamCollisionFilter , protocols::topology_broker::TopologyClaimer
• passes_filters() : protocols::match::output::MatchProcessor
• passes_hardsphere_filter() : protocols::match::output::UpstreamCollisionFilter , protocols::match::output::UpstreamDownstreamCollisionFilter
• passport() : protocols::environment::ClientMover , protocols::environment::EXCN_Env_Security_Exception
• passport_updated() : protocols::abinitio::abscript::AbscriptLoopCloserCM , protocols::abinitio::abscript::FragmentCM , protocols::abinitio::abscript::RigidChunkCM , protocols::environment::ClientMover , protocols::environment::CoMTrackerCM , protocols::environment::ScriptCM , protocols::loops::loop_mover::LoopCM , protocols::rigid::UniformRigidBodyCM
• passports_ : protocols::environment::ClientMover
• PassportStack : protocols::environment::ClientMover
• passthrough_ : protocols::electron_density::DockIntoDensityMover
• Patch() : core::chemical::Patch
• patch_map() : core::chemical::ResidueTypeSet
• patch_map_ : core::chemical::ResidueTypeSet
• patch_name : core::chemical::carbohydrates::SugarModificationsNomenclatureTableRow
• patch_name_from_affix() : core::chemical::carbohydrates::CarbohydrateInfoManager
• patch_names() : core::chemical::ResidueTypeFinder
• patch_names_ : core::chemical::ResidueTypeFinder
• patch_scores_ : protocols::toolbox::pose_metric_calculators::HPatchCalculator
• patch_str() : core::sequence::AnnotatedSequence
• patcharea_to_score_ : core::pack::interaction_graph::SurfacePotential
• patchdock_entry_num() : protocols::protein_interface_design::PatchdockReader
• patchdock_entry_num_ : protocols::protein_interface_design::PatchdockReader
• patchdock_fname() : protocols::protein_interface_design::PatchdockReader
• patchdock_fname_ : protocols::protein_interface_design::PatchdockReader
• PatchdockReader() : protocols::protein_interface_design::PatchdockReader
• PatchdockReaderOP : protocols::protein_interface_design::movers::PatchdockTransform
• PatchdockTransform() : protocols::protein_interface_design::movers::PatchdockTransform
• patches() : core::chemical::ResidueTypeSet
• patches_ : core::chemical::ResidueTypeSet
• PatchOperation() : protocols::canonical_sampling::PatchOperation
• path : protocols::hybridization::TMalign , protocols::motifs::Motif , protocols::sewing::Assembly
• path_ : core::chemical::NCAARotLibPath , core::pose::rna::RNA_IdealCoord , protocols::features::DatabaseJobOutputter , protocols::jd2::FileSystemJobDistributor , protocols::jd2::PDBJobOutputter , protocols::motifs::Motif , protocols::sewing::Assembly
• path_dist() : core::scoring::AtomNeighbor , core::scoring::SmallAtNb
• path_dist_ : core::scoring::AtomNeighbor , core::scoring::SmallAtNb
• path_dist_cutoff_ : core::scoring::carbon_hbonds::CarbonHBondEnergy
• path_distance() : core::chemical::ResidueType , core::conformation::Residue , core::scoring::etable::count_pair::CountPairGeneric
• path_distance_ : core::chemical::ResidueType , core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• path_distance_OK() : core::scoring::carbon_hbonds::CarbonHBondEnergy
• path_distances() : core::chemical::ResidueType , core::conformation::Residue
• path_distances_to_connection_points_ : core::scoring::etable::etrie::GenericResidueConnectionData
• path_dists_ : core::scoring::etable::count_pair::CountPairIntraRes< CrossoverBehavior >
• path_tightness() : protocols::simple_filters::AveragePathLengthFilter
• path_tightness_ : protocols::simple_filters::AveragePathLengthFilter
• path_to_parameter_files_ : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• path_to_torsion_files_ : core::scoring::rna::RNA_TorsionPotential
• pAtoms : core::scoring::sc::_PROBE
• pattern_ : protocols::hotspot_hashing::AddSearchPatternRotSetOp
• pb_bound_tag() : core::scoring::methods::EnergyMethodOptions
• pb_bound_tag_ : core::scoring::methods::EnergyMethodOptions
• pb_by_state_ : core::scoring::methods::PBLifetimeCache
• pb_cached_data_ : protocols::simple_moves::ddG
• pb_enabled_ : protocols::simple_filters::DdgFilter , protocols::simple_moves::ddG
• pb_lengths_ : core::scoring::etable::count_pair::CountPairGeneric
• PB_LIFETIME_CACHE : core::pose::datacache::CacheableDataType
• PB_potential_ : core::scoring::ScoringManager
• pb_unbound_tag() : core::scoring::methods::EnergyMethodOptions
• pb_unbound_tag_ : core::scoring::methods::EnergyMethodOptions
• pbe_mode : core::scoring::APBSConfig::I_PARAM
• pbest() : core::optimization::Particle
• pbest_ : core::optimization::Particle
• PBIter : core::conformation::PseudoBondCollection
• PBLifetimeCache() : core::scoring::methods::PBLifetimeCache , core::scoring::methods::PoissonBoltzmannEnergy
• PBLifetimeCacheOP : core::scoring::methods::PoissonBoltzmannEnergy
• PBP_clustering_at_chain_closure() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• PBP_clustering_at_chain_closure_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection , protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• pca_ : protocols::abinitio::AbrelaxApplication , protocols::abinitio::PcaEvaluator
• PcaEvaluator() : protocols::abinitio::PcaEvaluator
• PCluster() : protocols::pockets::PCluster
• PClusterSet : protocols::pockets::PCluster , protocols::pockets::PClusterSet
• pconf_creation() : protocols::environment::Environment
• pconf_destruction() : protocols::environment::Environment
• pconfs_ : protocols::environment::Environment
• pcs_d_ : protocols::scoring::methods::pcs::TensorsOptimizer , protocols::scoring::methods::pcsTs1::TensorsOptimizer_Ts1 , protocols::scoring::methods::pcsTs2::TensorsOptimizer_Ts2 , protocols::scoring::methods::pcsTs3::TensorsOptimizer_Ts3 , protocols::scoring::methods::pcsTs4::TensorsOptimizer_Ts4
• pcs_d_c_ : protocols::scoring::methods::pcs2::TensorsOptimizer , protocols::scoring::methods::pcs2::TensorsOptimizerFix , protocols::scoring::methods::pcs2::TensorsOptimizerSvd
• PCS_data() : protocols::scoring::methods::pcs::PCS_data
• PCS_data_all_ : protocols::scoring::methods::pcs2::PcsDataCenterManager , protocols::scoring::methods::pcs2::PcsDataCenterManagerSingleton
• PCS_data_from_pose() : protocols::scoring::methods::pcs::PCS_Energy , protocols::scoring::methods::pcsTs1::PCS_Energy_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_Ts4
• PCS_data_input() : protocols::scoring::methods::pcs::PCS_data_input
• PCS_data_input_manager() : protocols::scoring::methods::pcs::PCS_data_input_manager
• PCS_data_input_manager_Ts1() : protocols::scoring::methods::pcsTs1::PCS_data_input_manager_Ts1
• PCS_data_input_manager_Ts2() : protocols::scoring::methods::pcsTs2::PCS_data_input_manager_Ts2
• PCS_data_input_manager_Ts3() : protocols::scoring::methods::pcsTs3::PCS_data_input_manager_Ts3
• PCS_data_input_manager_Ts4() : protocols::scoring::methods::pcsTs4::PCS_data_input_manager_Ts4
• PCS_data_input_Ts1() : protocols::scoring::methods::pcsTs1::PCS_data_input_Ts1
• PCS_data_input_Ts2() : protocols::scoring::methods::pcsTs2::PCS_data_input_Ts2
• PCS_data_input_Ts3() : protocols::scoring::methods::pcsTs3::PCS_data_input_Ts3
• PCS_data_input_Ts4() : protocols::scoring::methods::pcsTs4::PCS_data_input_Ts4
• PCS_data_line_all_ : protocols::scoring::methods::pcs::PCS_file_data , protocols::scoring::methods::pcsTs1::PCS_file_data_Ts1 , protocols::scoring::methods::pcsTs2::PCS_file_data_Ts2 , protocols::scoring::methods::pcsTs3::PCS_file_data_Ts3 , protocols::scoring::methods::pcsTs4::PCS_file_data_Ts4
• PCS_data_line_all_spin_ : 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
• PCS_data_per_lanthanides() : protocols::scoring::methods::pcs::PCS_data_per_lanthanides
• PCS_data_per_lanthanides_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
• PCS_data_per_lanthanides_Ts1() : protocols::scoring::methods::pcsTs1::PCS_data_per_lanthanides_Ts1
• PCS_data_per_lanthanides_Ts2() : protocols::scoring::methods::pcsTs2::PCS_data_per_lanthanides_Ts2
• PCS_data_per_lanthanides_Ts3() : protocols::scoring::methods::pcsTs3::PCS_data_per_lanthanides_Ts3
• PCS_data_per_lanthanides_Ts4() : protocols::scoring::methods::pcsTs4::PCS_data_per_lanthanides_Ts4
• PCS_data_Ts1() : protocols::scoring::methods::pcsTs1::PCS_data_Ts1
• PCS_data_Ts2() : protocols::scoring::methods::pcsTs2::PCS_data_Ts2
• PCS_data_Ts3() : protocols::scoring::methods::pcsTs3::PCS_data_Ts3
• PCS_data_Ts4() : protocols::scoring::methods::pcsTs4::PCS_data_Ts4
• pcs_e_p_all_ : protocols::scoring::methods::pcs2::PcsEnergyParameterManager
• PCS_Energy() : protocols::scoring::methods::pcs::PCS_Energy
• PCS_Energy_parameters_manager() : protocols::scoring::methods::pcs::PCS_Energy_parameters_manager
• PCS_Energy_parameters_manager_Ts1() : protocols::scoring::methods::pcsTs1::PCS_Energy_parameters_manager_Ts1
• PCS_Energy_parameters_manager_Ts2() : protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2
• PCS_Energy_parameters_manager_Ts3() : protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3
• PCS_Energy_parameters_manager_Ts4() : protocols::scoring::methods::pcsTs4::PCS_Energy_parameters_manager_Ts4
• PCS_Energy_Ts1() : protocols::scoring::methods::pcsTs1::PCS_Energy_Ts1
• PCS_Energy_Ts2() : protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2
• PCS_Energy_Ts3() : protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3
• PCS_Energy_Ts4() : protocols::scoring::methods::pcsTs4::PCS_Energy_Ts4
• PCS_experimental() : 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
• PCS_experimental_ : 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
• PCS_file_data() : protocols::scoring::methods::pcs::PCS_file_data
• PCS_file_data_Ts1() : protocols::scoring::methods::pcsTs1::PCS_file_data_Ts1
• PCS_file_data_Ts2() : protocols::scoring::methods::pcsTs2::PCS_file_data_Ts2
• PCS_file_data_Ts3() : protocols::scoring::methods::pcsTs3::PCS_file_data_Ts3
• PCS_file_data_Ts4() : protocols::scoring::methods::pcsTs4::PCS_file_data_Ts4
• PCS_filename_and_data_ : protocols::scoring::methods::pcs::PCS_data_input , protocols::scoring::methods::pcsTs1::PCS_data_input_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_input_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_input_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_input_Ts4
• PCS_FragDistance() : protocols::frag_picker::scores::PCS_FragDistance
• PCS_line_data() : protocols::scoring::methods::pcs::PCS_line_data
• PCS_line_data_Ts1() : protocols::scoring::methods::pcsTs1::PCS_line_data_Ts1
• PCS_line_data_Ts2() : protocols::scoring::methods::pcsTs2::PCS_line_data_Ts2
• PCS_line_data_Ts3() : protocols::scoring::methods::pcsTs3::PCS_line_data_Ts3
• PCS_line_data_Ts4() : protocols::scoring::methods::pcsTs4::PCS_line_data_Ts4
• PCS_multi_data_from_noone() : protocols::scoring::methods::pcs2::PcsEnergy
• PCS_multi_data_from_pose() : protocols::scoring::methods::pcs2::PcsEnergy
• PCS_tensor() : protocols::scoring::methods::pcs::PCS_tensor
• PCS_tensor_Ts1() : protocols::scoring::methods::pcsTs1::PCS_tensor_Ts1
• PCS_tensor_Ts2() : protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2
• PCS_tensor_Ts3() : protocols::scoring::methods::pcsTs3::PCS_tensor_Ts3
• PCS_tensor_Ts4() : protocols::scoring::methods::pcsTs4::PCS_tensor_Ts4
• PCS_tolerance() : 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
• PCS_tolerance_ : 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
• pcs_weight_ : protocols::scoring::methods::pcs2::PcsEnergyParameter , protocols::scoring::methods::pcs::PCS_Energy_parameters_manager , protocols::scoring::methods::pcsTs1::PCS_Energy_parameters_manager_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_parameters_manager_Ts4
• pcs_weight_stage1_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter , protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• pcs_weight_stage2_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter , protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• pcs_weight_stage3_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter , protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• pcs_weight_stage4_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter , protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• PcsDataCenter() : protocols::scoring::methods::pcs2::PcsDataCenter
• PcsDataCenterManager() : protocols::scoring::methods::pcs2::PcsDataCenterManager
• PcsDataCenterManagerSingleton() : protocols::scoring::methods::pcs2::PcsDataCenterManagerSingleton
• PcsDataLanthanide() : protocols::scoring::methods::pcs2::PcsDataLanthanide
• PcsEnergy() : protocols::scoring::methods::pcs2::PcsEnergy
• PcsEnergyController() : protocols::topology_broker::PcsEnergyController
• PcsEnergyParameter() : protocols::scoring::methods::pcs2::PcsEnergyParameter
• PcsEnergyParameterManager() : protocols::scoring::methods::pcs2::PcsEnergyParameterManager
• PcsGridSearchParameter() : protocols::scoring::methods::pcs2::PcsGridSearchParameter
• PcsGridSearchParameterManager() : protocols::scoring::methods::pcs2::PcsGridSearchParameterManager
• PcsInputCenter() : protocols::scoring::methods::pcs2::PcsInputCenter
• PcsInputCenter_all_ : protocols::scoring::methods::pcs2::PcsInputCenterManager
• PcsInputCenterManager() : protocols::scoring::methods::pcs2::PcsInputCenterManager
• PcsInputFile() : protocols::scoring::methods::pcs2::PcsInputFile
• PcsInputFile_all_ : protocols::scoring::methods::pcs2::PcsInputCenter
• PcsInputLine() : protocols::scoring::methods::pcs2::PcsInputLine
• PcsInputLine_all_ : protocols::scoring::methods::pcs2::PcsInputFile
• PcsTensor() : protocols::scoring::methods::pcs2::PcsTensor
• pcut_ : protocols::hybridization::DDomainParse , protocols::hybridization::HybridizeProtocol
• pd_ : core::scoring::packstat::MultiProbePerSphereAccumulator
• pd_edge_table_all_zeros() : core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::PDEdge
• pd_reader() : protocols::protein_interface_design::movers::PatchdockTransform
• pd_reader_ : protocols::protein_interface_design::movers::PatchdockTransform
• pdamp() : core::scoring::MultipoleParameter
• pdamp_ : core::scoring::MultipoleParameter
• pdb() : core::scoring::motif::ResPairMotif , protocols::antibody::CDRDBPose , protocols::antibody::CDRDBSequence
• PDB() : protocols::sparta::PDB
• pdb2pose() : core::pose::PDBInfo
• Pdb2Pose : core::pose::PDBPoseMap
• pdb2pose_ : core::pose::PDBInfo , core::pose::PDBPoseMap
• pdb_ : core::scoring::motif::ResPairMotif
• pdb_chain() : protocols::pmut_scan::MutationData
• pdb_code_ : protocols::sewing::Model
• pdb_codes_ : core::io::sequence_comparation::DesignContrast
• pdb_comments() : core::io::StructFileRep , core::io::StructFileRepOptions
• pdb_comments_ : core::io::StructFileRep , core::io::StructFileRepOptions
• pdb_components_filename_ : core::chemical::ResidueTypeSet
• pdb_contains_target_ : protocols::seeded_abinitio::SeedFoldTree
• pdb_data_features_ : protocols::features::ProteinSilentReport
• PDB_DIR : protocols::sparta::Sparta::SpartaLib
• pdb_end() : protocols::antibody::clusters::CDRCluster
• pdb_end_ : protocols::antibody::clusters::CDRCluster
• pdb_end_insertion_code_ : protocols::antibody::clusters::CDRCluster
• pdb_file_names_ : core::io::sequence_comparation::DesignContrast , protocols::pmut_scan::PointMutScanDriver
• pdb_filenames_ : protocols::docking::DockingEnsemble
• pdb_hash_ : protocols::frag_picker::PdbIdChunkFilter
• pdb_id : protocols::loophash::BBExtraData
• pdb_info() : core::pose::Pose
• pdb_info_ : core::pose::Pose
• pdb_lines_ : core::import_pose::PDBSilentStruct
• pdb_name() : protocols::simple_filters::RelativePoseFilter
• pdb_name_ : protocols::pack_daemon::StructureFileNames
• pdb_num : core::io::raw_data::DisulfideFile
• pdb_numb() : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• pdb_numb_ : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• pdb_numbered_h3_loop_end : protocols::toolbox::task_operations::RestrictToCDRH3Loop
• pdb_numbered_h3_loop_start : protocols::toolbox::task_operations::RestrictToCDRH3Loop
• pdb_numbering_ : protocols::simple_filters::ScoreCutoffFilter
• pdb_output() : protocols::helical_bundle::BackboneGridSampler , protocols::helical_bundle::BundleGridSampler
• pdb_parents() : core::io::StructFileRepOptions
• pdb_parents_ : core::io::StructFileRepOptions
• pdb_pose_map_ : protocols::pack_daemon::EntityCorrespondence
• pdb_position_ : protocols::antibody::design::MutantPosition
• pdb_prefix() : protocols::helical_bundle::BackboneGridSampler , protocols::helical_bundle::BundleGridSampler
• pdb_prefix_ : protocols::helical_bundle::BackboneGridSampler , protocols::helical_bundle::BundleGridSampler
• pdb_resnum_ : protocols::pmut_scan::MutationData
• pdb_rotamers_file() : core::chemical::rotamers::PDBRotamerLibrarySpecification
• pdb_rotamers_file_ : core::chemical::rotamers::PDBRotamerLibrarySpecification
• pdb_seqpos : protocols::simple_filters::nmer_svm_res_data
• pdb_source_ : protocols::features::helixAssembly::HelicalFragment , protocols::features::strand_assembly::SandwichFragment , protocols::features::strand_assembly::StrandFragment
• pdb_start() : protocols::antibody::clusters::CDRCluster , protocols::forge::remodel::RemodelData
• pdb_start_ : protocols::antibody::clusters::CDRCluster
• pdb_start_insertion_code_ : protocols::antibody::clusters::CDRCluster
• pdb_stop : protocols::forge::remodel::RemodelData
• pdbContent : protocols::pockets::SmallMol
• pdbdata_string_ : protocols::rpc::JSON_RPC
• PdbDataFeatures() : protocols::features::PdbDataFeatures
• PdbDataFeaturesCreator() : protocols::features::PdbDataFeaturesCreator
• PDBDumpMover() : protocols::moves::PDBDumpMover
• PDBfileName : protocols::sparta::PDB
• pdbid() : core::fragment::AnnotatedFragData , core::fragment::FragData
• pdbid_ : core::fragment::AnnotatedFragData
• PDBInfo() : core::pose::PDBInfo
• PDBJobInputter() : protocols::jd2::PDBJobInputter
• PDBJobOutputter() : protocols::jd2::PDBJobOutputter
• PDBLandmark() : protocols::antibody::PDBLandmark
• pdbListName : protocols::sparta::Sparta::SpartaLib
• pdbname() : protocols::cryst::Spacegroup , protocols::cryst::WallpaperGroup , protocols::dna::DnaInterfacePacker , protocols::simple_filters::SSMotifFinder
• pdbname_ : protocols::dna::DnaInterfacePacker , protocols::metal_interface::AddZincSiteConstraints , protocols::simple_filters::SSMotifFinder
• pdbno_ : protocols::pockets::PocketGrid
• pdboutput() : protocols::dna::DnaInterfacePacker
• PDBOutput() : protocols::dna::PDBOutput
• pdboutput_ : protocols::dna::DnaInterfacePacker , protocols::motifs::MotifDnaPacker
• pdbpos() : core::fragment::AnnotatedFragData , core::fragment::FragData , protocols::dna::DnaDesignDef
• PDBPoseInputStream() : core::import_pose::pose_stream::PDBPoseInputStream
• PDBPoseInputter() : protocols::jd3::pose_inputters::PDBPoseInputter
• PDBPoseMap() : core::pose::PDBPoseMap
• PDBPoseOutputter() : protocols::jd3::pose_outputters::PDBPoseOutputter
• PDBReloadMover() : protocols::simple_moves::PDBReloadMover
• PDBRotamerLibrarySpecification() : core::chemical::rotamers::PDBRotamerLibrarySpecification
• pdbs_this_round_ : protocols::optimize_weights::IterativeOptEDriver
• PDBSilentStruct() : core::import_pose::PDBSilentStruct
• PDBSilentStructCreator() : core::import_pose::PDBSilentStructCreator
• PDBTrajectoryRecorder() : protocols::canonical_sampling::PDBTrajectoryRecorder
• PDBWriter() : protocols::match::output::PDBWriter
• PDDFEnergy() : protocols::scoring::methods::saxs::PDDFEnergy
• PDDFEnergyCreator() : protocols::scoring::methods::saxs::PDDFEnergyCreator
• PDDFScoreFilter() : protocols::simple_filters::PDDFScoreFilter
• PDEdge() : core::pack::interaction_graph::PDEdge
• pdf_ : protocols::nonlocal::BiasedFragmentMover
• pdie : core::scoring::APBSConfig::R_PARAM
• pdime : core::scoring::APBSConfig
• PDInteractionGraph() : core::pack::interaction_graph::PDInteractionGraph
• PDNode() : core::pack::interaction_graph::PDNode
• peak_id() : protocols::noesy_assign::CrossPeak
• peak_id_ : protocols::noesy_assign::CrossPeak
• peak_violation_counts_ : protocols::noesy_assign::DistanceScoreMover
• peak_volume() : protocols::noesy_assign::PeakAssignment
• PeakAssignment() : protocols::noesy_assign::PeakAssignment
• PeakAssignmentMap : protocols::noesy_assign::PeakAssignmentResidueMap
• PeakAssignmentParameters() : protocols::noesy_assign::PeakAssignmentParameters
• PeakAssignmentResidueMap() : protocols::noesy_assign::PeakAssignmentResidueMap
• PeakAssignments : protocols::noesy_assign::CrossPeak , protocols::noesy_assign::PeakAssignmentResidueMap
• PeakCalibrator() : protocols::noesy_assign::PeakCalibrator
• PeakCalibratorMap() : protocols::noesy_assign::PeakCalibratorMap
• PeakFileFormat() : protocols::noesy_assign::PeakFileFormat
• PeakFileFormat_Base() : protocols::noesy_assign::PeakFileFormat_Base
• PeakFileFormat_Sparky() : protocols::noesy_assign::PeakFileFormat_Sparky
• PeakFileFormat_xeasy() : protocols::noesy_assign::PeakFileFormat_xeasy
• PeakFileFormat_xpk() : protocols::noesy_assign::PeakFileFormat_xpk
• peaks() : protocols::noesy_assign::CrossPeakList , protocols::noesy_assign::PeakCalibrator
• peaks_ : protocols::noesy_assign::CrossPeakList , protocols::noesy_assign::PeakCalibrator
• PeakViolationCounts : protocols::noesy_assign::DistanceScoreMover
• peek_back() : protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering >
• peek_front() : protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering >
• penalties() : core::scoring::aa_repeat_energy::AARepeatEnergy
• penalties_ : core::scoring::aa_repeat_energy::AARepeatEnergy
• penalty() : core::fragment::picking_old::vall::eval::ABEGOEval , core::scoring::MembraneEmbed
• PENALTY : protocols::frag_picker::scores::ProlinePhiScore , protocols::frag_picker::scores::SecondaryIdentity , protocols::frag_picker::scores::SequenceIdentity
• penalty_ : core::fragment::picking_old::vall::eval::ABEGOEval , core::scoring::MembraneEmbed , protocols::simple_moves::FavorSymmetricSequence
• penalty_at_1M_ : core::scoring::methods::IntermolEnergy
• penalty_factor_ : protocols::simple_filters::ResidueIEFilter
• penalty_from_score() : protocols::simple_filters::ResidueIEFilter
• penalty_res_ : protocols::rbsegment_relax::SequenceShiftMover
• pending_notifications_ : protocols::jd2::archive::MPIArchiveJobDistributor
• pep1 : core::io::CisPeptideInformation
• pep2 : core::io::CisPeptideInformation
• pep_fold_only : protocols::flexpep_docking::FlexPepDockingFlags
• pep_lengths_ : protocols::analysis::PeptideDeriverFilter
• pep_next_ : core::environment::FoldTreeSketch::Node
• pep_prev_ : core::environment::FoldTreeSketch::Node
• pep_refine : protocols::flexpep_docking::FlexPepDockingFlags
• PEPTIDE : core::kinematics::Edge
• peptide_anchors : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_bonded_pair_indices_ : core::scoring::PolymerBondedEnergyContainer
• peptide_chain() : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_chain_ : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_chain_num_ : protocols::simple_moves::DisulfideInsertionMover
• peptide_cuts : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_entry() : protocols::analysis::PeptideDeriverBasicStreamOutputter , protocols::analysis::PeptideDeriverMarkdownStreamOutputter , protocols::analysis::PeptideDeriverOutputter , protocols::analysis::PeptideDeriverOutputterContainer , protocols::analysis::PeptideDeriverPoseOutputter
• peptide_first_res() : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_first_res_ : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_last_res() : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_length() : protocols::analysis::PeptideDeriverBasicStreamOutputter , protocols::analysis::PeptideDeriverMarkdownStreamOutputter , protocols::analysis::PeptideDeriverOutputter , protocols::analysis::PeptideDeriverOutputterContainer , protocols::analysis::PeptideDeriverPoseOutputter
• peptide_loop_model : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_nres() : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_nres_ : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_random_loop_model() : protocols::flexpep_docking::FlexPepDockingProtocol
• peptide_stub_mover_ : protocols::helical_bundle::BackboneGridSampler
• peptide_stub_mover_initialized() : protocols::helical_bundle::BackboneGridSampler
• peptide_stub_mover_initialized_ : protocols::helical_bundle::BackboneGridSampler
• PeptideBondEnergy() : core::scoring::methods::PeptideBondEnergy
• PeptideDeriverBasicStreamOutputter() : protocols::analysis::PeptideDeriverBasicStreamOutputter
• PeptideDeriverFilter() : protocols::analysis::PeptideDeriverFilter
• PeptideDeriverMarkdownStreamOutputter() : protocols::analysis::PeptideDeriverMarkdownStreamOutputter
• PeptideDeriverPoseOutputter() : protocols::analysis::PeptideDeriverPoseOutputter
• PeptideStapleDesignMover() : protocols::protein_interface_design::movers::PeptideStapleDesignMover
• PeptideStapleMover() : protocols::simple_moves::PeptideStapleMover
• PeptideStubMover() : protocols::cyclic_peptide::PeptideStubMover , protocols::helical_bundle::BackboneGridSampler
• PeptideStubMoverCOP : protocols::helical_bundle::BackboneGridSampler
• PeptideStubMoverOP : protocols::helical_bundle::BackboneGridSampler
• peptoid_rotlib_n_bin_per_rot() : core::chemical::rotamers::PeptoidRotamerLibrarySpecification
• peptoid_rotlib_n_bins_per_rot_ : core::chemical::rotamers::PeptoidRotamerLibrarySpecification
• peptoid_rotlib_n_rotameric_bins() : core::chemical::rotamers::PeptoidRotamerLibrarySpecification
• peptoid_rotlib_path() : core::chemical::rotamers::PeptoidRotamerLibrarySpecification
• peptoid_rotlib_path_ : core::chemical::rotamers::PeptoidRotamerLibrarySpecification
• PeptoidRotamerLibrarySpecification() : core::chemical::rotamers::PeptoidRotamerLibrarySpecification
• per_chain_renumbering() : core::io::StructFileRepOptions
• per_chain_renumbering_ : core::io::StructFileRepOptions
• per_constraint_build_points() : protocols::match::Matcher
• per_constraint_build_points_ : protocols::match::Matcher
• per_cst_build_resids_ : protocols::match::Matcher
• per_cst_pose_build_resids_ : protocols::match::MatcherTask
• per_native_recovery_ : protocols::rotamer_recovery::RRReporterHuman
• per_node_rotamer_sets_ : core::pack::interaction_graph::ResidueArrayAnnealingEvaluator
• per_res_atom_ind_ : protocols::match::output::UpstreamDownstreamCollisionFilter
• per_residue_data_ : protocols::analysis::InterfaceAnalyzerMover
• per_residue_ddg_ : protocols::simple_moves::ddG
• percent_native() : protocols::sewing::Assembly
• perform_bump_check() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• perform_checks() : core::chemical::ResidueType
• perform_electron_density_screen_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer
• perform_filters_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• perform_local_refinement() : protocols::hotspot_hashing::movers::PlaceProbeMover
• perform_minimizer_run_ : protocols::farna::movers::RNA_Minimizer
• perform_rama_check() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• perform_score_diff_cut_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• perform_VDW_rep_screen_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• performing_pure_insertion() : protocols::forge::build::SegmentInsert
• performs_orientation() : protocols::denovo_design::connection::Connection
• performs_orientation_ : protocols::denovo_design::connection::Connection
• period() : core::scoring::methods::BBDepCartBondedParameters , core::scoring::methods::BBIndepCartBondedParameters , core::scoring::methods::CartBondedParameters
• period_ : core::chemical::Element , core::scoring::methods::BBIndepCartBondedParameters
• periodic_range() : protocols::canonical_sampling::CanonicalSamplingMover
• PeriodicBoundFunc() : core::scoring::constraints::PeriodicBoundFunc
• PeriodicBoxMover() : protocols::simple_moves::PeriodicBoxMover
• PeriodicFunc() : core::scoring::func::PeriodicFunc
• periodicity() : core::scoring::dna::TorsionFourierComponent , protocols::toolbox::match_enzdes_util::GeomSampleInfo
• periodicity_ : core::scoring::constraints::OffsetPeriodicBoundFunc , core::scoring::constraints::PeriodicBoundFunc , core::scoring::dna::TorsionFourierComponent , protocols::match::downstream::AtomDihedralSecMatchRPE , protocols::toolbox::match_enzdes_util::GeomSampleInfo
• permanent_ : protocols::topology_broker::claims::JumpClaim
• permitted_overlap() : protocols::match::MatcherTask
• permitted_overlap_ : protocols::match::MatcherTask
• permutate_n_vv_of_pairs() : protocols::motif_grafting::movers::MotifGraftMover
• PerNativeRRReporterHuman() : protocols::rotamer_recovery::PerNativeRRReporterHuman
• PerResidueAAProbSet : protocols::toolbox::task_operations::ResidueProbDesignOperation
• perrsd_dens_ : protocols::hybridization::FragmentBiasAssigner
• perrsd_geometry_ : protocols::hybridization::FragmentBiasAssigner
• perrsd_nbrdens_ : protocols::hybridization::FragmentBiasAssigner
• perrsd_rama_ : protocols::hybridization::FragmentBiasAssigner
• PerSphereAccumulator() : core::scoring::packstat::PerSphereAccumulator
• pert_dock_rot_mag_ : protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• pert_dock_trans_mag_ : protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• pert_mc_temp_ : protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• pert_num_ : protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• pert_pep_num_rep_ : protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• pert_pep_shear_E_ : protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• pert_pep_shear_H_ : protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• pert_pep_shear_L_ : protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• pert_pep_shear_temp_ : protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• pert_pep_small_E_ : protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• pert_pep_small_H_ : protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• pert_pep_small_L_ : protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• pert_pep_small_temp_ : protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• pertinent_property_ : core::chemical::Metapatch
• perturb() : protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionSampler , protocols::kinematic_closure::perturbers::Perturber , protocols::mpi_refinement::Serial_Refine , protocols::protein_interface_design::movers::LoopMoverFromCommandLine , protocols::protein_interface_design::movers::LoopRemodel
• perturb_ : protocols::protein_interface_design::movers::LoopMoverFromCommandLine , protocols::protein_interface_design::movers::LoopRemodel , protocols::topology_broker::CoordConstraintClaimer , protocols::topology_broker::StartStructClaimer
• perturb_amplitude_ : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• perturb_anchor() : protocols::anchored_design::AnchoredDesignMover
• perturb_angles() : protocols::kinematic_closure::ClosureProblem
• perturb_beta_residue() : protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber
• perturb_c_n() : protocols::kinematic_closure::ClosureProblem
• perturb_c_n_ca() : protocols::kinematic_closure::ClosureProblem
• perturb_ca_c() : protocols::kinematic_closure::ClosureProblem
• perturb_ca_c_n() : protocols::kinematic_closure::ClosureProblem
• perturb_CCD_off_ : protocols::anchored_design::AnchoredPerturbMover
• perturb_chain() : protocols::loops::loop_closure::kinematic_closure::BaseTabooPerturber , protocols::loops::loop_closure::kinematic_closure::KinematicPerturber , protocols::loops::loop_closure::kinematic_closure::NeighborDependentTorsionSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::VicinitySamplingKinematicPerturber
• perturb_chi() : protocols::simple_moves::sidechain_moves::SidechainMCMover , protocols::simple_moves::sidechain_moves::SidechainMover
• perturb_cycles_ : protocols::anchored_design::AnchoredPerturbMover
• perturb_dBR_and_relax() : core::pack::interaction_graph::FASTERInteractionGraph
• perturb_KIC_off_ : protocols::anchored_design::AnchoredPerturbMover
• perturb_lengths() : protocols::kinematic_closure::ClosureProblem
• perturb_molecule_move() : protocols::simple_moves::PeriodicBoxMover
• perturb_n_ca() : protocols::kinematic_closure::ClosureProblem
• perturb_n_ca_c() : protocols::kinematic_closure::ClosureProblem
• perturb_omega() : protocols::kinematic_closure::ClosureProblem
• perturb_phi() : protocols::kinematic_closure::ClosureProblem
• perturb_psi() : protocols::kinematic_closure::ClosureProblem
• perturb_rot_within_well() : protocols::simple_moves::sidechain_moves::SidechainMover
• perturb_sBR_and_relax() : core::pack::interaction_graph::FASTERInteractionGraph
• perturb_show_ : protocols::anchored_design::AnchoredPerturbMover
• perturb_start_structures_ : protocols::abinitio::IterativeFullatom
• perturb_subset() : protocols::kinematic_closure::perturbers::BondAnglePerturber , protocols::kinematic_closure::perturbers::FragmentPerturber , protocols::kinematic_closure::perturbers::IdealizeNonPhiPsi , protocols::kinematic_closure::perturbers::LogFilePerturber , protocols::kinematic_closure::perturbers::OmegaPerturber , protocols::kinematic_closure::perturbers::Perturber , protocols::kinematic_closure::perturbers::PerturberSet , protocols::kinematic_closure::perturbers::Rama2bPerturber , protocols::kinematic_closure::perturbers::RamaPerturber , protocols::kinematic_closure::perturbers::UniformPerturber , protocols::kinematic_closure::perturbers::VicinityPerturber , protocols::kinematic_closure::perturbers::WalkingBondAnglePerturber , protocols::kinematic_closure::perturbers::WalkingPerturber
• perturb_subset_with_balance() : protocols::kinematic_closure::perturbers::IdealizeNonPhiPsi , protocols::kinematic_closure::perturbers::Perturber , protocols::kinematic_closure::perturbers::PerturberSet , protocols::kinematic_closure::perturbers::RamaPerturber , protocols::kinematic_closure::perturbers::UniformPerturber , protocols::kinematic_closure::perturbers::VicinityPerturber , protocols::kinematic_closure::perturbers::WalkingBondAnglePerturber , protocols::kinematic_closure::perturbers::WalkingPerturber
• perturb_temp_ : protocols::anchored_design::AnchoredPerturbMover
• perturb_torsion() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• perturb_torsion_ : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger
• perturb_torsions() : protocols::kinematic_closure::ClosureProblem
• perturb_trial() : protocols::cryst::DockLatticeMover
• perturb_values() : protocols::helical_bundle::PerturbBundle
• perturb_weights() : core::scoring::ScoreFunction
• perturb_with_balance() : protocols::kinematic_closure::perturbers::Perturber
• perturbable_ : protocols::helical_bundle::PerturbBundleOptions
• perturbation_magnitude() : protocols::helical_bundle::PerturbBundleOptions , protocols::simple_moves::SetTorsion
• perturbation_magnitude_ : protocols::helical_bundle::PerturbBundleOptions , protocols::simple_moves::SetTorsion
• perturbation_type() : protocols::helical_bundle::PerturbBundleOptions , protocols::simple_moves::SetTorsion
• perturbation_type_ : protocols::helical_bundle::PerturbBundleOptions , protocols::simple_moves::SetTorsion
• PerturbBundle() : protocols::helical_bundle::PerturbBundle
• PerturbBundleHelix() : protocols::helical_bundle::PerturbBundleHelix
• PerturbBundleOptions() : protocols::helical_bundle::PerturbBundleOptions
• PerturbByBins() : protocols::simple_moves::bin_transitions::PerturbByBins
• PerturbChiSidechainMover() : protocols::simple_moves::sidechain_moves::PerturbChiSidechainMover
• perturbed_ : core::pack::interaction_graph::FASTERNode
• perturbed_angles_ : protocols::kinematic_closure::ClosureProblem::Memento , protocols::kinematic_closure::ClosureProblem
• perturbed_lengths_ : protocols::kinematic_closure::ClosureProblem::Memento , protocols::kinematic_closure::ClosureProblem
• perturbed_res_ : protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionSampler
• perturbed_torsions_ : protocols::kinematic_closure::ClosureProblem::Memento , protocols::kinematic_closure::ClosureProblem
• perturbed_two_body_energies_ : core::pack::interaction_graph::FASTERNode
• perturber() : protocols::docking::DockingProtocol , protocols::loops::loop_closure::kinematic_closure::KinematicMover
• perturber_ : protocols::docking::DockingProtocol , protocols::loops::loop_closure::kinematic_closure::KinematicMover
• perturber_exhausted() : protocols::loops::loop_closure::kinematic_closure::KinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber
• perturber_type() : protocols::loops::loop_closure::kinematic_closure::KinematicPerturber , protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::NeighborDependentTorsionSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TabooSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::VicinitySamplingKinematicPerturber
• perturberlist_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• perturbers_ : protocols::kinematic_closure::BalancedKicMover , protocols::kinematic_closure::KicMover , protocols::kinematic_closure::perturbers::PerturberSet
• PerturberSet() : protocols::kinematic_closure::perturbers::PerturberSet
• PerturbRotamerSidechainMover() : protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover
• pfp_ : protocols::pockets::DarcParticleSwarmMinimizer , protocols::pockets::FingerprintMultifunc
• pfront_poses_ : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• pfront_poses_filter_ranks_ : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• pfront_poses_filter_vals_ : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• pg : protocols::pockets::PocketExemplarMultifunc
• pH_ : core::scoring::methods::pHEnergy
• phase() : core::scoring::dna::TorsionFourierComponent
• phase_ : core::scoring::dna::TorsionFourierComponent
• pHEnergy() : core::scoring::methods::pHEnergy
• phenix_home_ : core::scoring::cryst::PhenixInterface
• PhenixInterface() : core::scoring::cryst::PhenixInterface
• phi() : core::chemical::Adduct , core::chemical::AtomICoor , core::chemical::orbitals::ICoorOrbitalData , core::fragment::picking_old::vall::VallResidue , core::fragment::torsions , core::io::raw_data::DecoyStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::pose::Pose , core::scoring::motif::Xfres , protocols::fldsgn::topology::DimerPairing , protocols::frag_picker::PhiPsiTalosIO
• Phi() : protocols::frag_picker::scores::Phi
• phi() : protocols::frag_picker::VallResidue , protocols::frags::RMSVallData , protocols::frags::VallData , protocols::jumping::DisulfTemplate , protocols::jumping::PairingTemplate , protocols::kinematic_closure::ClosureProblem , protocols::loophash::BackboneSegment , protocols::match::upstream::ProteinBackboneBuildPoint , protocols::optimize_weights::PNatRotOptEPositionData , protocols::pockets::spherical_coor_triplet , protocols::pockets::triplet_and_originnum , protocols::simple_moves::MinimalRotamer , protocols::stepwise::modeler::protein::MainChainTorsionSet
• phi_ : core::chemical::AddConnect , core::chemical::Adduct , core::chemical::AtomICoor , core::chemical::orbitals::ICoorOrbitalData , core::chemical::SetICoor , core::fragment::picking_old::vall::VallResidue , core::io::raw_data::DecoyStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::kinematics::tree::BondedAtom , core::scoring::motif::Xfres , protocols::fldsgn::topology::DimerPairing , protocols::frag_picker::DiversifyDihedralsSelector , protocols::frag_picker::VallResidue , protocols::frags::RMSVallData , protocols::frags::VallData , protocols::loophash::BackboneSegment , protocols::match::upstream::ProteinBackboneBuildPoint , protocols::membrane::benchmark::MakeCanonicalHelix , protocols::optimize_weights::PNatRotOptEPositionData , protocols::pose_length_moves::InsertResMover , protocols::stepwise::modeler::protein::MainChainTorsionSet
• phi_angle_ : protocols::rigid::RigidBodyRandomizeMover , protocols::simple_moves::a3b_hbs::A3BHbsMover , protocols::simple_moves::oop::OopMover , protocols::simple_moves::triazolamer::TriazolamerMover
• phi_bin_width_ : protocols::qsar::scoring_grid::ShapeGrid
• PHI_BINRANGE : core::pack::rotamers::RotamericSingleResiduePeptoidLibrary< T, N >
• phi_index() : core::scoring::OmegaTether
• phi_max() : core::sequence::ABEGO
• phi_max_ : core::sequence::ABEGO
• phi_min() : core::sequence::ABEGO
• phi_min_ : core::sequence::ABEGO
• phi_offsets_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger
• phi_psi_bins_above_thold_ : core::scoring::Ramachandran
• phi_sampler_mover_ : protocols::carbohydrates::LinkageConformerMover
• PHIPSI_BINRANGE : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary , core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >
• phipsi_in_allowed_rama() : core::scoring::Ramachandran
• phipsi_in_forbidden_rama() : core::scoring::Ramachandran
• PhiPsiRmsd() : protocols::frag_picker::scores::PhiPsiRmsd
• PhiPsiSquareWell() : protocols::frag_picker::scores::PhiPsiSquareWell
• PhiPsiTalosIO() : protocols::frag_picker::PhiPsiTalosIO
• phis : protocols::antibody::clusters::ClusterData
• PhiSelector() : core::select::residue_selector::PhiSelector
• phithetascore_ : protocols::fldsgn::potentials::sspot::HSPairPotential , protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential
• phosphate_move_ : protocols::stepwise::modeler::rna::phosphate::PhosphateMover
• phosphate_move_list() : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• phosphate_move_list_ : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• phosphate_sample_pose_ : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• phosphate_sampler_ : protocols::stepwise::modeler::packer::StepWiseMasterPacker , protocols::stepwise::screener::PhosphateScreener
• phosphate_sampler_for_restoration_ : protocols::stepwise::screener::PhosphateScreener
• phosphate_scorefxn_ : protocols::stepwise::modeler::packer::StepWiseMasterPacker
• phosphate_takeoff_donor_distance_cutoff2_ : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• PhosphateMove() : protocols::stepwise::modeler::rna::phosphate::PhosphateMove
• PhosphateMover() : protocols::stepwise::modeler::rna::phosphate::PhosphateMover
• PhosphateScreener() : protocols::stepwise::screener::PhosphateScreener
• physical() : protocols::environment::claims::JumpClaim
• physical_cut_ : protocols::environment::claims::JumpClaim
• physical_pose_clash_dist_cutoff_ : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• pi_charge_to_en_inflection_ : core::chemical::gasteiger::GasteigerAtomTypeData
• pi_contribution_ : core::chemical::gasteiger::GasteigerAtomTypeData
• pi_orbitals_binding_ : core::chemical::gasteiger::GasteigerAtomTypeData
• pi_pi_total_ : protocols::toolbox::pose_metric_calculators::PiPiCalculator
• pick() : protocols::kinematic_closure::pivot_pickers::EndToEndPivots , protocols::kinematic_closure::pivot_pickers::FixedOffsetPivots , protocols::kinematic_closure::pivot_pickers::FixedPivots , protocols::kinematic_closure::pivot_pickers::LoopPivots , protocols::kinematic_closure::pivot_pickers::PivotPicker , protocols::kinematic_closure::pivot_pickers::StandardPivots
• pick_a_rotamer() : core::pack::annealer::RotamerAssigningAnnealer , protocols::flexpack::annealer::FlexbbSimAnnealer
• pick_a_rotamer_for_node() : core::pack::annealer::RotamerAssigningAnnealer
• pick_a_rotamer_for_sBR() : core::pack::annealer::FASTERAnnealer
• pick_all_fragments() : protocols::forge::components::VarLengthBuild
• pick_and_apply() : protocols::kinematic_closure::solution_pickers::FilteredSolutions , protocols::kinematic_closure::solution_pickers::RandomSolutions , protocols::kinematic_closure::solution_pickers::SolutionPicker
• pick_and_cache_fragments() : protocols::denovo_design::components::Picker
• pick_baserotamer_from_rotblock() : core::pack::rotamer_set::ContinuousRotamerSet
• pick_boundary_ : core::select::util::SelectResiduesByLayer
• pick_candidates() : protocols::frag_picker::FragmentPicker
• pick_chunk_candidates() : protocols::frag_picker::FragmentPicker
• pick_core_ : core::select::util::SelectResiduesByLayer
• pick_enrich_methods() : protocols::mpi_refinement::Scheduler
• pick_fragment_library() : protocols::farna::fragments::FullAtomRNA_Fragments
• pick_fragments() : protocols::forge::components::VarLengthBuild
• pick_frags() : protocols::abinitio::Templates
• pick_large_frags() : protocols::abinitio::Template , protocols::abinitio::Templates
• pick_loop_frags() : protocols::protein_interface_design::movers::LoopRemodel
• pick_new_cutpoint() : protocols::anchored_design::AnchorMoversData
• pick_new_cutpoints() : protocols::anchored_design::AnchorMoversData
• pick_objfunction() : protocols::mpi_refinement::Scheduler
• pick_objfunction_ : protocols::mpi_refinement::Scheduler
• pick_pivots() : protocols::generalized_kinematic_closure::GeneralizedKIC
• pick_random_chunk() : protocols::hybridization::ChunkTrialMover
• pick_random_fragment() : protocols::coarse_rna::CoarseRNA_Fragments , protocols::farna::fragments::FullAtomRNA_Fragments
• pick_random_template() : protocols::hybridization::ChunkTrialMover
• pick_rotamer_for_node() : core::pack::annealer::FASTERAnnealer
• pick_sequence_from_database() : protocols::toolbox::task_operations::DatabaseThread
• pick_solution() : protocols::kinematic_closure::BalancedKicMover
• pick_starting_template() : protocols::hybridization::HybridizeProtocol
• pick_strategy() : protocols::mpi_refinement::Scheduler
• pick_strategy_ : protocols::mpi_refinement::Scheduler
• pick_surface_ : core::select::util::SelectResiduesByLayer
• Picker() : protocols::denovo_design::components::Picker
• picking_rounds() : protocols::toolbox::task_operations::ResidueProbDesignOperation
• picking_rounds_ : protocols::antibody::task_operations::AddCDRProfileSetsOperation , protocols::antibody::task_operations::AddCDRProfilesOperation , protocols::toolbox::task_operations::MutationSetDesignOperation , protocols::toolbox::task_operations::ResidueProbDesignOperation
• PiContributionType : core::chemical::gasteiger::GasteigerAtomTypeData
• piece() : protocols::grafting::GraftMoverBase
• piece_ : protocols::grafting::GraftMoverBase
• PiOrbitalElectronegativityMulliken : core::chemical::gasteiger::GasteigerAtomTypeData
• PiOrbitalElectronegativityPauling : core::chemical::gasteiger::GasteigerAtomTypeData
• PiPiCalculator() : protocols::toolbox::pose_metric_calculators::PiPiCalculator
• PiValenceStateElectronAffinity : core::chemical::gasteiger::GasteigerAtomTypeData
• PiValenceStateIonizationPotential : core::chemical::gasteiger::GasteigerAtomTypeData
• pivot_1_atmname_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• pivot_1_rsd_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• pivot_2_atmname_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• pivot_2_rsd_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• pivot_3_atmname_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• pivot_3_rsd_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• pivot_atoms() : protocols::backrub::BackrubMover , protocols::kinematic_closure::ClosureProblem
• pivot_atoms_ : protocols::backrub::BackrubMover , protocols::backrub::BackrubProtocol
• pivot_loop() : protocols::kinematic_closure::ClosureProblem
• pivot_picker_ : protocols::kinematic_closure::BalancedKicMover , protocols::kinematic_closure::KicMover
• pivot_range_randomly() : protocols::simple_moves::BBGaussianMover
• pivot_res_ : protocols::coarse_rna::CoarseRNA_LoopCloser
• pivot_residues() : protocols::backrub::BackrubMover , protocols::backrub::BackrubSidechainMover , protocols::kinematic_closure::ClosureProblem
• pivot_residues_ : protocols::backrub::BackrubMover , protocols::backrub::BackrubProtocol
• pivot_to_scratch_res_ : protocols::coarse_rna::CoarseRNA_LoopCloser
• pivots_ : protocols::kinematic_closure::ClosureProblem
• place() : core::conformation::Residue
• place_atom() : protocols::motifs::Motif
• place_atom_() : protocols::motifs::Motif
• place_atoms() : protocols::motifs::Motif
• place_atoms_() : protocols::motifs::Motif
• place_c() : protocols::kinmatch::BruteFunGroupTK , protocols::kinmatch::FunGroupTK , protocols::kinmatch::KinFunGroupTK
• place_d() : protocols::kinmatch::BruteFunGroupTK , protocols::kinmatch::FunGroupTK , protocols::kinmatch::KinFunGroupTK
• place_h() : protocols::kinmatch::BruteFunGroupTK , protocols::kinmatch::FunGroupTK , protocols::kinmatch::KinFunGroupTK
• place_near_origin() : protocols::cryst::MakeLatticeMover , protocols::cryst::MakeLayerMover
• place_origin_point() : protocols::pockets::NonPlaidFingerprint
• place_peptide : protocols::flexpep_docking::FlexPepDockingFlags
• place_peptide_on_binding_site() : protocols::flexpep_docking::FlexPepDockingProtocol
• place_residue() : protocols::motifs::Motif
• place_residue_() : protocols::motifs::Motif
• place_residue_helper() : protocols::motifs::Motif
• place_scaffold_ : protocols::protein_interface_design::movers::PlaceStubMover
• place_sidechain_in_pose() : core::scoring::motif::Xfres
• place_stub() : protocols::protein_interface_design::movers::PlaceStubMover
• place_stubs() : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• placed_stubs_ : protocols::protein_interface_design::movers::PlaceStubMover
• placeholder_clone() : core::chemical::ResidueType
• placeholder_info() : core::scoring::FACTSPoseInfo , core::scoring::GenBornPoseInfo , core::scoring::MultipoleElecPoseInfo , core::scoring::VdWTinkerPoseInfo
• placeholder_info_ : core::scoring::FACTSPoseInfo , core::scoring::GenBornPoseInfo , core::scoring::MultipoleElecPoseInfo , core::scoring::VdWTinkerPoseInfo
• placeholder_residue() : core::scoring::FACTSPoseInfo , core::scoring::GenBornPoseInfo , core::scoring::MultipoleElecPoseInfo , core::scoring::VdWTinkerPoseInfo
• placeholder_residue_ : core::scoring::FACTSPoseInfo , core::scoring::GenBornPoseInfo , core::scoring::MultipoleElecPoseInfo , core::scoring::VdWTinkerPoseInfo
• PlacementAuctionMover() : protocols::protein_interface_design::movers::PlacementAuctionMover
• PlacementMinimizationMover() : protocols::protein_interface_design::movers::PlacementMinimizationMover
• PlaceOnLoop() : protocols::protein_interface_design::movers::PlaceOnLoop
• PlaceProbeMover() : protocols::hotspot_hashing::movers::PlaceProbeMover
• placeResidueAtTransform() : protocols::hotspot_hashing::StubGenerator
• placeResidueOnPose() : protocols::hotspot_hashing::StubGenerator
• PlaceSimultaneouslyMover() : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• PlaceStubMover() : protocols::protein_interface_design::movers::PlaceStubMover
• PlaceSurfaceProbe() : protocols::hotspot_hashing::movers::PlaceSurfaceProbe
• PlaidFingerprint() : protocols::pockets::PlaidFingerprint
• plain_text : protocols::sparta::GDB
• PlainPdbJobDistributor() : protocols::jobdist::PlainPdbJobDistributor
• PlainRawJobDistributor() : protocols::jobdist::PlainRawJobDistributor
• PlainSilentFileJobDistributor() : protocols::jobdist::PlainSilentFileJobDistributor
• plane_tolerance_ : protocols::simple_moves::symmetry::DetectSymmetry
• pleat_weird : core::scoring::dssp::StrandPairing
• Pleating() : core::scoring::dssp::Pairing
• pleating1 : core::scoring::dssp::StrandPairing
• pleating_ : core::scoring::dssp::Pairing
• pleats1() : protocols::fldsgn::topology::StrandPairing
• pleats1_ : protocols::fldsgn::topology::StrandPairing
• pleats2() : protocols::fldsgn::topology::StrandPairing
• pleats2_ : protocols::fldsgn::topology::StrandPairing
• pmatch() : protocols::noesy_assign::FloatingResonance , protocols::noesy_assign::Resonance
• PNatAAOptEPositionData() : protocols::optimize_weights::PNatAAOptEPositionData
• PNatAAOptERotamerData() : protocols::optimize_weights::PNatAAOptERotamerData
• PNatLigPoseOptEData() : protocols::optimize_weights::PNatLigPoseOptEData
• PNatRotOptEPositionData() : protocols::optimize_weights::PNatRotOptEPositionData
• PNatRotOptERotamerData() : protocols::optimize_weights::PNatRotOptERotamerData
• PNatStructureOptEData() : protocols::optimize_weights::PNatStructureOptEData
• PO_BURIED : protocols::pockets::ComparisonGrid , protocols::pockets::PocketGrid
• PO_EDGE : protocols::pockets::ComparisonGrid , protocols::pockets::PocketGrid
• PO_SURF : protocols::pockets::ComparisonGrid , protocols::pockets::PocketGrid
• POCKET : protocols::pockets::ComparisonGrid , protocols::pockets::PocketGrid
• pocket_CoM_ : protocols::pockets::NonPlaidFingerprint
• PocketConstraint() : protocols::pockets::PocketConstraint
• PocketConstraintCreator() : protocols::pockets::PocketConstraintCreator
• PocketExemplarMultifunc() : protocols::pockets::PocketExemplarMultifunc
• PocketGrid : protocols::pockets::CCluster , protocols::pockets::CClusterSet , protocols::pockets::ElectrostaticpotentialGrid , protocols::pockets::PCluster , protocols::pockets::PClusterSet , protocols::pockets::PocketGrid
• pocketgrid_ : protocols::pockets::PocketConstraint
• pocketGrid_dim_ : protocols::pockets::FingerprintBase
• pocketGrid_mid_ : protocols::pockets::FingerprintBase
• pocketGrid_spacing_ : protocols::pockets::FingerprintBase
• pockets_ : protocols::pockets::PocketGrid
• Point() : core::scoring::packstat::Point
• point : core::scoring::sc::_PROBE
• point_ : protocols::match::VoxelSetIterator
• point_for_nonchitip_atom() : protocols::match::upstream::UpstreamResTypeGeometry
• point_graph : core::conformation::AddEdgeVisitor< Vertex, Edge > , core::scoring::Energies
• point_graph_ : core::scoring::Energies
• point_on_ellipsoid() : protocols::docking::EllipsoidalRandomizationMover
• point_orbitals_to_closest_ligands() : protocols::magnesium::MgOrbitalFrameFinder
• pointer : core::io::silent::SilentFileData::const_iterator , core::io::silent::SilentFileData::iterator , protocols::toolbox::OP_const_iterator< const_iterator, SomeOP >
• PointGraphEdgeData() : core::conformation::PointGraphEdgeData
• PointGraphVertexData() : core::conformation::PointGraphVertexData
• PointMutationCalculator() : protocols::design_opt::PointMutationCalculator
• PointMutScanDriver : protocols::pmut_scan::Mutant , protocols::pmut_scan::MutationData , protocols::pmut_scan::PointMutScanDriver
• PointPair() : core::scoring::packstat::PointPair
• points_ : core::scoring::func::FourPointsFunc , protocols::pockets::CCluster , protocols::pockets::PCluster , protocols::scoring::ImplicitFastClashCheck , protocols::sic_dock::CBScore
• points_defined_ : protocols::electron_density::DockIntoDensityMover
• points_for_nonchitip_atoms() : protocols::match::upstream::UpstreamResTypeGeometry
• points_for_nonchitip_atoms_ : protocols::match::upstream::UpstreamResTypeGeometry
• points_in_D3_frame_ : protocols::toolbox::match_enzdes_util::LigandConformer
• points_in_global_orintation_frame_ : protocols::toolbox::match_enzdes_util::LigandConformer
• points_to_search_ : protocols::electron_density::DockIntoDensityMover
• poisson_boltzmann_potential_ : core::scoring::methods::PoissonBoltzmannEnergy
• PoissonBoltzmannEnergy() : core::scoring::methods::PoissonBoltzmannEnergy
• PoissonBoltzmannPotential() : core::scoring::PoissonBoltzmannPotential
• polar_ : core::pack::task::operation::ResidueTypeFilter , protocols::simple_filters::InterfaceSasaFilter , protocols::simple_filters::TotalSasaFilter
• polar_charge_cutoff_ : core::scoring::sasa::SasaCalc
• polar_energy_pack_corrector() : core::scoring::FACTSPotential
• polar_expansion_radius_ : core::pack::interaction_graph::RotamerDotsRadiusData
• polar_gap_ : protocols::toolbox::task_operations::CrystalContactsOperation
• polar_hydrogens() : core::chemical::ResidueType
• polar_max : protocols::hotspot_hashing::SphericalRotationSearchPattern
• polar_min : protocols::hotspot_hashing::SphericalRotationSearchPattern
• polar_rotation_sampling : protocols::hotspot_hashing::SphericalRotationSearchPattern
• PolarHydrogenFilter() : core::chemical::PolarHydrogenFilter
• PolarHydrogenPacker() : protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker
• polarity() : core::scoring::MultipoleParameter
• polarity_ : core::scoring::MultipoleParameter
• polars : protocols::sic_dock::BuriedPolarScore
• Policy() : protocols::nonlocal::Policy
• policy_ : protocols::nonlocal::BiasedFragmentMover , protocols::nonlocal::SingleFragmentMover
• poly_A_seq_ : protocols::frag_picker::VallProvider
• polyAla() : protocols::flexpep_docking::FlexPepDockingProtocol
• polymer_bond_exists() : protocols::denovo_design::components::StructureData
• polymer_connection() : protocols::denovo_design::connection::BridgeChains , protocols::denovo_design::connection::BridgeTomponents , protocols::denovo_design::connection::Connection , protocols::denovo_design::connection::ConnectTerminiWithDisulfide , protocols::denovo_design::connection::ExtendChain , protocols::denovo_design::connection::GenericConnection , protocols::denovo_design::connection::StapleChains
• polymer_direction() : core::kinematics::Edge
• POLYMER_LOWER : core::chemical::ICoorAtomID
• polymer_type_ : protocols::make_rot_lib::MakeRotLibOptionsData
• POLYMER_UPPER : core::chemical::ICoorAtomID
• PolymerBondedEnergyContainer() : core::scoring::PolymerBondedEnergyContainer
• PolymerBondedNeighborConstIterator() : core::scoring::PolymerBondedNeighborConstIterator
• PolymerBondedNeighborIterator() : core::scoring::PolymerBondedNeighborIterator
• polymeric_oriented_sequence_distance() : core::conformation::Residue
• polymeric_sequence_distance() : core::conformation::Residue
• Polynomial_1d() : core::scoring::hbonds::Polynomial_1d
• polys_ : protocols::sasa_scores::PPoly
• pool_ : protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD , protocols::canonical_sampling::mc_convergence_checks::PoolData
• pool_cache_ : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• Pool_ConvergenceCheck() : protocols::canonical_sampling::mc_convergence_checks::Pool_ConvergenceCheck
• pool_defs_ : protocols::frag_picker::quota::ABEGO_SS_Config
• Pool_Evaluator() : protocols::canonical_sampling::mc_convergence_checks::Pool_Evaluator
• pool_exists() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• pool_master_node_ : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD
• pool_name_ : protocols::frag_picker::FragmentCandidate , protocols::frag_picker::quota::QuotaPool
• pool_names_ : protocols::frag_picker::quota::QuotaConfig
• pool_npes_ : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• pool_rank_ : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• pool_rms_ : protocols::canonical_sampling::CanonicalSamplingMover
• Pool_RMSD() : protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD
• pool_size() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• pool_size_ : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD
• pool_weights_ : protocols::frag_picker::quota::QuotaConfig
• PoolData() : protocols::canonical_sampling::mc_convergence_checks::PoolData
• PoolEvaluatorCreator() : protocols::simple_filters::PoolEvaluatorCreator
• pop() : core::graph::NegSpaceElement< T > , protocols::electron_density::ResultDB< T, Tcomp > , protocols::forge::remodel::RemodelAccumulator , protocols::pack_daemon::TopEntitySet
• pop_back() : protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD , protocols::evaluation::MetaPoseEvaluator
• pop_back_CA_xyz() : protocols::toolbox::DecoySetEvaluation
• pop_const_const_iter : protocols::genetic_algorithm::GeneticAlgorithmBase
• pop_const_iter : protocols::genetic_algorithm::GeneticAlgorithmBase
• pop_from_ss_ : protocols::dna::DnaInterfaceMultiStateDesign , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• pop_iter : protocols::genetic_algorithm::GeneticAlgorithmBase
• pop_mutation() : protocols::pmut_scan::Mutant
• pop_next() : protocols::wum::WorkUnitQueue
• pop_passport() : core::conformation::Conformation , protocols::environment::ClientMover , protocols::environment::ProtectedConformation
• pop_size_ : protocols::dna::DnaInterfaceMultiStateDesign , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• popular_bin() : protocols::noesy_assign::FragsToAtomDist::DistanceRecord
• populate_all_cdrs() : protocols::antibody_legacy::Antibody
• populate_batch_list_from_cmd() : protocols::jd2::JobDistributor
• populate_matrix() : core::scoring::bin_transitions::BinTransitionCalculator
• populate_next_n_jobs() : protocols::jd2::LargeNstructJobInputter
• population : core::chemical::carbohydrates::LinkageConformerData , protocols::genetic_algorithm::GeneticAlgorithmBase
• population_weight_ : protocols::cluster::ClusterBase
• pore_radius() : core::select::util::SelectResiduesByLayer , protocols::flxbb::LayerDesignOperation
• pore_radius_ : core::select::util::SelectResiduesByLayer
• pos() : core::fragment::NonContinuousFrame , protocols::environment::EnvClaimBroker::BrokeredJumpData , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight
• Pos1() : core::scoring::dssp::Pairing
• pos1() : protocols::environment::claims::JumpClaim , protocols::jumping::DisulfPairing
• pos1_ : core::scoring::DenseNeighborConstIterator , core::scoring::DenseNeighborIterator , core::scoring::dssp::Pairing , core::scoring::OneToAllNeighborConstIterator , core::scoring::OneToAllNeighborIterator , protocols::environment::claims::JumpClaim
• Pos2() : core::scoring::dssp::Pairing
• pos2() : protocols::environment::claims::JumpClaim , protocols::jumping::DisulfPairing
• pos2_ : core::scoring::DenseNeighborConstIterator , core::scoring::DenseNeighborIterator , core::scoring::dssp::Pairing , core::scoring::OneToAllNeighborConstIterator , core::scoring::OneToAllNeighborIterator , protocols::environment::claims::JumpClaim
• pos2select() : protocols::flxbb::LayerDesignOperation
• pos_ : core::fragment::NonContinuousFrame , core::pack::task::operation::ResiduePDBIndexIs::ChainPos , core::scoring::PolymerBondedNeighborConstIterator , core::scoring::PolymerBondedNeighborIterator , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::kinmatch::FunGroupTK
• pos_in_bg_edge_vector_ : core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >
• pos_in_bg_nodes_edge_list_ : core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >
• pos_in_fc_edge_vector_ : core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >
• pos_in_fc_nodes_edge_list_ : core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >
• pos_in_nodes_edge_list_ : core::graph::Edge , core::pack::interaction_graph::EdgeBase
• pos_in_nodes_edge_vector_ : core::pack::interaction_graph::EdgeBase
• pos_in_owners_edge_list_ : core::graph::Edge , core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G > , core::pack::interaction_graph::EdgeBase
• pos_list_ : protocols::idealize::IdealizeMover , protocols::simple_moves::BackboneMover
• pos_map_ : core::sequence::AnnotatedSequence
• Pose : core::fragment::IndependentBBTorsionSRFD , core::fragment::picking_old::vall::eval::EnergyEval
• pose() : core::fragment::picking_old::vall::eval::EnergyEval , core::optimization::AtomTreeMultifunc , core::optimization::CartesianMultifunc , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• Pose : core::pack::interaction_graph::OnTheFlyInteractionGraph
• pose() : core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::SimpleInteractionGraph , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• Pose : core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• pose() : core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• Pose : 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::ResFilter , core::pack::task::operation::TaskOperation
• pose() : core::pose::datacache::CacheablePoseRawPtr
• Pose() : core::pose::Pose , core::pose::signals::DestructionEvent
• pose : core::pose::signals::DestructionEvent
• Pose : core::pose::signals::GeneralEvent
• pose : core::pose::signals::GeneralEvent
• Pose : core::scoring::constraints::ConstraintSet , core::scoring::constraints::SequenceProfileConstraint , core::scoring::MinimizationEdge , core::scoring::MinimizationNode , core::scoring::OmegaTether , core::scoring::Ramachandran2B , core::scoring::Ramachandran , core::scoring::RamaPrePro , core::select::util::SelectResiduesByLayer , core::sequence::ABEGOManager
• pose : protocols::antibody::CDRDBPose
• Pose : protocols::boinc::BoincCurrentPoseObserver
• pose : protocols::canonical_sampling::DbTrajectoryRecorder::Frame , protocols::cartesian::MolecularDynamics
• Pose : protocols::constraints_additional::SequenceCoupling1BDConstraint , protocols::constraints_additional::SequenceCouplingConstraint
• pose() : protocols::denovo_design::components::StructureData
• Pose : protocols::denovo_design::constraints::FileConstraintGenerator , protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::dna::PDBOutput , protocols::dna::RestrictDesignToProteinDNAInterface , protocols::dna::WatsonCrickRotamerCouplings
• pose : protocols::environment::EnvClaimBroker::BrokerResult
• Pose : protocols::enzdes::AddLigandMotifRotamers , protocols::enzdes::AddRigidBodyLigandConfs , protocols::enzdes::BackboneSampler , protocols::enzdes::DetectProteinLigandInterface , protocols::enzdes::ProteinLigandInterfaceUpweighter , protocols::enzdes::RemoveLigandFilter , protocols::enzdes::SetCatalyticResPackBehavior , protocols::filters::FilterFactory , protocols::fldsgn::BluePrintBDR , protocols::fldsgn::CircularPermutation , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::filters::FragQualFilter , 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::MatchResidues , protocols::fldsgn::MatchResiduesMover , protocols::fldsgn::NcontactsCalculator , protocols::fldsgn::potentials::AACompositionEnergy , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::fldsgn::potentials::sspot::HSPairPotential , protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy , protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential , protocols::fldsgn::SheetConstraintGenerator , protocols::fldsgn::topology::BB_Pos , protocols::fldsgn::topology::Sheet , protocols::fldsgn::topology::SS_Info2 , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::flexpack::rotamer_set::FlexbbRotamerSets , protocols::flxbb::DesignTask , protocols::flxbb::DesignTask_Layer , protocols::flxbb::DesignTask_Normal , protocols::flxbb::FilterStructs , protocols::flxbb::FilterStructs_Packstat , protocols::flxbb::FilterStructs_TotalCharge , protocols::flxbb::FlxbbDesign , protocols::flxbb::InterlockAroma , protocols::flxbb::LayerDesignOperation , 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::RelativeConnectRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap , protocols::forge::components::BDR , protocols::forge::components::VarLengthBuild , protocols::forge::constraints::NtoCConstraintGenerator , protocols::forge::constraints::RemoveConstraints , protocols::forge::remodel::RemodelAccumulator , protocols::forge::remodel::RemodelDesignMover , protocols::forge::remodel::RemodelGlobalFrame , protocols::forge::remodel::RemodelLigandHandler , protocols::forge::remodel::RemodelLoopMover , protocols::forge::remodel::RemodelMover , protocols::forge::remodel::RemodelRotamerLinks , protocols::idealize::IdealizeMover , protocols::indexed_structure_store::filters::FragmentLookupFilter , protocols::jd2::parser::BluePrint , protocols::jd2::parser::FragmentReader , protocols::jd2::Parser
• pose() : protocols::jd3::MoverAndPoseJob , protocols::jd3::PoseJobResult
• Pose : protocols::loophash::FastGapMover , protocols::match::output::PoseInserter , protocols::matdes::ClashCheckFilter , protocols::matdes::GetRBDOFValues , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator , protocols::matdes::OligomericAverageDegreeFilter , protocols::matdes::SymDofMover , protocols::matdes::SymUnsatHbondFilter , protocols::metal_interface::MatchGrafter , protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch , protocols::moves::FilterMover , protocols::moves::MonteCarlo , protocols::moves::Mover , protocols::moves::MoverFactory
• pose() : protocols::multistate_design::SingleState
• Pose : protocols::nonlocal::SingleFragmentMover
• pose() : protocols::normalmode::NormalModeMultifunc
• Pose : protocols::pack_daemon::DaemonSet , protocols::pack_daemon::MultistateFitnessFunction
• pose() : protocols::pack_daemon::PackDaemon
• Pose : protocols::pack_daemon::PackDaemon
• pose() : protocols::pack_daemon::QuickRepacker , protocols::pockets::PlaidFingerprint
• Pose : protocols::protein_interface_design::DockDesignFilterFactory , protocols::protein_interface_design::FavorNativeResidue , protocols::protein_interface_design::FavorNonNativeResidue , protocols::protein_interface_design::movers::BackrubDDMover , protocols::protein_interface_design::movers::BuildAlaPose , protocols::protein_interface_design::movers::DesignMinimizeHbonds , protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover , protocols::protein_interface_design::movers::LoopLengthChange , protocols::protein_interface_design::movers::MapHotspot , protocols::protein_interface_design::movers::PatchdockTransform , protocols::protein_interface_design::movers::RandomMutation , protocols::protein_interface_design::movers::RepackMinimize , protocols::protein_interface_design::movers::SaveAndRetrieveSidechains , protocols::protein_interface_design::movers::SetTemperatureFactor , protocols::protein_interface_design::movers::SpinMover , protocols::protein_interface_design::movers::TaskAwareCsts , protocols::protein_interface_design::movers::TopologyBrokerMover , protocols::protein_interface_design::movers::TryRotamers , protocols::protein_interface_design::ReportPSSMDifferences , protocols::protein_interface_design::ReportSequenceDifferences , protocols::rosetta_scripts::ParsedProtocol , protocols::rosetta_scripts::PosePropertyReporterFactory , protocols::rosetta_scripts::PoseSelectorFactory , protocols::seeded_abinitio::CAcstGenerator , protocols::seeded_abinitio::CoordinateCst , protocols::seeded_abinitio::SegmentHybridizer , protocols::seeded_abinitio::SwapSegment , protocols::sic_dock::RigidScore , protocols::sic_dock::Rose
• pose() : protocols::sic_dock::Rose
• Pose : protocols::simple_filters::HolesFilter , protocols::simple_filters::InterRepeatContactFilter , protocols::simple_filters::IntraRepeatContactFilter , protocols::simple_filters::LeastNativeLike9merFilter , protocols::simple_filters::PackStatFilter , protocols::simple_filters::RangeFilter
• pose() : protocols::simple_filters::RelativePoseFilter
• Pose : protocols::simple_filters::SaveResfileToDiskFilter , protocols::simple_filters::ShapeComplementarityFilter , protocols::simple_filters::SSElementMotifContactFilter , protocols::simple_filters::TaskAwareSASAFilter
• pose() : protocols::simple_moves::AlignChainMover
• Pose : protocols::simple_moves::BBGaussianMover , protocols::simple_moves::ConsensusDesignMover , protocols::simple_moves::ddG , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::GreenPacker , protocols::simple_moves::GroupDiscriminator , protocols::simple_moves::MonteCarloRecover , protocols::simple_moves::MonteCarloReset , protocols::simple_moves::MonteCarloTest , protocols::simple_moves::rational_mc::RationalMonteCarlo , protocols::simple_moves::symmetry::DetectSymmetry , protocols::simple_moves::UserDefinedGroupDiscriminator
• pose() : protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker , protocols::stepwise::modeler::rna::o2prime::O2PrimePacker , protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler , protocols::stepwise::sampler::copy_dofs::ResidueAlternativeSet , protocols::stepwise::screener::SampleApplier
• Pose : protocols::toolbox::pose_metric_calculators::FragQualCalculator , protocols::toolbox::task_operations::ImportUnboundRotamersOperation , protocols::toolbox::task_operations::JointSequenceOperation , protocols::toolbox::task_operations::LimitAromaChi2_RotamerSetOperation , protocols::toolbox::task_operations::LimitAromaChi2Operation , protocols::toolbox::task_operations::RestrictNativeResiduesOperation , protocols::toolbox::task_operations::SeqprofConsensusOperation
• pose : protocols::trajectory::DbTrajectoryWriter::Frame
• Pose : protocols::viewer::SilentObserver
• pose0_ : protocols::md::MDBase , protocols::mpi_refinement::MPI_Refinement , protocols::ncbb::SecStructMinimizeMultiFunc , protocols::normalmode::NormalModeMultifunc
• pose1() : core::scoring::motif::MotifHit , core::scoring::motif::ResPairMotifQuery
• pose1_ : core::scoring::motif::MotifHit , core::scoring::motif::ResPairMotifQuery , protocols::hybridization::DomainAssembly , protocols::sic_dock::LinkerScore , protocols::sic_dock::scores::MotifHashRigidScore
• pose1ptr() : core::scoring::motif::MotifHit
• pose2() : core::scoring::motif::MotifHit , core::scoring::motif::ResPairMotifQuery
• pose2_ : core::scoring::motif::MotifHit , core::scoring::motif::ResPairMotifQuery , protocols::hybridization::DomainAssembly , protocols::sic_dock::LinkerScore , protocols::sic_dock::scores::MotifHashRigidScore
• pose2pdb() : core::pose::PDBInfo
• pose2ptr() : core::scoring::motif::MotifHit
• pose_ : core::fragment::picking_old::vall::eval::EnergyEval , core::optimization::AtomTreeMultifunc , core::optimization::CartesianMultifunc , core::optimization::symmetry::SymAtomTreeMultifunc , core::optimization::symmetry::SymMinimizerMap , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::SimpleInteractionGraph , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph , core::pack::scmin::CartSCMinMultifunc , core::pack::scmin::SCMinMultifunc , core::pose::datacache::CacheablePoseRawPtr , core::pose::datacache::ObserverCache , core::scoring::packstat::MultiProbePoseAccumulator , protocols::abinitio::Template , protocols::denovo_design::components::StructureData , protocols::electron_density::BfactorMultifunc , protocols::electron_density::RefinementResult , protocols::flexpack::interaction_graph::OTFFlexbbEdge , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::helical_bundle::FitSimpleHelixMultiFunc , protocols::hotspot_hashing::HotspotStub , protocols::hotspot_hashing::HotspotStubSet , protocols::jd2::InnerJob , protocols::jd3::MoverAndPoseJob , protocols::jd3::PoseJobResult , protocols::kinmatch::FunGroupTK , protocols::ligand_docking::rdf::RDFBinaryOrbitalFunction , protocols::ligand_docking::rdf::RDFOrbitalFunction , protocols::LoopRebuild , protocols::match::output::PoseInserter , protocols::ncbb::SecStructMinimizeMultiFunc , protocols::normalmode::NormalModeMultifunc , protocols::pack_daemon::BasicSimAnnealerRepacker , protocols::pack_daemon::EntityCorrespondence , protocols::pack_daemon::PackDaemon , protocols::pack_daemon::QuickRepacker , protocols::pockets::PlaidFingerprint , protocols::residue_optimization::MetapatchEnumeration , protocols::scoring::ImplicitFastClashCheck , protocols::sic_dock::scores::TrisBpyScore , protocols::simple_filters::RelativePoseFilter , protocols::simple_moves::AlignChainMover , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::stepwise::legacy::screener::SimplePoseSelection , protocols::stepwise::legacy::screener::SimpleRMSD_Screener , protocols::stepwise::screener::PartitionContactScreener , protocols::stepwise::screener::PoseSelectionScreener , protocols::stepwise::screener::SampleApplier , protocols::stepwise::screener::Scorer , protocols::stepwise::screener::TagDefinition
• pose_aligner_ : protocols::stepwise::modeler::align::StepWiseClusterer , protocols::stepwise::screener::AlignRMSD_Screener
• pose_at_origin() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler
• pose_at_origin_ : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler
• POSE_BEFORE_CAVITIES_ADDED : core::pose::datacache::CacheableDataType
• pose_build_resids_ : protocols::match::Matcher
• pose_by_state_ : core::scoring::methods::PBLifetimeCache
• pose_comments_features_ : protocols::features::ProteinSilentReport
• pose_conformation_features_ : protocols::features::ProteinSilentReport
• pose_coords_are_same() : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• pose_copy_ : protocols::dna::PDBOutput
• pose_count_ : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger
• pose_data_uptodate_ : protocols::toolbox::match_enzdes_util::EnzCstTemplateResCache
• pose_end_ : protocols::protein_interface_design::filters::ClashWithTargetFilter
• pose_for_job() : protocols::jd3::StandardJobQueen
• pose_frag_moves_ : protocols::forge::remodel::RemodelMover::instruction_flags
• pose_free_ : protocols::stepwise::modeler::rna::phosphate::PhosphateMover
• pose_from_input_source() : protocols::jd3::pose_inputters::PDBPoseInputter , protocols::jd3::PoseInputter
• pose_from_job() : protocols::comparative_modeling::GenericJobInputter , protocols::comparative_modeling::ThreadingJobInputter , protocols::enzdes::EnzdesJobInputter , protocols::features::DatabaseJobInputter , protocols::jd2::AtomTreeDiffJobInputter , protocols::jd2::BatchJobInputter , protocols::jd2::JD2ResourceManagerJobInputter , protocols::jd2::JobInputter , protocols::jd2::LargeNstructJobInputter , protocols::jd2::LazySilentFileJobInputter , protocols::jd2::PDBJobInputter , protocols::jd2::PoseInputStreamJobInputter , protocols::jd2::ScreeningJobInputter , protocols::jd2::SilentFileJobInputter , protocols::make_rot_lib::MakeRotLibJobInputter , protocols::protein_interface_design::ParserJobInputter
• pose_has_chainbreak() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer
• pose_has_resolved_loop_indices_ : protocols::loops::GuardedLoopsFromFile
• pose_idx_ : protocols::electron_density::RBfitResult
• pose_index() : core::pose::ResidueIndexDescription
• pose_index_ : core::pose::ResidueIndexDescription
• pose_init_ : protocols::stepwise::modeler::packer::StepWisePacker
• pose_input_cache_ : protocols::rosetta_scripts::MultiplePoseMover
• pose_input_stream() : protocols::stepwise::modeler::protein::InputStreamWithResidueInfo
• pose_input_stream_ : protocols::stepwise::modeler::protein::InputStreamWithResidueInfo
• pose_inputter() : protocols::jd3::StandardJobQueen
• pose_inputter_ : protocols::jd3::StandardJobQueen
• pose_intensities_ : core::scoring::saxs::SAXSEnergy
• pose_is_proper : core::scoring::electron_density::ElecDensAllAtomCenEnergy , core::scoring::electron_density::ElecDensCenEnergy , core::scoring::electron_density::ElecDensEnergy , core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy
• pose_is_setup_for_density_scoring() : core::scoring::electron_density::FastDensEnergy
• pose_length() : protocols::denovo_design::components::StructureData
• pose_length_ : protocols::denovo_design::components::StructureData
• pose_list() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection , protocols::stepwise::legacy::screener::SimplePoseSelection , protocols::stepwise::modeler::align::StepWiseClusterer , protocols::stepwise::modeler::rna::sugar::SugarModeling , protocols::stepwise::modeler::StepWiseMinimizer , protocols::stepwise::sampler::copy_dofs::ResidueAlternativeSet
• pose_list_ : protocols::farna::FARNA_Optimizer , protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection , protocols::stepwise::legacy::screener::SimplePoseSelection , protocols::stepwise::modeler::align::StepWiseClusterer , protocols::stepwise::modeler::StepWiseConnectionSampler , protocols::stepwise::modeler::StepWiseMinimizer , protocols::stepwise::modeler::StepWiseModeler , protocols::stepwise::sampler::copy_dofs::CopyDofStepWiseSampler , protocols::stepwise::sampler::copy_dofs::ResidueAlternativeSet
• pose_loop_anchors() : protocols::sewing::Assembly
• pose_minobj_ : protocols::md::MDBase
• pose_name() : protocols::moves::StructureRestrictor , protocols::stepwise::modeler::rna::checker::VDW_RepScreenInfo
• pose_num() : protocols::sewing::Assembly
• pose_numb() : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• pose_numb_ : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• pose_number() : protocols::sewing::Model
• pose_numbered() : core::pose::ResidueIndexDescription
• pose_numbered_ : core::pose::ResidueIndexDescription
• pose_output_cache_ : protocols::rosetta_scripts::MultiplePoseMover
• pose_output_list_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• pose_outputter() : protocols::jd3::StandardJobQueen
• pose_outputter_ : protocols::jd3::StandardJobQueen
• pose_p_ : protocols::multistate_design::SingleState
• pose_passes_ss_length_check() : protocols::frags::TorsionFragmentMover
• pose_pddf_ : protocols::scoring::methods::saxs::PDDFEnergy
• pose_ptr_ : core::pose::metrics::PoseMetricContainer
• pose_raw_unfolded_state_energymap() : core::scoring::UnfoldedStatePotential
• pose_ref() : protocols::simple_moves::CombinePoseMover
• pose_ref_ : protocols::simple_moves::CombinePoseMover
• pose_relax_ : protocols::forge::remodel::RemodelMover::instruction_flags
• pose_res_no() : core::scoring::constraints::FabConstraint
• pose_residue() : protocols::denovo_design::components::StructureData
• pose_resnum() : protocols::pmut_scan::MutationData
• pose_resnum_ : protocols::pmut_scan::MutationData
• pose_right() : protocols::forge::build::ConnectRight
• pose_right_ : protocols::forge::build::ConnectRight
• pose_secstruct_ : core::select::residue_selector::SecondaryStructureSelector
• pose_segment_ends_ : protocols::sewing::AppendAssemblyMover
• pose_segment_starts_ : protocols::sewing::AppendAssemblyMover
• pose_selection_by_full_score() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection
• pose_sequence_ : protocols::toolbox::task_operations::ConservativeDesignOperation
• pose_start_ : protocols::protein_interface_design::filters::ClashWithTargetFilter
• pose_store_ : protocols::forge::remodel::RemodelAccumulator
• pose_string() : protocols::simple_moves::CopyDofMover
• pose_string_ : protocols::simple_moves::CopyDofMover
• pose_tag() : protocols::simple_moves::CombinePoseMover
• pose_tag_ : protocols::simple_moves::CombinePoseMover
• pose_temps_ : core::io::pose_from_sfr::PoseFromSFRBuilder
• pose_to_local_numbers_ : core::environment::SequenceAnnotation
• pose_to_native_map_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer
• pose_to_rinfo_ : core::io::pose_from_sfr::PoseFromSFRBuilder
• pose_with_original_HO2prime_torsion_ : protocols::stepwise::modeler::rna::o2prime::O2PrimePacker
• pose_with_original_phosphates_ : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• pose_with_original_terminal_phosphates_ : protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler
• PoseBalls() : core::scoring::packing::PoseBalls
• PoseBallsLite() : core::scoring::packing::PoseBallsLite
• poseBfacts2multivec() : protocols::electron_density::BfactorMultifunc
• PoseComment() : protocols::simple_filters::PoseComment
• PoseCommentsFeatures() : protocols::features::PoseCommentsFeatures
• PoseCommentsFeaturesCreator() : protocols::features::PoseCommentsFeaturesCreator
• PoseCondition() : protocols::moves::PoseCondition
• PoseConformationFeatures() : protocols::features::PoseConformationFeatures
• PoseConformationFeaturesCreator() : protocols::features::PoseConformationFeaturesCreator
• PoseCOP : protocols::dna::PDBOutput , protocols::dna::RestrictDesignToProteinDNAInterface , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::moves::MonteCarlo , protocols::moves::Mover , protocols::pack_daemon::PackDaemon , protocols::sic_dock::Rose , protocols::simple_moves::BBGaussianMover
• PoseEvaluator() : protocols::evaluation::PoseEvaluator
• PoseFoundResiduesCombination() : protocols::enzdes::PoseFoundResiduesCombination
• PoseFromPDBLoader() : core::import_pose::PoseFromPDBLoader
• PoseFromSFRBuilder() : core::io::pose_from_sfr::PoseFromSFRBuilder
• PoseInfoFilter() : protocols::simple_filters::PoseInfoFilter
• PoseInputSource() : protocols::jd3::PoseInputSource
• PoseInputStream() : core::import_pose::pose_stream::PoseInputStream
• PoseInputStreamJobInputter() : protocols::jd2::PoseInputStreamJobInputter
• PoseInputter() : protocols::jd3::PoseInputter
• PoseInserter() : protocols::match::output::PoseInserter
• PoseJobResult() : protocols::jd3::PoseJobResult
• poselist : protocols::cluster::GatherPosesMover
• PoseList : protocols::denovo_design::DisulfidizeMover
• PoseMap : protocols::comparative_modeling::ThreadingJobInputter
• PoseMatchOutputWriter() : protocols::match::output::PoseMatchOutputWriter
• PoseMetricCalculator() : core::pose::metrics::PoseMetricCalculator
• PoseMetricCalculatorOP : protocols::fldsgn::NcontactsCalculator , protocols::toolbox::pose_metric_calculators::FragQualCalculator
• PoseMetricContainer() : core::pose::metrics::PoseMetricContainer
• PoseMetricEvaluator() : protocols::simple_filters::PoseMetricEvaluator< T >
• posename_ : protocols::analysis::InterfaceAnalyzerMover
• posename_base_ : protocols::analysis::InterfaceAnalyzerMover
• PoseNumberedLoopFileReader() : protocols::loops::PoseNumberedLoopFileReader
• PoseOP : core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph , protocols::dna::PDBOutput , protocols::fldsgn::BluePrintBDR , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::flxbb::FilterStructs , protocols::forge::remodel::RemodelLoopMover , protocols::moves::MonteCarlo , protocols::pack_daemon::DaemonSet , protocols::pack_daemon::MultistateFitnessFunction , protocols::pack_daemon::PackDaemon , protocols::pack_daemon::QuickRepacker , protocols::protein_interface_design::movers::SaveAndRetrieveSidechains , protocols::simple_moves::BBGaussianMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::MonteCarloRecover , protocols::simple_moves::MonteCarloReset , protocols::simple_moves::MonteCarloTest , protocols::simple_moves::symmetry::DetectSymmetry
• PoseOPs : protocols::comparative_modeling::ThreadingJobInputter
• PoseOutputter() : protocols::jd3::PoseOutputter
• PosePropertyReporter() : protocols::rosetta_scripts::PosePropertyReporter
• PosePropertyReporterCreator() : protocols::rosetta_scripts::PosePropertyReporterCreator
• PosePropertyReporterFactory() : protocols::rosetta_scripts::PosePropertyReporterFactory
• PosePropertyReporterMap : protocols::rosetta_scripts::PosePropertyReporterFactory
• PosePropertyReporterRegistrator() : protocols::rosetta_scripts::PosePropertyReporterRegistrator< T >
• Poses : protocols::comparative_modeling::MultiThreadingMover
• poses_ : core::pack::rotamer_set::UnboundRotamersOperation , protocols::abinitio::StructureStore , protocols::docking::membrane::MPDockingSetupMover , protocols::hybridization::DomainAssembly , protocols::moves::VectorPoseMover , protocols::mpi_refinement::StructAvrgMover , protocols::simple_filters::StructuralSimilarityEvaluator
• poses_from_cmd_line() : protocols::comparative_modeling::AlignmentClustering
• poses_input_ : protocols::rosetta_scripts::MultiplePoseMover
• poses_output_ : protocols::rosetta_scripts::MultiplePoseMover
• PoseSelectionScreener() : protocols::stepwise::screener::PoseSelectionScreener
• PoseSelector() : protocols::rosetta_scripts::PoseSelector
• poseselector_creator_map_ : protocols::rosetta_scripts::PoseSelectorFactory
• PoseSelectorCreator() : protocols::rosetta_scripts::PoseSelectorCreator
• PoseSelectorFactory() : protocols::rosetta_scripts::PoseSelectorFactory
• PoseSelectorMap : protocols::rosetta_scripts::PoseSelectorFactory
• PoseSelectorRegistrator() : protocols::rosetta_scripts::PoseSelectorRegistrator< T >
• posesOutputed_ : protocols::pose_length_moves::InsertResMover
• poseSphericalSamples() : protocols::electron_density::DockIntoDensityMover
• posestart_ : protocols::denovo_design::components::Segment
• posesToOutput_ : protocols::pose_length_moves::InsertResMover
• PoseToStructFileRepConverter() : core::io::pose_to_sfr::PoseToStructFileRepConverter
• PoseVector : protocols::noesy_assign::DistanceScoreMover , protocols::noesy_assign::StructureDependentPeakCalibrator
• position() : core::chemical::sdf::MolFileIOAtom , core::conformation::signals::IdentityEvent , core::conformation::signals::LengthEvent , core::environment::LocalPosition , core::kinematics::tree::Atom
• Position : core::kinematics::tree::Atom
• position() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_ , core::scoring::motif::Xfrag , core::scoring::rna::data::RNA_Datum , core::scoring::rna::data::RNA_Reactivity , protocols::cartesian::CartesianAtom , protocols::dna::PositionType , protocols::hotspot_hashing::VectorPair , protocols::optimize_weights::PNatAAOptEPositionData
• position_ : core::chemical::sdf::MolFileIOAtom , core::chemical::Selector_UPPER_POSITION , core::environment::LocalPosition , core::kinematics::tree::Atom_ , core::scoring::methods::D2H_SA_Energy , core::scoring::motif::Xfrag , core::scoring::rna::data::RNA_Datum , core::scoring::rna::data::RNA_Reactivity , protocols::optimize_weights::PNatAAOptEPositionData , protocols::topology_broker::claims::CutClaim
• position_above_surface_ : protocols::surface_docking::SurfaceDockingProtocol
• position_ala_ddG() : protocols::toolbox::task_operations::RestrictConservedLowDdgOperation
• POSITION_CONSERVED_RESIDUES : core::pose::datacache::CacheableDataType
• position_data_begin() : protocols::optimize_weights::OptEData
• position_data_end() : protocols::optimize_weights::OptEData
• position_ddGs_ : protocols::toolbox::task_operations::RestrictConservedLowDdgOperation
• position_index() : core::fragment::picking_old::vall::VallResidue
• position_index_ : core::fragment::picking_old::vall::VallResidue
• position_membrane_at_topology_com() : protocols::symmetric_docking::membrane::MPSymDockMover
• position_stub() : protocols::protein_interface_design::movers::PlaceOnLoop
• position_untouchable() : protocols::toolbox::task_operations::RestrictConservedLowDdgOperation
• position_vector_setup() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• PositionConservedResiduesStore() : core::pose::datacache::PositionConservedResiduesStore
• PositionDdGInfo() : core::io::PositionDdGInfo::PositionDdGInfo
• PositionMap : core::sequence::AnnotatedSequence
• positions() : protocols::dna::DnaChains , protocols::enzdes::EnzdesFlexibleRegion
• Positions : protocols::forge::build::Bridge , protocols::forge::build::BuildInstruction , protocols::forge::build::BuildManager
• positions() : protocols::forge::build::BuildManager
• Positions : protocols::forge::build::ConnectRight , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::forge::build::RelativeConnectRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap , protocols::forge::components::VarLengthBuild
• positions_ : protocols::analysis::LoopAnalyzerMover , protocols::carbohydrates::GlycanRelaxMover , protocols::carbohydrates::SimpleGlycosylateMover , protocols::dna::DnaChains , protocols::environment::claims::EnvLabelSelector , protocols::enzdes::EnzdesFlexibleRegion , protocols::simple_filters::ScoreCutoffFilter , protocols::toolbox::task_operations::ConservativeDesignOperation
• positions_to_replace_ : protocols::enzdes::PredesignPerturbMover
• PositionType() : protocols::dna::PositionType
• positive_filters_ : protocols::protein_interface_design::filters::BoltzmannFilter
• positive_scores_ : protocols::jd2::archive::NormalizedEvaluatedArchive
• positive_states() : protocols::multistate_design::MultiStateFitnessFunction
• PosList : core::fragment::NonContinuousFrame
• possible_hbond_acceptors_ : protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker
• possible_root() : core::kinematics::FoldTree
• possible_working_res_1 : protocols::stepwise::modeler::rna::InternalWorkingResidueParameter
• possible_working_res_2 : protocols::stepwise::modeler::rna::InternalWorkingResidueParameter
• PossibleAtomTypesForAtom() : core::chemical::gasteiger::PossibleAtomTypesForAtom
• PossibleLoop() : protocols::pose_length_moves::PossibleLoop
• possibleLoops_ : protocols::pose_length_moves::NearNativeLoopCloser
• post_catalog_op() : core::fragment::picking_old::vall::eval::VallFragmentEval
• post_catalog_ops() : core::fragment::picking_old::vall::VallLibrarian
• post_loop_closure_protocol() : protocols::abinitio::AbrelaxMover
• post_loop_closure_protocol_ : protocols::abinitio::AbrelaxMover
• post_packing() : protocols::dna::DnaInterfacePacker
• post_placement_sdev_ : protocols::protein_interface_design::movers::PlaceStubMover
• post_process() : protocols::relax::WorkUnit_BatchRelax , protocols::relax::WorkUnit_BatchRelax_and_PostRescore
• post_process_permutation() : protocols::denovo_design::connection::Connection
• post_trans_ : protocols::electron_density::RBfitResult
• PostDockAssemblyScorer() : protocols::domain_assembly::PostDockAssemblyScorer
• PosType : protocols::dna::DnaInterfaceMultiStateDesign , protocols::multistate_design::PosType , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• potential_ : core::scoring::disulfides::CentroidDisulfideEnergy , core::scoring::disulfides::DisulfideMatchingEnergy , core::scoring::disulfides::FullatomDisulfideEnergy , core::scoring::dna::DNAChiEnergy , core::scoring::methods::CenHBEnergy , core::scoring::methods::CenPairEnergy , core::scoring::methods::CenRotEnvEnergy , core::scoring::methods::CenRotPairEnergy , core::scoring::methods::dfire::DFIRE_Potential , core::scoring::methods::DirectReadoutEnergy , core::scoring::methods::DNA_BaseEnergy , core::scoring::methods::DNA_DihedralEnergy , core::scoring::methods::DNA_EnvPairEnergy , core::scoring::methods::EnvEnergy , core::scoring::methods::Fa_MbenvEnergy , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::methods::FACTSEnergy , core::scoring::methods::GenBornEnergy , core::scoring::methods::MembraneCbetaEnergy , core::scoring::methods::MembraneCenPairEnergy , core::scoring::methods::MembraneEnvEnergy , core::scoring::methods::MembraneEnvPenalties , core::scoring::methods::MembraneLipo , core::scoring::methods::MMBondAngleEnergy , core::scoring::methods::MMBondLengthEnergy , core::scoring::methods::MMLJEnergyInter , core::scoring::methods::MMLJEnergyIntra , core::scoring::methods::MMTorsionEnergy , core::scoring::methods::MultipoleElecEnergy , core::scoring::methods::OmegaTetherEnergy , core::scoring::methods::PairEnergy , core::scoring::methods::ProQ_Energy , core::scoring::methods::RamachandranEnergy2B , core::scoring::methods::RamachandranEnergy , core::scoring::methods::RamaPreProEnergy , core::scoring::methods::SecondaryStructureEnergy , core::scoring::methods::SmoothCenPairEnergy , core::scoring::methods::SmoothEnvEnergy , core::scoring::methods::VdWTinkerEnergy , core::scoring::methods::WaterAdductHBondEnergy , core::scoring::PoissonBoltzmannPotential , protocols::protein_interface_design::filters::DisulfideFilter , protocols::protein_interface_design::movers::DisulfideMover
• potential_energy_ : protocols::md::MDBase
• potential_is_loaded_ : core::scoring::methods::dfire::DFIRE_Energy , core::scoring::methods::dfire::DFIRE_Potential
• potential_twobody_memory_use() : core::pack::interaction_graph::DoubleLazyEdge
• potential_vect_ : core::scoring::func::SplineFunc
• potential_vect_size_ : core::scoring::func::SplineFunc
• power_ : core::scoring::func::CircularPowerFunc
• PowExpression() : protocols::pack_daemon::PowExpression
• ppk_only : protocols::flexpep_docking::FlexPepDockingFlags
• pqr : core::scoring::APBSWrapper
• PQR() : core::scoring::PQR
• pqr_filename_ : core::scoring::PoissonBoltzmannPotential
• pr_idx_ : core::scoring::packstat::MultiProbePerSphereAccumulator , core::scoring::packstat::MultiProbePoseAccumulator
• pre_align() : protocols::constraints_additional::BindingSiteConstraint
• pre_catalog_op() : core::fragment::picking_old::vall::eval::ABEGOEval , core::fragment::picking_old::vall::eval::EnergyEval , core::fragment::picking_old::vall::eval::IdentityEval , core::fragment::picking_old::vall::eval::VallFragmentEval
• pre_catalog_ops() : core::fragment::picking_old::vall::VallLibrarian
• pre_chitip_transform() : protocols::match::upstream::UpstreamResTypeGeometry
• pre_chitip_transforms_ : protocols::match::upstream::UpstreamResTypeGeometry
• pre_compute_grid_points() : protocols::topology_broker::TMHTopologySamplerClaimer
• pre_ligand_atom_id_ : protocols::metal_interface::MetalSiteResidue
• pre_load_data() : protocols::antibody::task_operations::AddCDRProfileSetsOperation , protocols::antibody::task_operations::AddCDRProfilesOperation
• pre_loaded_data_ : protocols::antibody::task_operations::AddCDRProfileSetsOperation , protocols::antibody::task_operations::AddCDRProfilesOperation
• pre_loop_closure_protocol() : protocols::abinitio::AbrelaxMover
• pre_loop_closure_protocol_ : protocols::abinitio::AbrelaxMover
• pre_minimization_ : protocols::antibody::SnugDock
• pre_nresidue_change() : core::conformation::Conformation
• pre_pre_ligand_atom_id_ : protocols::metal_interface::MetalSiteResidue
• pre_process() : protocols::relax::WorkUnit_BatchRelax , protocols::relax::WorkUnit_BatchRelax_and_PostRescore , protocols::topology_broker::MembraneTopologyClaimer , protocols::topology_broker::TMHTopologySamplerClaimer , protocols::topology_broker::TopologyClaimer
• pre_scoring() : protocols::flexpack::OtherContextScoreFunction
• pre_scoring_filter_ : protocols::helical_bundle::BackboneGridSampler
• pre_scoring_filter_exists_ : protocols::helical_bundle::BackboneGridSampler
• pre_scoring_mover_ : protocols::helical_bundle::BackboneGridSampler
• pre_scoring_mover_exists_ : protocols::helical_bundle::BackboneGridSampler
• pre_selection_filter_ : protocols::helical_bundle::BundleGridSampler
• pre_selection_filter_exists_ : protocols::helical_bundle::BundleGridSampler
• pre_selection_mover_ : protocols::generalized_kinematic_closure::GeneralizedKIC , protocols::helical_bundle::BundleGridSampler
• pre_selection_mover_exists_ : protocols::generalized_kinematic_closure::GeneralizedKIC , protocols::helical_bundle::BundleGridSampler
• pre_talaris2013_geometries : core::init::pre_talaris_2013_behavior_settings
• pre_talaris_2013_behavior_settings() : core::init::pre_talaris_2013_behavior_settings
• pre_trans_ : protocols::electron_density::RBfitResult
• preallocate() : core::fragment::picking_old::vall::VallLibrarian
• preallocate_ : core::fragment::picking_old::vall::VallLibrarian
• preamble() : protocols::ligand_docking::rdf::RDFBase , protocols::ligand_docking::rdf::RDFBinaryOrbitalFunction , protocols::ligand_docking::rdf::RDFHbondFunction , protocols::ligand_docking::rdf::RDFOrbitalFunction
• preapply() : protocols::simple_moves::GenericMonteCarloMover
• preapply_ : protocols::simple_moves::GenericMonteCarloMover
• precalc_context() : core::scoring::elec::FA_GrpElecEnergy
• precalc_etable_coefficients() : core::scoring::etable::Etable , core::scoring::etable::MembEtable
• precalculate_bb_bb_energy_for_design() : core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• precalculated_bb_bb_energy_ : core::scoring::geometric_solvation::ContextDependentGeometricSolEnergy , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy
• precision() : core::io::silent::SilentStruct
• precision_ : core::io::silent::SilentStruct , protocols::frag_picker::scores::FragmentScoreManager , protocols::rotamer_recovery::RRReporterHuman
• precompute_all_energies() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• precompute_energies() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• precompute_transforms() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• precompute_two_body_energies() : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::symmetry::SymmetricRotamerSets
• precompute_unweighted_score() : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• precomputed_library_mover() : protocols::stepwise::modeler::StepWiseModeler
• precomputed_library_mover_ : protocols::stepwise::modeler::StepWiseModeler
• PrecomputedLibraryMover() : protocols::stepwise::modeler::precomputed::PrecomputedLibraryMover
• PrecomputedPairEnergiesEdge() : core::pack::interaction_graph::PrecomputedPairEnergiesEdge
• PrecomputedPairEnergiesInteractionGraph() : core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph , protocols::simple_moves::GreenPacker
• PrecomputedPairEnergiesInteractionGraphOP : protocols::simple_moves::GreenPacker
• PrecomputedPairEnergiesNode() : core::pack::interaction_graph::PrecomputedPairEnergiesNode
• pred_ : core::scoring::ExcludedResPredicate , core::scoring::ResRangePredicate , core::scoring::SelectedResPredicate
• pred_burial_ : core::scoring::methods::BurialEnergy
• PRED_DIR : protocols::sparta::Sparta::SpartaLib
• pred_ss : core::io::external::PsiPredResult
• pred_ss_ : protocols::medal::MedalExchangeMover , protocols::star::Extender , protocols::star::StarAbinitio
• predefine_search() : protocols::electron_density::DockIntoDensityMover
• predefined_torsions_ : protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber
• predefined_window_start_ : protocols::simple_moves::ClassicFragmentMover
• PredesignPerturbMover() : protocols::enzdes::PredesignPerturbMover
• Predicate() : core::scoring::Predicate
• predict_H3_base_type() : protocols::antibody::AntibodyInfo
• predict_n_matches_for_hit_subsets() : protocols::match::Matcher
• predict_pos_rd1() : protocols::ss_prediction::SS_predictor
• predict_pos_rd2() : protocols::ss_prediction::SS_predictor
• predict_rd1() : protocols::ss_prediction::SS_predictor
• predict_rd2() : protocols::ss_prediction::SS_predictor
• predict_region() : protocols::mpi_refinement::StructAvrgMover
• predict_ss() : protocols::ss_prediction::SS_predictor
• predicted_burial_ : protocols::simple_filters::PredictedBurialEvaluator
• predicted_H3_base_type_ : protocols::antibody::AntibodyInfo
• predicted_sa_norm_ : protocols::frag_picker::scores::SolventAccessibility
• PredictedBurialEvaluator() : protocols::simple_filters::PredictedBurialEvaluator
• PredictedBurialFnEvaluatorCreator() : protocols::simple_filters::PredictedBurialFnEvaluatorCreator
• prediction_name_ : protocols::frag_picker::scores::PartialSecondarySimilarity , protocols::frag_picker::scores::RamaScore , protocols::frag_picker::scores::SecondaryIdentity , protocols::frag_picker::scores::SecondarySimilarity , protocols::frag_picker::scores::TalosSSSimilarity
• preexisting_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
• prefactor_ : core::scoring::rna::RNA_FullAtomStackingEnergy
• preferred_root_res() : core::pose::full_model_info::FullModelInfo
• prefilter_scorefxn_ : protocols::loophash::LoopHashMoverWrapper
• prefix() : protocols::match::output::PDBWriter
• prefix_ : protocols::analysis::PeptideDeriverBasicStreamOutputter , protocols::analysis::PeptideDeriverMarkdownStreamOutputter , protocols::forge::remodel::RemodelMover::instruction_flags , protocols::frag_picker::FragmentPicker , protocols::jd2::JobOutputter , protocols::ligand_docking::InterfaceScoreCalculator , protocols::ligand_docking::WriteLigandMolFile , protocols::match::output::PDBWriter , protocols::matdes::ExtractSubposeMover , protocols::membrane::benchmark::SampleTiltAngles
• PREFIX_FINAL : protocols::nonlocal::StarTreeBuilder
• PREFIX_INITIAL : protocols::nonlocal::StarTreeBuilder
• prefix_len : core::kinematics::Node
• preload_motif_data : core::scoring::motif::MotifHashManager
• preminimize() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• preminimize_ : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• preminimize_pose() : protocols::stepwise::monte_carlo::mover::StepWiseMasterMover
• prep_aa_submatrix() : core::pack::interaction_graph::DoubleLazyEdge
• prep_for_neighbors_perturbation() : core::pack::interaction_graph::FASTERNode
• prep_grid() : protocols::match::downstream::ActiveSiteGrid
• prepack() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• prepack_ : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• prepack_full_repack_ : protocols::docking::DockingEnsemblePrepackProtocol , protocols::docking::DockingPrepackProtocol
• prepack_only() : protocols::flexpep_docking::FlexPepDockingProtocol
• prepack_only_ : protocols::docking::DockTaskFactory
• prepack_res_was_inputted_ : protocols::stepwise::modeler::StepWiseModeler
• prepacked_ : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• PrepackMover() : protocols::protein_interface_design::movers::PrepackMover
• prepare() : protocols::abinitio::abscript::ConstraintPreparer , protocols::abinitio::abscript::StagePreparer
• prepare_constraints_energy_container() : core::scoring::constraints::ConstraintsEnergy
• prepare_coord() : protocols::normalmode::NormalMode
• prepare_enrich_stage() : protocols::mpi_refinement::Scheduler
• prepare_fold_tree_for_erraser() : protocols::stepwise::monte_carlo::mover::TransientCutpointHandler
• prepare_for_altbb_move_to_closest_state() : protocols::flexpack::interaction_graph::MinimalistFlexbbNode
• prepare_for_altbb_move_to_state() : protocols::flexpack::interaction_graph::MinimalistFlexbbNode
• prepare_for_centroid_ : protocols::loop_modeling::LoopModeler
• prepare_for_FASTER() : core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::FASTERNode
• prepare_for_fullatom_ : protocols::loop_modeling::LoopModeler
• prepare_for_hit_generation() : protocols::match::downstream::SecondaryMatcherToDownstreamResidue , protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• prepare_for_hit_generation_at_target_build_point() : protocols::match::downstream::SecondaryMatcherToDownstreamResidue , protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• prepare_for_hit_generation_for_constraint() : protocols::match::Matcher
• prepare_for_hit_generation_for_geomcst() : protocols::match::downstream::SecondaryMatcherToDownstreamResidue
• prepare_for_match_enumeration() : protocols::match::downstream::DownstreamAlgorithm , protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• prepare_for_new_residue_type() : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• prepare_for_output_writing() : protocols::match::output::CloudPDBWriter , protocols::match::output::OutputWriter , protocols::match::output::PDBWriter
• prepare_for_packing() : protocols::sewing::Assembly
• prepare_for_perturbation() : core::pack::interaction_graph::FASTERNode
• prepare_for_residue_pair() : core::scoring::etable::BaseEtableEnergy< Derived >
• prepare_for_scoring() : core::scoring::NeighborList
• prepare_for_simulated_annealing() : core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > , core::pack::interaction_graph::AnnealableGraphBase , core::pack::interaction_graph::BackgroundNode< V, E, G > , core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G > , core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::EdgeBase , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::FASTERNode , 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::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::MultiplexedAnnealableGraph , core::pack::interaction_graph::NodeBase , core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::ResidueArrayAnnealingEvaluator , core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G > , core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceEdge< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistEdge , core::pack::interaction_graph::SymmMinimalistInteractionGraph , core::pack::interaction_graph::SymmMinimalistNode , protocols::flexpack::interaction_graph::FlexbbNode , protocols::flexpack::interaction_graph::MinimalistFlexbbEdge , protocols::flexpack::interaction_graph::MinimalistFlexbbNode , protocols::flexpack::interaction_graph::OTFFlexbbEdge
• prepare_for_simulated_annealing_no_deletion() : core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::PDEdge
• prepare_from_prior_sampled_sugar_jobs() : protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator
• prepare_from_prior_sampled_sugar_jobs_for_chain_break() : protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator
• prepare_ghost_pose() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• prepare_hashing_packer_task_() : protocols::hotspot_hashing::HotspotStubSet
• prepare_loop_in_stage3() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints , protocols::abinitio::FragmentSampler , protocols::abinitio::KinematicAbinitio , protocols::abinitio::MembraneAbinitio
• prepare_loop_in_stage4() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints , protocols::abinitio::FragmentSampler , protocols::abinitio::KinematicAbinitio , protocols::abinitio::MembraneAbinitio
• prepare_neighbor_graphs() : core::scoring::Energies
• prepare_otf_graph() : core::pack::rotamer_set::RotamerSets
• prepare_pose() : protocols::analysis::PeptideDeriverFilter , protocols::constraints_additional::ConstraintEvaluator
• prepare_pose_for_sampling() : protocols::abinitio::KinematicControl
• prepare_preliminary_job_list() : protocols::jd3::StandardJobQueen
• prepare_push_back() : protocols::toolbox::DecoySetEvaluation
• prepare_rotamers_for_packing() : core::scoring::elec::FA_ElecEnergy , core::scoring::elec::FA_ElecEnergyAroAll , core::scoring::elec::FA_ElecEnergyAroAro , core::scoring::elec::FA_GrpElecEnergy , core::scoring::elec::RNA_FA_ElecEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::hbonds::HBondEnergy , core::scoring::lkball::LK_BallEnergy , core::scoring::methods::CustomAtomPairEnergy , core::scoring::methods::EnergyMethod , core::scoring::methods::FACTSEnergy , core::scoring::methods::GenBornEnergy , core::scoring::methods::MMLJEnergyInter , core::scoring::methods::MultipoleElecEnergy , core::scoring::methods::PairEnergy , core::scoring::methods::VdWTinkerEnergy , core::scoring::orbitals::OrbitalsScore , core::scoring::ScoreFunction , core::scoring::vdwaals::VDW_Energy
• prepare_scoring() : protocols::noesy_assign::DistanceScoreMover
• prepare_search_stage() : protocols::mpi_refinement::Scheduler
• prepare_send_new_coords() : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• prepare_sets_for_packing() : core::pack::rotamer_set::RotamerSets
• prepare_simulation() : protocols::canonical_sampling::MetropolisHastingsMover
• prepare_stage1() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints , protocols::abinitio::FragmentSampler , protocols::abinitio::KinematicAbinitio , protocols::abinitio::MembraneAbinitio
• prepare_stage2() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints , protocols::abinitio::FragmentSampler , protocols::abinitio::KinematicAbinitio , protocols::abinitio::MembraneAbinitio
• prepare_stage3() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::KinematicAbinitio , protocols::abinitio::MembraneAbinitio
• prepare_stage4() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FoldConstraints , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• prepare_stage5() : protocols::abinitio::ClassicAbinitio
• prepare_symm_otf_interaction_graph() : core::pack::rotamer_set::symmetry::SymmetricRotamerSets
• prepare_to_note_hits_for_completed_round() : protocols::match::OccupiedSpaceHash
• prepared_for_simA_ : core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G > , core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >
• prepared_for_simulated_annealing_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• PrepareForCentroid() : protocols::loop_modeling::utilities::PrepareForCentroid
• PrepareForFullatom() : protocols::loop_modeling::utilities::PrepareForFullatom
• preparers_ : protocols::abinitio::abscript::AbscriptStageMover
• PreparerSet : protocols::abinitio::abscript::AbscriptStageMover
• preped_for_sim_annealing_ : core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmMinimalistEdge
• prepend_Aform_residue() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• prepend_edge() : core::kinematics::FoldTree
• prepend_n_residues_ : protocols::ncbb::oop::OopCreatorMover
• prepend_other_pose() : protocols::stepwise::monte_carlo::mover::AddMover
• prepend_output_name() : protocols::canonical_sampling::MetricRecorder
• prepend_output_name_ : protocols::canonical_sampling::MetricRecorder
• prepend_polymer_residue_before_seqpos() : core::conformation::Conformation , core::pose::Pose , protocols::environment::ProtectedConformation
• prepend_res() : core::pose::PDBInfo
• prepend_residue() : protocols::stepwise::monte_carlo::mover::AddMover
• PrependMainchainAtom() : core::chemical::PrependMainchainAtom
• prepro_restype_data_ : core::scoring::methods::IdealParametersDatabase
• preprocess_data() : core::scoring::ResidualDipolarCoupling
• preprocess_pose() : core::import_pose::pose_stream::PoseInputStream
• preprocessing_script_version_ : protocols::antibody::GraftOneCDRLoop
• PreProlineFilter() : protocols::denovo_design::filters::PreProlineFilter
• presample_added_residue_ : protocols::stepwise::monte_carlo::mover::AddMover
• presample_by_swa_ : protocols::stepwise::monte_carlo::mover::AddMover
• presample_virtual_sugars() : protocols::stepwise::modeler::StepWiseConnectionSampler
• prescoring_filter_exists() : protocols::helical_bundle::BackboneGridSampler
• prescoring_mover_exists() : protocols::helical_bundle::BackboneGridSampler
• preselection_filter_exists() : protocols::helical_bundle::BundleGridSampler
• preselection_mover_exists() : protocols::generalized_kinematic_closure::GeneralizedKIC , protocols::helical_bundle::BundleGridSampler
• preserve_atom_coords() : protocols::simple_moves::MutateResidue
• preserve_atom_coords_ : protocols::simple_moves::MutateResidue
• preserve_buried_contacts() : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• preserve_buried_contacts_ : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• preserve_c_beta() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• preserve_c_beta_ : core::pack::task::ResidueLevelTask_
• preserve_crystinfo() : core::io::StructFileRepOptions
• preserve_crystinfo_ : core::io::StructFileRepOptions
• preserve_detailed_balance() : protocols::backrub::BackrubMover , protocols::backrub::BackrubSidechainMover , protocols::canonical_sampling::ThermodynamicMover , protocols::kinematic_closure::BalancedKicMover , protocols::rigid::RigidBodyMover , protocols::rigid::UniformRigidBodyMover , protocols::simple_moves::BackboneMover , protocols::simple_moves::BBGaussianMover , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• preserve_detailed_balance_ : protocols::backrub::BackrubMover , protocols::simple_moves::BackboneMover , protocols::simple_moves::BBGaussianMover , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• preserve_header() : core::io::StructFileRepOptions
• preserve_header_ : core::io::StructFileRepOptions
• preserve_whole_input_tag_ : protocols::jobdist::BasicJob
• PreserveCBetaRLT() : core::pack::task::operation::PreserveCBetaRLT
• presetClass() : protocols::sparta::GDB
• pretty_print() : core::scoring::mm::MMBondAngleLibrary , core::scoring::mm::MMBondLengthLibrary
• preturb_rot_and_dunbrack_eval() : protocols::simple_moves::sidechain_moves::SidechainMover
• prev_residue_skipping_merges() : core::io::pose_from_sfr::PoseFromSFRBuilder
• prev_residue_skipping_null_residue_types() : core::io::pose_from_sfr::PoseFromSFRBuilder
• prev_state_hash_ : protocols::pack_daemon::PackDaemon
• PREV_Tab : protocols::sparta::Sparta::SpartaLib
• prevburied : core::scoring::sc::MolecularSurfaceCalculator
• prevent_repacking() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_ , protocols::simple_moves::DesignRepackMover , protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation , protocols::toolbox::task_operations::RestrictIdentitiesOperation , protocols::toolbox::task_operations::RestrictNativeResiduesOperation
• prevent_repacking_ : protocols::simple_moves::DesignRepackMover , protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation , protocols::toolbox::task_operations::RestrictIdentitiesOperation , protocols::toolbox::task_operations::RestrictNativeResiduesOperation
• PreventChainFromRepackingOperation() : protocols::toolbox::task_operations::PreventChainFromRepackingOperation
• PreventResiduesFromRepackingOperation() : protocols::toolbox::task_operations::PreventResiduesFromRepackingOperation
• prevFileName : protocols::sparta::Sparta::SpartaLib
• previous() : core::graph::EdgeListElement , protocols::sewing::SegmentGraph
• previous_ : core::graph::EdgeListElement , protocols::simple_moves::sidechain_moves::SidechainMCMover
• previous_child() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• previous_hash_value_ : core::scoring::methods::LinearChainbreakEnergy
• previous_mover_ : protocols::rosetta_scripts::MultiplePoseMover
• previous_round_geometry_still_matchable() : protocols::match::OccupiedSpaceHash
• previous_sequence_ : protocols::docking::DockingProtocol , protocols::docking::TemperedDocking
• previous_sibling() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• previous_tree_ : protocols::nonlocal::SingleFragmentMover
• previous_vertex1 : protocols::viewer::GraphicsState
• previous_vertex2 : protocols::viewer::GraphicsState
• previous_width_vector : protocols::viewer::GraphicsState
• previous_working_pack_res() : protocols::stepwise::modeler::packer::StepWisePacker
• previous_working_pack_res_ : protocols::stepwise::modeler::packer::StepWisePacker
• previously_builded_res_clash_filter() : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• previously_builded_res_contact_filter() : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• previously_builded_res_VDW_filter() : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• previously_grown_ : protocols::seeded_abinitio::SwapSegment
• prevp : core::scoring::sc::MolecularSurfaceCalculator
• primary_atom_id_ : core::scoring::constraints::BackboneStubConstraint
• primary_backbone_target_ : core::scoring::constraints::BackboneStubConstraint
• primary_seq_distance_cutoff_for_beta_sheet_capping_after_C_term_capping_ : protocols::features::strand_assembly::SandwichFeatures
• primary_seq_distance_cutoff_for_beta_sheet_capping_after_N_term_capping_ : protocols::features::strand_assembly::SandwichFeatures
• primary_seq_distance_cutoff_for_beta_sheet_capping_before_C_term_capping_ : protocols::features::strand_assembly::SandwichFeatures
• primary_seq_distance_cutoff_for_beta_sheet_capping_before_N_term_capping_ : protocols::features::strand_assembly::SandwichFeatures
• primary_sidechain_target_ : core::scoring::constraints::BackboneStubConstraint
• PrimarySequenceNeighborhoodSelector() : core::select::residue_selector::PrimarySequenceNeighborhoodSelector
• principal_component() : protocols::features::helixAssembly::HelicalFragment
• principal_component_ : protocols::features::helixAssembly::HelicalFragment
• PrincipalQuantumNumber : core::chemical::ElectronConfiguration
• PrincipalQuantumNumber_strings() : core::chemical::ElectronConfiguration
• print() : core::chemical::AtomType , core::chemical::Bond , core::chemical::Orbital , core::graph::Node , core::pack::interaction_graph::BackgroundNode< V, E, G > , core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DotSphere , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::NodeBase , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::RotamerDots , core::pack::interaction_graph::RotamerDotsCache , core::pack::interaction_graph::SimpleNode , core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode , core::pose::metrics::EnergyDependentCalculator , core::pose::metrics::PoseMetricCalculator , core::pose::metrics::PoseMetricContainer , core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator , core::pose::metrics::simple_calculators::InterfaceDeltaEnergeticsCalculator , core::pose::metrics::simple_calculators::InterfaceNeighborDefinitionCalculator , core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator , core::pose::metrics::simple_calculators::SasaCalculator2 , core::pose::metrics::simple_calculators::SasaCalculatorLegacy , core::pose::metrics::StructureDependentCalculator , core::scoring::elec::ElecAtom , core::scoring::EMapVector , core::scoring::EnergyNode , core::scoring::etable::etrie::CountPairData_1_1 , core::scoring::etable::etrie::CountPairData_1_2 , core::scoring::etable::etrie::CountPairData_1_3 , core::scoring::etable::etrie::CountPairDataGeneric , core::scoring::etable::etrie::EtableAtom , core::scoring::etable::etrie::TrieCountPair1BC3 , core::scoring::etable::etrie::TrieCountPairAll , core::scoring::etable::etrie::TrieCountPairGeneric , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::hbonds::hbtrie::HBAtom , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::hbonds::hbtrie::HBCPData , core::scoring::lkball::lkbtrie::LKBAtom , core::scoring::MembraneTopology , core::scoring::MinimizationNode , core::scoring::mm::mmtrie::MMEnergyTableAtom , core::scoring::trie::RotamerTrie< AT, CPDATA > , core::scoring::trie::RotamerTrieBase , core::scoring::trie::TrieNode< AT, CPDATA > , core::scoring::vdwaals::VDWAtom , protocols::dna::DnaChains , protocols::fldsgn::NcontactsCalculator , protocols::flexpack::interaction_graph::FlexbbNode , protocols::flexpack::interaction_graph::MinimalistFlexbbNode , protocols::flexpack::interaction_graph::OTFFlexbbNode , protocols::frag_picker::nonlocal::NonlocalPair , protocols::frags::TorsionFragmentLibrary , protocols::jd2::ScoreMap , protocols::loophash::BackboneSegment , protocols::match::downstream::AtomAngleSecMatchRPE , protocols::match::downstream::AtomDihedralSecMatchRPE , protocols::match::downstream::AtomDistanceSecMatchRPE , protocols::match::downstream::AtomGeometrySecMatchRPE , protocols::motifs::Motif , protocols::moves::MoverStatistics , protocols::moves::PyMolMover , protocols::pockets::PocketGrid , protocols::rbsegment_relax::RBSegmentMover , protocols::scoring::Interface , protocols::simple_moves::LookupResultPlus , protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator , protocols::toolbox::pose_metric_calculators::CatPiCalculator , protocols::toolbox::pose_metric_calculators::ChargeCalculator , protocols::toolbox::pose_metric_calculators::ClashCountCalculator , protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator , protocols::toolbox::pose_metric_calculators::FragQualCalculator , protocols::toolbox::pose_metric_calculators::HPatchCalculator , protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculator , protocols::toolbox::pose_metric_calculators::NeighborhoodByDistanceCalculator , protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator , protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator , protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator , protocols::toolbox::pose_metric_calculators::PackstatCalculator , protocols::toolbox::pose_metric_calculators::PiPiCalculator , protocols::toolbox::pose_metric_calculators::ResidueDecompositionCalculator , protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator , protocols::toolbox::pose_metric_calculators::SaltBridgeCalculator , protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator , protocols::toolbox::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator , protocols::toolbox::pose_metric_calculators::SurfaceCalculator , protocols::wum::SilentStructStore , protocols::wum::WorkUnitBase
• print_address() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel , protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• print_addresses_at_level() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• print_all_bond_lengths() : core::chemical::IdealBondLengthSet
• print_all_info() : protocols::toolbox::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator
• print_all_types() : core::chemical::MMAtomTypeSet
• print_allowed_types() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• print_alt_energies() : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• print_atom_info() : protocols::toolbox::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator
• print_atom_subset() : protocols::toolbox::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator
• print_avg_cluster_centroid_dist() : protocols::make_rot_lib::MakeRotLibMover
• print_best_rms() : protocols::electron_density::DockIntoDensityMover
• print_bit_string() : core::pack::interaction_graph::RotamerDotsCache
• print_bondangles() : core::chemical::ResidueType
• print_cache() : protocols::genetic_algorithm::GeneticAlgorithmBase
• print_cluster_assignment() : protocols::cluster::ClusterBase , protocols::toolbox::ClusterBase
• print_cluster_PDBs() : protocols::cluster::ClusterBase
• print_clusters_silentfile() : protocols::cluster::ClusterBase
• print_comments() : core::io::silent::SilentStruct
• print_conformation() : core::import_pose::PDBSilentStruct , core::io::raw_data::DecoyStruct , core::io::raw_data::RawStruct , core::io::raw_data::ScoreStructJSON , core::io::raw_data::ScoreStructText , core::io::silent::BinarySilentStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RigidBodySilentStruct , core::io::silent::RNA_SilentStruct , core::io::silent::ScoreFileSilentStruct , core::io::silent::ScoreJumpFileSilentStruct , core::io::silent::SilentStruct
• print_current_energy() : 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
• print_current_state_assignment() : core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistInteractionGraph , protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph
• print_debug() : protocols::abinitio::MembraneAbinitio
• print_definitions() : protocols::make_rot_lib::MakeRotLibMover
• print_dihedrals() : core::chemical::ResidueType
• print_dofs() : protocols::optimize_weights::WrapperOptEMultifunc
• print_dot_bit_string() : core::pack::interaction_graph::InvRotamerDots , core::scoring::sasa::LeGrandSasa
• print_dunbrack02_rotlib() : protocols::make_rot_lib::MakeRotLibMover
• print_dunbrack10_rotlib() : protocols::make_rot_lib::MakeRotLibMover
• print_energies() : protocols::optimize_weights::IterativeOptEDriver
• print_entity_history() : protocols::pack_daemon::PackDaemon
• print_fragment() : protocols::frag_picker::FragmentCandidate
• print_fragment_index() : protocols::frag_picker::FragmentCandidate
• print_fragment_seq() : protocols::frag_picker::FragmentCandidate
• print_generation_statistics() : protocols::genetic_algorithm::GeneticAlgorithmBase
• print_grid_param() : protocols::scoring::methods::pcs::PCS_Energy_parameters_manager , protocols::scoring::methods::pcsTs1::PCS_Energy_parameters_manager_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_parameters_manager_Ts4
• print_header() : core::import_pose::PDBSilentStruct , core::io::raw_data::RawStruct , core::io::raw_data::ScoreStructJSON , core::io::silent::BinarySilentStruct , core::io::silent::RNA_SilentStruct , core::io::silent::ScoreFileSilentStruct , core::io::silent::ScoreJumpFileSilentStruct , core::io::silent::SilentStruct , core::scoring::motif::ResPairMotif
• print_hpatch_avoidance_stats() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• print_info() : core::pose::rna::BasePair
• print_internal_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
• print_internal_energies_for_current_state_assignment() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• print_library() : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• print_metric() : core::pose::Pose
• print_mutation_data() : protocols::pmut_scan::MutationData
• print_ngb_mask() : protocols::neighbor::Neighborhood
• print_pack_report() : protocols::vip::VIP_Mover
• print_parent_remarks() : core::io::silent::SilentStruct
• print_particles() : core::optimization::ParticleSwarmMinimizer
• print_peak_info() : protocols::noesy_assign::CrossPeak
• print_population() : protocols::genetic_algorithm::GeneticAlgorithmBase
• print_pretty_path_distances() : core::chemical::ResidueType
• print_pymol_selection_of_hbond_unsat() : protocols::analysis::InterfaceAnalyzerMover
• print_pymol_selection_of_interface_residues() : protocols::analysis::InterfaceAnalyzerMover
• print_pymol_selection_of_packing() : protocols::analysis::InterfaceAnalyzerMover
• print_quantiles() : core::scoring::motif::XformScore
• print_raw_numbers() : protocols::cluster::ClusterBase
• print_relax_report() : protocols::vip::VIP_Mover
• print_report() : 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
• print_residue_numbers() : core::io::silent::SilentStruct
• print_rot_data() : protocols::make_rot_lib::MakeRotLibMover
• print_rot_data_vec() : protocols::make_rot_lib::MakeRotLibMover
• print_rot_vec() : protocols::toolbox::pose_metric_calculators::RotamerRecovery
• print_score() : protocols::optimize_weights::ConstraintedOptimizationWeightFunc , protocols::optimize_weights::DDGBindOptEData , protocols::optimize_weights::DDGMutationOptEData , protocols::optimize_weights::DGBindOptEData , protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData , protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData , protocols::optimize_weights::OptEPositionData , protocols::optimize_weights::PNatAAOptEPositionData , protocols::optimize_weights::PNatLigPoseOptEData , protocols::optimize_weights::PNatRotOptEPositionData , protocols::optimize_weights::PNatStructureOptEData , protocols::optimize_weights::PSSMOptEPositionData , protocols::relax::RangeRelaxMover
• print_score_functions() : core::scoring::disulfides::FullatomDisulfidePotential
• print_score_header() : core::io::silent::SilentStruct
• print_scores() : core::io::raw_data::RawStruct , core::io::raw_data::ScoreStructJSON , core::io::silent::SilentStruct , core::scoring::motif::XformScore
• print_scores_norm() : core::scoring::motif::XformScore
• print_sequence() : protocols::frag_picker::CSTalosIO , protocols::frag_picker::PhiPsiTalosIO
• print_sho_energies() : protocols::toolbox::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator
• print_stats() : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement , protocols::wum::MPI_WorkUnitManager
• print_stats_auto() : protocols::wum::MPI_WorkUnitManager
• print_statw_interval_ : protocols::wum::MPI_WorkUnitManager
• print_str_vec() : protocols::antibody::design::AntibodyDesignMover
• print_string_to_PDBfile() : protocols::pockets::GenPharmacophore
• print_submotif_info() : core::io::silent::SilentStruct
• print_summary() : protocols::cluster::ClusterBase , protocols::mpi_refinement::MPI_Refinement , protocols::toolbox::ClusterBase
• print_surface_avoidance_stats() : core::pack::interaction_graph::SurfaceNode< V, E, G >
• print_timing_stats() : protocols::wum::MPI_WorkUnitManager
• print_to_file() : protocols::pockets::FingerprintBase
• print_to_oegrid() : protocols::pockets::ElectrostaticpotentialGrid
• print_to_pdb() : protocols::pockets::FingerprintBase
• print_tracer_info_ : protocols::antibody::design::AntibodyDesignMover
• print_verbose_ddgs() : protocols::ddg::ddGMover
• print_vertex_groups() : core::pack::interaction_graph::InteractionGraphBase
• print_vertices() : core::graph::Graph , core::pack::interaction_graph::InteractionGraphBase
• printContent() : protocols::pockets::SmallMol
• printCoordinates() : protocols::pockets::SmallMol
• PrintErrorAndQuit() : protocols::hybridization::TMalign
• printGrishinFormat() : core::sequence::SequenceAlignment
• prior_probs_ : core::sequence::ProfSimScoringScheme
• priority() : protocols::topology_broker::claims::SequenceClaim
• priority_ : protocols::frag_picker::scores::FragmentScoringMethod , protocols::topology_broker::claims::SequenceClaim , protocols::topology_broker::SequenceClaimer
• PrioSubtype : protocols::environment::claims::ClaimStrength
• private_data_to_public_array() : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• pro_cd_cprev_n_ca_interres_torsion_params() : core::scoring::methods::ResidueCartBondedParameters
• pro_cd_cprev_n_ca_interres_torsion_params_ : core::scoring::methods::ResidueCartBondedParameters
• pro_CD_index() : core::scoring::methods::ResidueCartBondedParameters
• pro_CD_index_ : core::scoring::methods::ResidueCartBondedParameters
• pro_nv_ : core::scoring::methods::CartesianBondedEnergy
• prob() : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• prob_ : core::pack::dunbrack::BBDepNRChiSample< P > , core::pack::dunbrack::BBIndNRChiSample< P > , core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• prob_cutoff_ : protocols::antibody::design::AntibodySeqDesignTFCreator
• PROB_DELTA : core::pack::dunbrack::SingleResidueDunbrackLibrary
• prob_larger_current_ : protocols::toolbox::task_operations::SeqprofConsensusOperation
• prob_level_ : protocols::noesy_assign::PeakAssignmentParameters
• prob_profile_ : core::scoring::methods::ProQ_Energy
• prob_random_pert_current() : protocols::backrub::BackrubSidechainMover , protocols::simple_moves::sidechain_moves::SidechainMover
• prob_random_pert_to_current_ : protocols::simple_moves::sidechain_moves::SidechainMover
• prob_set_ : protocols::antibody::task_operations::AddCDRProfilesOperation , protocols::toolbox::task_operations::ResidueProbDesignOperation
• prob_sigmoid_m_ : protocols::noesy_assign::PeakAssignmentParameters
• prob_sigmoid_tau_ : protocols::noesy_assign::PeakAssignmentParameters
• prob_sigmoid_w_ : protocols::noesy_assign::PeakAssignmentParameters
• prob_sum_of_gaussians() : core::scoring::func::SOGFunc_Impl
• prob_table_ : protocols::docking::ConformerSwitchMover
• prob_terminus_ramapert_ : protocols::mpi_refinement::MPI_Refine_Master
• prob_to_accumulate() : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::rotamers::SingleResiduePeptoidLibrary
• prob_to_accumulate_buried() : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::rotamers::SingleResiduePeptoidLibrary
• prob_to_accumulate_buried_ : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::rotamers::SingleResiduePeptoidLibrary
• prob_to_accumulate_nonburied() : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::rotamers::SingleResiduePeptoidLibrary
• prob_to_accumulate_nonburied_ : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::rotamers::SingleResiduePeptoidLibrary
• prob_uniform() : protocols::backrub::BackrubSidechainMover , protocols::simple_moves::sidechain_moves::SidechainMover
• prob_uniform_ : protocols::simple_moves::sidechain_moves::SidechainMover
• prob_withinrot() : protocols::backrub::BackrubSidechainMover , protocols::simple_moves::sidechain_moves::SidechainMover
• prob_withinrot_ : protocols::simple_moves::sidechain_moves::SidechainMover
• probA() : core::scoring::packstat::PackingScore
• probA_ : core::scoring::packstat::PackingScore
• probabilistically_commit_relaxation() : core::pack::interaction_graph::FASTERInteractionGraph
• probabilities : core::scoring::carbohydrates::CHIDihedralSamplingData
• Probabilities : protocols::medal::MedalMover , protocols::nonlocal::BiasedFragmentMover
• probability : core::pack::dunbrack::ChiSet , core::pack::dunbrack::DunbrackRotamerSampleData , protocols::frag_picker::quota::ABEGO_SS_Config , protocols::noesy_assign::CrossPeak
• probability_ : core::pack::dunbrack::DunbrackRotamerSampleData , core::pack::dunbrack::ProbSortClass , protocols::make_rot_lib::RotData
• Probability_AA : core::scoring::P_AA
• Probability_AA_n : core::scoring::P_AA
• Probability_AA_n_n : protocols::simple_moves::StructProfileMover
• Probability_AA_pp : core::scoring::P_AA
• probability_limit() : protocols::match::upstream::BuildSet
• probability_matrix() : core::scoring::bin_transitions::BinTransitionData
• probability_matrix_ : core::scoring::bin_transitions::BinTransitionData
• probability_rigid_ : protocols::simple_moves::PeriodicBoxMover
• probability_row() : core::sequence::SequenceProfile
• probability_to_accumulate_while_building_rotamers() : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::rotamers::SingleResiduePeptoidLibrary
• probabilty_row() : core::sequence::SequenceProfile
• probB() : core::scoring::packstat::PackingScore
• probB_ : core::scoring::packstat::PackingScore
• Probe : protocols::hotspot_hashing::movers::PlaceProbeMover
• probe_atom_type_ : protocols::qsar::scoring_grid::SolvationGrid
• probe_rad_ : protocols::pockets::PocketGrid
• probe_radii : core::scoring::packstat::SasaOptions
• probe_radius() : protocols::match::BumpGrid , protocols::simple_filters::TaskAwareSASAFilter
• probe_radius_ : core::pack::interaction_graph::RotamerDots , core::pose::metrics::simple_calculators::SasaCalculatorLegacy , core::scoring::sasa::SasaCalc , core::scoring::sasa::SasaMethod , protocols::simple_filters::TaskAwareSASAFilter , protocols::toolbox::task_operations::SelectBySASAOperation
• probe_scorefxn_ : core::scoring::rna::data::RNA_DMS_Potential
• probe_specificity_ : protocols::dna::DnaInterfacePacker
• probes : core::scoring::sc::MolecularSurfaceCalculator
• problem_ : protocols::kinematic_closure::ClosureProblem::Memento , protocols::kinematic_closure::ClosureSolution
• probs_ : protocols::frag_picker::LAMBEGO_IO , protocols::frag_picker::TorsionBinIO , protocols::nonlocal::SingleFragmentMover
• proc_id_ : protocols::jobdist::BaseJobDistributor
• proceed() : protocols::mpi_refinement::Scheduler
• process_AA_SET_line() : protocols::pack_daemon::EntityFunc
• process_add_daemon_message() : protocols::pack_daemon::DaemonSet
• process_algorithm_info() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• process_continuous_design_string() : protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover
• process_data() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• process_decoy() : protocols::abinitio::AbrelaxApplication
• process_discard_entity_message() : protocols::pack_daemon::DaemonSet
• process_elements() : protocols::environment::EnvClaimBroker
• process_energy_change() : core::pose::metrics::PoseMetricContainer
• process_ENTITY_FUNCTION_line() : protocols::pack_daemon::DynamicAggregateFunction
• process_exception_from_job() : protocols::jd3::JobDistributor
• process_FITNESS_line() : protocols::pack_daemon::DynamicAggregateFunction
• process_fragments() : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• process_hit() : protocols::match::downstream::SecondaryMatcherToUpstreamResidue , protocols::match::downstream::SecondaryMatchUpstreamResProcessor , protocols::match::output::PoseInserter , protocols::match::output::UpstreamHitCacher , protocols::match::output::WriteUpstreamHitKinemage , protocols::match::upstream::UpstreamResidueProcessor
• process_inbound_wus() : protocols::loophash::MPI_LoopHashRefine_Emperor , protocols::loophash::MPI_LoopHashRefine_Master , protocols::mpi_refinement::MPI_Refine_Emperor , protocols::mpi_refinement::MPI_Refine_Master , protocols::wum::MPI_WorkUnitManager , protocols::wum::MPI_WorkUnitManager_Slave
• process_include_xml() : protocols::rosetta_scripts::RosettaScriptsParser
• process_includes() : protocols::rosetta_scripts::RosettaScriptsParser
• process_incoming_msgs() : protocols::wum::MPI_WorkUnitManager
• process_input_line_tokens() : protocols::toolbox::match_enzdes_util::ResInteractions
• process_insert_design_string() : protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover
• process_job_result() : protocols::jd3::JobDistributor
• process_match() : protocols::match::output::MatchConsolidator , protocols::match::output::MatchOutputter , protocols::match::output::MatchProcessor
• process_match_list() : protocols::canonical_sampling::AsyncMPITemperingBase
• process_matches() : protocols::match::Matcher
• process_matches_all_hit_combos_for_hit_subsets() : protocols::match::Matcher
• process_matches_main_loop_enumerating_all_hit_combos() : protocols::match::Matcher
• process_matches_where_one_geomcst_defines_downstream_location() : protocols::match::Matcher
• process_matching_exchange_requests() : protocols::canonical_sampling::AsyncMPITemperingBase
• process_message() : protocols::jd2::archive::MPIArchiveJobDistributor , protocols::jd2::MPIFileBufJobDistributor
• process_motifs() : protocols::simple_filters::SymmetricMotifFilter
• process_NPD_PROPERTY_line() : protocols::pack_daemon::DynamicAggregateFunction
• process_outbound_wus() : protocols::loophash::MPI_LoopHashRefine_Emperor , protocols::loophash::MPI_LoopHashRefine_Master , protocols::mpi_refinement::MPI_Refine_Emperor , protocols::mpi_refinement::MPI_Refine_Master , protocols::wum::MPI_WorkUnitManager , protocols::wum::MPI_WorkUnitManager_Slave
• process_pdb_header() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• process_permutation() : protocols::denovo_design::components::NamedMover , protocols::denovo_design::connection::Connection , protocols::denovo_design::connection::ExtendChain
• process_pose() : protocols::denovo_design::DisulfidizeMover , protocols::match::MatcherMover , protocols::rosetta_scripts::MultiplePoseMover
• process_POSE_ENERGY_line() : protocols::pack_daemon::DynamicAggregateFunction
• process_POSE_ENERGY_VECTOR_line() : protocols::pack_daemon::DynamicAggregateFunction
• process_pose_request_for_entity() : protocols::pack_daemon::DaemonSet
• process_poses() : protocols::rosetta_scripts::MultiplePoseMover
• process_rotamers() : protocols::optimize_weights::PNatAAOptEPositionData
• process_round() : protocols::mpi_refinement::MPI_Refine_Master
• process_SCALAR_EXPRESSION_line() : protocols::pack_daemon::DynamicAggregateFunction
• process_score() : protocols::optimize_weights::DDGBindOptEData , protocols::optimize_weights::DDGMutationOptEData , protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData , protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData , protocols::optimize_weights::PNatRotOptEPositionData , protocols::optimize_weights::PNatStructureOptEData
• process_SCORE_line() : protocols::pack_daemon::EntityFunc
• process_SET_CONDITION_line() : protocols::pack_daemon::EntityFunc
• process_state_energy_evaluations_for_entity() : protocols::pack_daemon::DaemonSet
• process_STATE_line() : protocols::pack_daemon::DynamicAggregateFunction
• process_STATE_VECTOR_line() : protocols::pack_daemon::DynamicAggregateFunction
• process_structure_change() : core::pose::metrics::PoseMetricContainer
• process_SUB_EXPRESSION_line() : protocols::pack_daemon::EntityFunc
• process_symmdef_file() : protocols::simple_moves::symmetry::SetupForSymmetryMover
• process_termination() : protocols::mpi_refinement::MPI_Refine_Emperor , protocols::mpi_refinement::MPI_Refine_Master
• process_termination_ : protocols::mpi_refinement::MPI_Refine_Emperor
• process_VECTOR_EXPRESSION_line() : protocols::pack_daemon::DynamicAggregateFunction
• process_VECTOR_VARIABLE_line() : protocols::pack_daemon::DynamicAggregateFunction
• ProcessorFactory() : protocols::match::output::ProcessorFactory
• ProClosureEnergy() : core::scoring::methods::ProClosureEnergy
• procorr_alt_conf_ : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• procorr_curr_conf_ : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• procorr_energies_ : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• procrastinated_ : core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::LazyNode
• prof_row() : core::sequence::SequenceProfile , protocols::frag_picker::LAMBEGO_IO , protocols::frag_picker::TorsionBinIO
• profile() : core::fragment::picking_old::vall::VallResidue , core::sequence::SequenceProfile , protocols::frag_picker::VallResidue
• profile_ : core::fragment::picking_old::vall::VallResidue , core::sequence::SequenceProfile , protocols::frag_picker::VallResidue
• profile_feature() : core::scoring::methods::ProQ_Energy
• profile_index_to_aa() : core::scoring::methods::ProQ_Energy
• profile_mapping() : core::scoring::constraints::SequenceProfileConstraint
• profile_picking_rounds_ : protocols::antibody::design::AntibodySeqDesignTFCreator
• profile_scoring_ : protocols::frag_picker::scores::ProfileScore
• profile_sets_task_ : protocols::antibody::task_operations::AddCDRProfilesOperation
• profile_struct() : protocols::frag_picker::VallResidue
• profile_struct_ : protocols::frag_picker::VallResidue
• profile_wgt_ : protocols::simple_moves::SequenceProfileMover
• ProfilerMover() : protocols::moves::ProfilerMover
• ProfileScore() : protocols::frag_picker::scores::ProfileScore
• ProfileScoreBlosum62() : protocols::frag_picker::scores::ProfileScoreBlosum62
• ProfileScoreDistWeight() : protocols::frag_picker::scores::ProfileScoreDistWeight
• ProfileScoreL1() : protocols::frag_picker::scores::ProfileScoreL1
• ProfileScoreStructL1() : protocols::frag_picker::scores::ProfileScoreStructL1
• ProfileScoreSubMatrix() : protocols::frag_picker::scores::ProfileScoreSubMatrix
• ProfSimScoringScheme() : core::sequence::ProfSimScoringScheme
• progress_ : protocols::canonical_sampling::ProgressBarObserver
• progress_file() : protocols::simple_moves::GenericMonteCarloMover
• progress_file_ : protocols::simple_moves::GenericMonteCarloMover
• progress_through_sBR_ : core::pack::annealer::FASTERAnnealer
• ProgressBarObserver() : protocols::canonical_sampling::ProgressBarObserver
• prohibit_property_i() : core::scoring::bin_transitions::BinTransitionData
• prohibit_property_iplus1() : core::scoring::bin_transitions::BinTransitionData
• prohibit_res_identity_i() : core::scoring::bin_transitions::BinTransitionData
• prohibit_res_identity_iplus1() : core::scoring::bin_transitions::BinTransitionData
• prohibit_single_residue_loops() : protocols::loops::LoopFromFileData , protocols::loops::LoopsFileOptions
• prohibit_single_residue_loops_ : protocols::loops::LoopFromFileData , protocols::loops::LoopsFileOptions
• prohibited_properties_i_ : core::scoring::bin_transitions::BinTransitionData
• prohibited_properties_iplus1_ : core::scoring::bin_transitions::BinTransitionData
• prohibited_res_identities_i_ : core::scoring::bin_transitions::BinTransitionData
• prohibited_res_identities_iplus1_ : core::scoring::bin_transitions::BinTransitionData
• prohibited_types_ : core::chemical::ResidueTypeSetCache
• project_deltaE_for_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 , protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph , protocols::flexpack::interaction_graph::MinimalistFlexbbNode
• project_deltaE_for_substitution_surface() : core::pack::interaction_graph::SurfaceNode< V, E, G >
• project_point_to_3d() : protocols::match::OccupiedSpaceHash
• project_pref_max_cpu_run_time_ : protocols::boinc::Boinc
• project_pref_max_gfx_cpu_ : protocols::boinc::Boinc
• project_pref_max_gfx_fps_ : protocols::boinc::Boinc
• project_surface_deltaE() : core::pack::interaction_graph::SurfaceNode< V, E, G >
• project_surface_deltaE_for_substitution() : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >
• ProjectionVector : protocols::evaluation::PCA
• proline_corrections_ : core::pack::interaction_graph::OnTheFlyEdge , core::pack::interaction_graph::SymmOnTheFlyEdge
• ProlineFixMover() : protocols::simple_moves::ProlineFixMover
• ProlinePhiScore() : protocols::frag_picker::scores::ProlinePhiScore
• promote_sameresidue_nonjump_child() : core::kinematics::AtomTree
• propagate_best_from_previous_generation() : protocols::genetic_algorithm::GeneticAlgorithmBase
• propeller() : protocols::dna::DNABasepair
• propeller_ : protocols::dna::DNABasepair
• properties() : core::chemical::Atom
• Properties : core::chemical::Element , core::chemical::gasteiger::GasteigerAtomTypeData
• properties() : core::chemical::ResidueType , core::chemical::ResidueTypeFinder
• properties_ : core::chemical::Atom , core::chemical::Element , core::chemical::gasteiger::GasteigerAtomTypeData , core::chemical::ResidueType , core::chemical::ResidueTypeFinder , core::chemical::Selector_PROPERTY
• properties_i_ : core::scoring::bin_transitions::BinTransitionData
• properties_iplus1_ : core::scoring::bin_transitions::BinTransitionData
• properties_match_this() : core::scoring::aa_composition_energy::AACompositionPropertiesSet
• property() : core::pack::task::operation::ResidueHasProperty , core::pack::task::operation::ResiduePDBInfoHasLabel
• property_ : core::chemical::AddProperty , core::chemical::DeleteProperty , core::pack::task::operation::ResidueHasProperty , core::pack::task::operation::ResiduePDBInfoHasLabel
• property_deviation_ranges_ : core::scoring::aa_composition_energy::AACompositionEnergySetup
• property_from_string() : core::chemical::AtomPropertiesManager
• property_penalties_ : core::scoring::aa_composition_energy::AACompositionEnergySetup
• property_penalty() : core::scoring::aa_composition_energy::AACompositionEnergySetup
• property_set_indices_matching_residue() : core::scoring::aa_composition_energy::AACompositionEnergySetup
• property_sets_ : core::scoring::aa_composition_energy::AACompositionEnergySetup
• property_tailfunctions_ : core::scoring::aa_composition_energy::AACompositionEnergySetup
• property_to_string_map() : core::chemical::AtomPropertiesManager
• property_to_string_map_ : core::chemical::AtomPropertiesManager
• proposal_density() : protocols::simple_moves::sidechain_moves::SidechainMover
• proposal_density_ratio() : protocols::stepwise::monte_carlo::mover::StepWiseMasterMover
• proposal_density_ratio_ : protocols::stepwise::monte_carlo::mover::StepWiseMasterMover
• proposal_hists_ : protocols::backrub::BackrubSidechainMover
• proposal_probabilities_ : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• proposal_probability() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• proposed_energy_ : core::pack::interaction_graph::SimpleEdge
• proposed_one_body_energy() : core::pack::interaction_graph::SimpleNode
• proposed_since_last_batch() : protocols::jd2::archive::ArchiveBase
• proposed_since_last_batch_ : protocols::jd2::archive::ArchiveBase
• ProQ_Energy() : core::scoring::methods::ProQ_Energy
• ProQ_potential_ : core::scoring::ScoringManager
• ProQPotential() : core::scoring::ProQPotential
• ProtectedConformation() : protocols::environment::ProtectedConformation
• PROTEIN : protocols::pockets::ComparisonGrid , protocols::pockets::ElectrostaticpotentialGrid , protocols::pockets::PocketGrid
• protein_ : protocols::membrane::MPMutateRelaxMover
• protein_atom : protocols::ligand_docking::rdf::AtomPairData
• protein_atom_charge : protocols::ligand_docking::rdf::AtomPairData
• protein_atom_coords : protocols::ligand_docking::rdf::AtomPairData
• protein_atom_id : protocols::ligand_docking::rdf::AtomPairData
• protein_atom_type : protocols::ligand_docking::rdf::AtomPairData
• protein_atr_rep_screening_pose_ : protocols::stepwise::modeler::StepWiseConnectionSampler
• protein_CA_stddev_Ang_ : protocols::ligand_docking::LigandDockProtocol
• protein_calculate() : protocols::scoring::Interface
• protein_ccd_closer_ : protocols::stepwise::modeler::StepWiseMinimizer
• protein_ccd_closers_ : protocols::stepwise::modeler::StepWiseConnectionSampler
• protein_ccd_poses_ : protocols::stepwise::modeler::StepWiseConnectionSampler
• protein_connection_ : protocols::stepwise::modeler::StepWiseConnectionSampler
• protein_cutpoints_closed_ : protocols::stepwise::modeler::StepWiseConnectionSampler
• protein_dielectric() : core::scoring::methods::EnergyMethodOptions
• protein_dielectric_ : core::scoring::methods::EnergyMethodOptions
• protein_dna_motif() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• protein_DNA_motif_build_positions_JA() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• protein_DNA_motif_target_positions_JA() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• protein_gaussian_variance_per_residue_ : core::scoring::loop_graph::LoopGraph
• protein_interface_design() : protocols::toolbox::task_operations::SeqprofConsensusOperation
• protein_interface_design_ : protocols::toolbox::task_operations::SeqprofConsensusOperation
• protein_neighbors() : protocols::dna::DnaInterfaceFinder
• protein_neighbors_ : protocols::dna::DnaInterfaceFinder
• protein_position_equal_within() : core::scoring::methods::PoissonBoltzmannEnergy
• protein_positions() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• protein_positions_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• protein_prepack() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• protein_prepack_ : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• protein_protein_rdf() : protocols::ligand_docking::ComputeLigandRDF
• protein_residue_conformation_features_ : protocols::features::ProteinSilentReport
• protein_scan() : protocols::dna::DnaInterfacePacker
• protein_scan_ : protocols::dna::DnaInterfacePacker
• protein_silent_report_ : protocols::features::DatabaseJobInputter , protocols::features::DatabaseJobOutputter
• ProteinAtrRepChecker() : protocols::stepwise::modeler::protein::checker::ProteinAtrRepChecker
• ProteinAtrRepScreener() : protocols::stepwise::legacy::screener::ProteinAtrRepScreener
• ProteinBackboneAtomAtomPairFeatures() : protocols::features::ProteinBackboneAtomAtomPairFeatures
• ProteinBackboneAtomAtomPairFeaturesCreator() : protocols::features::ProteinBackboneAtomAtomPairFeaturesCreator
• ProteinBackboneBuildPoint() : protocols::match::upstream::ProteinBackboneBuildPoint
• ProteinBackboneTorsionAngleFeatures() : protocols::features::ProteinBackboneTorsionAngleFeatures
• ProteinBackboneTorsionAngleFeaturesCreator() : protocols::features::ProteinBackboneTorsionAngleFeaturesCreator
• ProteinBetaAntiParallelStepWiseSampler() : protocols::stepwise::sampler::protein::ProteinBetaAntiParallelStepWiseSampler
• ProteinBondGeometryFeatures() : protocols::features::ProteinBondGeometryFeatures
• ProteinBondGeometryFeaturesCreator() : protocols::features::ProteinBondGeometryFeaturesCreator
• ProteinCCD_ClosureScreener() : protocols::stepwise::screener::ProteinCCD_ClosureScreener
• ProteinCore() : protocols::toolbox::task_operations::ProteinCore
• ProteinFragmentStepWiseSampler() : protocols::stepwise::sampler::protein::ProteinFragmentStepWiseSampler
• ProteinInterfaceDesignOperation() : protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• ProteinInterfaceMultiStateDesignMover() : protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• ProteinLigandInterfaceUpweighter() : protocols::enzdes::ProteinLigandInterfaceUpweighter
• ProteinMainChainStepWiseSampler() : protocols::stepwise::sampler::protein::ProteinMainChainStepWiseSampler
• ProteinResidueConformationFeatures() : protocols::features::ProteinResidueConformationFeatures
• ProteinResidueConformationFeaturesCreator() : protocols::features::ProteinResidueConformationFeaturesCreator
• ProteinRMSDFeatures() : protocols::features::ProteinRMSDFeatures
• ProteinRMSDFeaturesCreator() : protocols::features::ProteinRMSDFeaturesCreator
• ProteinRMSDNoSuperpositionFeatures() : protocols::features::ProteinRMSDNoSuperpositionFeatures
• ProteinRMSDNoSuperpositionFeaturesCreator() : protocols::features::ProteinRMSDNoSuperpositionFeaturesCreator
• ProteinSilentReport() : protocols::features::ProteinSilentReport
• ProteinSilentStruct_SinglePrecCreator() : core::io::silent::ProteinSilentStruct_SinglePrecCreator
• ProteinSilentStruct_Template() : core::io::silent::ProteinSilentStruct_Template< T >
• ProteinSilentStructCreator() : core::io::silent::ProteinSilentStructCreator
• ProteinUpstreamBuilder() : protocols::match::upstream::ProteinUpstreamBuilder
• Protocol() : protocols::abinitio::Protocol
• protocol_ : protocols::features::RotamerRecoveryFeatures , protocols::ligand_docking::LigandDockProtocol , protocols::loop_modeling::LoopProtocol , protocols::protein_interface_design::movers::LoopMoverFromCommandLine , protocols::protein_interface_design::movers::LoopRemodel , protocols::rotamer_recovery::RotamerRecovery
• protocol_features_ : protocols::features::ProteinSilentReport , protocols::features::ReportToDB
• protocol_id_ : protocols::features::ProteinSilentReport , protocols::features::ReportToDB
• protocol_name_ : protocols::rotamer_recovery::RRReporterHuman , protocols::rotamer_recovery::RRReporterSQLite
• protocol_params_ : protocols::rotamer_recovery::RRReporterHuman , protocols::rotamer_recovery::RRReporterSQLite
• protocol_types_ : protocols::rotamer_recovery::RotamerRecoveryFactory
• ProtocolFeatures() : protocols::features::ProtocolFeatures
• protocols::jd2::JobDistributor : protocols::jd2::InnerJob
• protocols::jd2::JobDistributorFactory : protocols::jd2::archive::MPIArchiveJobDistributor
• protocols::jd2::JobInputter : protocols::jd2::InnerJob
• protocols::jd2::Parser : protocols::jd2::InnerJob
• proton() : protocols::noesy_assign::CrossPeak
• proton1_ : protocols::noesy_assign::CrossPeak
• proton2_ : protocols::noesy_assign::CrossPeak
• proton_atom_name_ : protocols::noesy_assign::CrossPeakInfo
• proton_chi_2_chi() : core::chemical::ResidueType
• proton_chi_extra_samples() : core::chemical::ResidueType
• proton_chi_extra_samples_ : core::chemical::ResidueType
• proton_chi_samples() : core::chemical::ResidueType
• proton_chi_samples_ : core::chemical::ResidueType
• proton_chis_ : core::chemical::ResidueType
• proton_index() : protocols::noesy_assign::MethylNames
• proton_tolerance() : protocols::noesy_assign::CrossPeakInfo
• proton_tolerance_ : protocols::noesy_assign::CrossPeakInfo
• protonated_H1_adenosine_list() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• protonated_H1_adenosine_list_ : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• ProtonResonance() : protocols::noesy_assign::ProtonResonance
• protons_ : protocols::simple_filters::AtomicContactFilter
• provide_selector_xsd() : core::pack::task::residue_selector::ClashBasedRepackShellSelector , core::pack::task::residue_selector::ClashBasedRepackShellSelectorCreator , core::select::residue_selector::AndResidueSelector , core::select::residue_selector::AndResidueSelectorCreator , core::select::residue_selector::ChainSelector , core::select::residue_selector::ChainSelectorCreator , core::select::residue_selector::InterGroupInterfaceByVectorSelector , core::select::residue_selector::InterGroupInterfaceByVectorSelectorCreator , core::select::residue_selector::JumpDownstreamSelector , core::select::residue_selector::JumpDownstreamSelectorCreator , core::select::residue_selector::JumpUpstreamSelector , core::select::residue_selector::JumpUpstreamSelectorCreator , core::select::residue_selector::LayerSelector , core::select::residue_selector::LayerSelectorCreator , core::select::residue_selector::NeighborhoodResidueSelector , core::select::residue_selector::NeighborhoodResidueSelectorCreator , core::select::residue_selector::NotResidueSelector , core::select::residue_selector::NotResidueSelectorCreator , core::select::residue_selector::NumNeighborsSelector , core::select::residue_selector::NumNeighborsSelectorCreator , core::select::residue_selector::OrResidueSelector , core::select::residue_selector::OrResidueSelectorCreator , core::select::residue_selector::PhiSelector , core::select::residue_selector::PhiSelectorCreator , core::select::residue_selector::PrimarySequenceNeighborhoodSelectorCreator , core::select::residue_selector::ResidueIndexSelector , core::select::residue_selector::ResidueIndexSelectorCreator , core::select::residue_selector::ResidueNameSelectorCreator , core::select::residue_selector::ResiduePDBInfoHasLabelSelector , core::select::residue_selector::ResiduePDBInfoHasLabelSelectorCreator , core::select::residue_selector::ResidueSelectorCreator , core::select::residue_selector::SecondaryStructureSelector , core::select::residue_selector::SecondaryStructureSelectorCreator , core::select::residue_selector::TrueResidueSelector , core::select::residue_selector::TrueResidueSelectorCreator , protocols::residue_selectors::TaskSelector , protocols::residue_selectors::TaskSelectorCreator
• provide_stored_derivatives() : core::optimization::ArmijoLineMinimization , core::optimization::LineMinimizationAlgorithm , core::optimization::StrongWolfeLineMinimization
• prsa_feature() : core::scoring::methods::ProQ_Energy
• prune_cavity_burial_probe_radii : core::scoring::packstat::SasaOptions
• prune_extra_atoms() : protocols::generalized_kinematic_closure::GeneralizedKIC
• prune_max_delta : core::scoring::packstat::SasaOptions
• prune_max_iters : core::scoring::packstat::SasaOptions
• prune_small_bins() : core::scoring::motif::XformScore
• prune_symmetric_disulfides() : protocols::denovo_design::DisulfidizeMover
• prv_eqxyz_ : protocols::md::MDBase
• pSer2Asp_centroid : protocols::flexpep_docking::FlexPepDockingFlags
• pSer2Glu_centroid : protocols::flexpep_docking::FlexPepDockingFlags
• pseudo_bonds_ : core::conformation::PseudoBondCollection
• PSEUDO_PROTEIN : protocols::pockets::ElectrostaticpotentialGrid
• PseudoBond() : core::conformation::PseudoBond
• PseudoBondCollection() : core::conformation::PseudoBondCollection
• pseudobonds() : core::conformation::Residue
• pseudobonds_ : core::conformation::Residue
• PSEUDOCONTACT_SHIFT_DATA : core::pose::datacache::CacheableDataType
• PSEUDOCONTACT_SHIFT_MULTI_DATA : core::pose::datacache::CacheableDataType
• PseudocontactShiftEnergyController() : protocols::topology_broker::PseudocontactShiftEnergyController
• PseudocontactShiftEnergyController_Ts1() : protocols::topology_broker::PseudocontactShiftEnergyController_Ts1
• PseudocontactShiftEnergyController_Ts2() : protocols::topology_broker::PseudocontactShiftEnergyController_Ts2
• PseudocontactShiftEnergyController_Ts3() : protocols::topology_broker::PseudocontactShiftEnergyController_Ts3
• PseudocontactShiftEnergyController_Ts4() : protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• pseudorotation() : protocols::dna::DNABase
• pseudorotation_ : protocols::dna::DNABase
• psi() : core::fragment::picking_old::vall::VallResidue , core::fragment::torsions , core::io::raw_data::DecoyStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::pose::Pose , core::scoring::motif::Xfres , protocols::frag_picker::PhiPsiTalosIO
• Psi() : protocols::frag_picker::scores::Psi
• psi() : protocols::frag_picker::VallResidue , protocols::frags::RMSVallData , protocols::frags::VallData , protocols::jumping::DisulfTemplate , protocols::jumping::PairingTemplate , protocols::kinematic_closure::ClosureProblem , protocols::loophash::BackboneSegment , protocols::match::upstream::ProteinBackboneBuildPoint , protocols::optimize_weights::PNatRotOptEPositionData , protocols::pockets::spherical_coor_triplet , protocols::pockets::triplet_and_originnum , protocols::stepwise::modeler::protein::MainChainTorsionSet
• psi_ : core::fragment::picking_old::vall::VallResidue , core::io::raw_data::DecoyStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::scoring::motif::Xfres , protocols::frag_picker::DiversifyDihedralsSelector , protocols::frag_picker::VallResidue , protocols::frags::RMSVallData , protocols::frags::VallData , protocols::loophash::BackboneSegment , protocols::match::upstream::ProteinBackboneBuildPoint , protocols::membrane::benchmark::MakeCanonicalHelix , protocols::optimize_weights::PNatRotOptEPositionData , protocols::pose_length_moves::InsertResMover , protocols::stepwise::modeler::protein::MainChainTorsionSet
• psi_angle_ : protocols::rigid::RigidBodyRandomizeMover , protocols::simple_moves::a3b_hbs::A3BHbsMover , protocols::simple_moves::oop::OopMover , protocols::simple_moves::triazolamer::TriazolamerMover
• PSI_BINRANGE : core::pack::rotamers::RotamericSingleResiduePeptoidLibrary< T, N >
• psi_index() : core::scoring::OmegaTether
• psi_max() : core::sequence::ABEGO
• psi_max_ : core::sequence::ABEGO
• psi_min() : core::sequence::ABEGO
• psi_min_ : core::sequence::ABEGO
• psi_offsets_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger
• psi_sampler_mover_ : protocols::carbohydrates::LinkageConformerMover
• psipred2_confidence : core::io::external::PsiPredResult
• psipred_interface_ : protocols::denovo_design::filters::SSPredictionFilter , protocols::frag_picker::frag_movers::FragSetFromH5Mover
• psipred_output_ : core::io::external::PsiPredInterface
• psipred_prob : core::io::external::PsiPredResult
• PsiPredInterface() : core::io::external::PsiPredInterface
• PsiPredResult() : core::io::external::PsiPredResult
• psis : protocols::antibody::clusters::ClusterData
• PSP : protocols::pockets::ComparisonGrid , protocols::pockets::PocketGrid
• PSSM2BfactorMover() : protocols::simple_moves::PSSM2BfactorMover
• pssm_ : protocols::protein_interface_design::movers::InterfaceRecapitulationMover , protocols::protein_interface_design::ReportPSSMDifferences
• pssm_data_ : protocols::optimize_weights::IterativeOptEDriver , protocols::protein_interface_design::ReportPSSMDifferences
• pssm_energy_at_frame_seqpos() : core::scoring::methods::NMerPSSMEnergy
• pssm_probabilities_ : protocols::optimize_weights::PSSMOptEPositionData
• PSSMOptEPositionData() : protocols::optimize_weights::PSSMOptEPositionData
• PSURFACE : protocols::pockets::ComparisonGrid , protocols::pockets::PocketGrid
• ptask() : protocols::multistate_design::PackingState
• ptask_ : protocols::enzdes::RepackLigandSiteWithoutLigandMover , protocols::simple_moves::ConsensusDesignMover
• ptask_p_ : protocols::multistate_design::PackingState
• pts_ : core::scoring::SecondaryStructurePotential , protocols::cluster::APCluster
• PtType : protocols::pockets::ComparisonGrid , protocols::pockets::ElectrostaticpotentialGrid , protocols::pockets::PocketGrid
• public_array_to_private_data() : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• pucker() : protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler
• pucker_flip_rate_ : protocols::stepwise::sampler::rna::RNA_MC_Suite
• pucker_state() : protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler
• pucker_state_ : protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler , protocols::stepwise::sampler::rna::RNA_KIC_Sampler , protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler
• pucker_states_ : protocols::stepwise::sampler::rna::RNA_NucleosideStepWiseSampler , protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler
• pucker_states_lower_ : protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler
• pucker_states_upper_ : protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler
• pulldomain() : protocols::hybridization::DDomainParse
• PURE_TOPO_RESAMPLING : protocols::abinitio::IterativeBase
• purge_similar_jobs_which_have_bad_inputs() : protocols::jd3::JobDistributor
• push() : protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering > , protocols::frag_picker::quota::ABEGO_SS_Pool , protocols::frag_picker::quota::QuotaPool , protocols::frag_picker::quota::SecondaryStructurePool
• push_back() : core::conformation::PseudoBondCollection , core::graph::EdgeList , core::id::SequenceMapping , core::io::silent::SilentFileData , core::pack::task::TaskFactory , core::pose::copydofs::CopyDofsInfo , core::scoring::dssp::StrandPairingSet , core::scoring::motif::MotifHits , protocols::analysis::PeptideDeriverOutputterContainer , protocols::cluster::Cluster , protocols::cluster::GatherPosesMover , protocols::coarse_rna::SourcePositions , protocols::fldsgn::topology::BetaAlphaBetaMotifSet , protocols::fldsgn::topology::HelixPairingSet , protocols::fldsgn::topology::HSSTripletSet , protocols::fldsgn::topology::SheetSet , protocols::fldsgn::topology::StrandPairingSet , protocols::frag_picker::VallChunk , protocols::frag_picker::VallProvider , protocols::jd2::JobsContainer , protocols::loops::Loops , protocols::loops::LoopsFileData , protocols::moves::MonteCarlo , protocols::toolbox::DecoySetEvaluation , protocols::wum::WorkUnitQueue
• push_back_and_finalize() : protocols::fldsgn::topology::StrandPairingSet
• push_back_CA_xyz() : protocols::toolbox::DecoySetEvaluation
• push_back_CA_xyz_from_silent_file() : protocols::toolbox::DecoySetEvaluation
• push_back_raw() : core::scoring::motif::MotifHits
• push_back_rotamer() : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• push_back_rotamers() : core::pack::rotamer_set::RotamerSet_
• push_chain_residue_indices() : protocols::analysis::PeptideDeriverFilter
• push_front() : core::graph::EdgeList , protocols::cluster::Cluster , protocols::wum::WorkUnitQueue
• push_passport() : core::conformation::Conformation , protocols::environment::ClientMover , protocols::environment::ProtectedConformation
• push_the_limits() : protocols::frag_picker::quota::QuotaSelector
• push_the_limits_to_the_winner() : protocols::frag_picker::quota::QuotaSelector
• put_constraints_on_base_step() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• put_in_cutpoints() : protocols::stepwise::monte_carlo::mover::TransientCutpointHandler
• put_intra_into_total() : core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::hbonds::HBondOptions , core::scoring::methods::EnergyMethodOptions
• put_intra_into_total_ : core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::hbonds::HBondOptions , core::scoring::methods::EnergyMethodOptions
• put_jump_stub_intra_residue : protocols::environment::EnvClaimBroker::BrokeredJumpData
• put_jump_stubs_intra_residue() : core::kinematics::FoldTree
• put_lock_on_silent_file() : protocols::stepwise::setup::StepWiseCSA_JobDistributor
• PValuedFragmentScoreManager() : protocols::frag_picker::scores::PValuedFragmentScoreManager
• Px : core::chemical::gasteiger::GasteigerAtomTypeData
• Py : core::chemical::gasteiger::GasteigerAtomTypeData
• PyEnergyMethodRegistrator() : core::scoring::methods::PyEnergyMethodRegistrator
• pymol() : protocols::moves::PyMolObserver
• pymol_ : protocols::moves::PyMolObserver , protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• pymol_movie_ : protocols::carbohydrates::GlycanRelaxMover
• pymol_name() : protocols::moves::PyMolMover
• pymol_name_ : protocols::moves::PyMolMover
• PYMOL_OBSERVER : core::pose::datacache::CacheableObserverType
• pymol_sel_hbond_unsat : protocols::analysis::InterfaceData
• pymol_sel_interface : protocols::analysis::InterfaceData
• pymol_sel_packing : protocols::analysis::InterfaceData
• PyMolMover() : protocols::moves::PyMolMover
• PyMolObserver() : protocols::moves::PyMolObserver
• pythag() : core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl
• Pz : core::chemical::gasteiger::GasteigerAtomTypeData