- p -

• p : protocols::environment::claims::CutBiasElement , protocols::environment::claims::CutElement , protocols::forge::build::CountFromLeft , protocols::sic_dock::Rose
• p1 : protocols::environment::claims::JumpElement
• p2 : protocols::environment::claims::JumpElement
• p_cond_ : protocols::moves::WhileMover
• 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_input_ : protocols::analysis::InterfaceAnalyzerMover
• pack_interface_repack_ : protocols::symmetric_docking::SymDockingHiRes
• pack_o2prime_hydrogens_ : protocols::stepwise::modeler::packer::StepWisePacker
• pack_operations_ : protocols::docking::DockingEnsemble , protocols::docking::DockingEnsemblePrepackProtocol , protocols::docking::DockingPrepackProtocol
• pack_region_ala_pose_ : protocols::enzdes::EnzdesFlexBBProtocol
• pack_rotamers_ : protocols::abinitio::ClassicAbinitio
• pack_rotamers_fullatom_ : protocols::surface_docking::SurfaceDockingProtocol
• pack_rottrial_ : protocols::relax::ClassicRelax , protocols::symmetric_docking::SymDockingHiRes
• 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_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
• packable_ : protocols::protein_interface_design::filters::DesignableResiduesFilter , protocols::simple_filters::MutationsFilter , protocols::simple_filters::ResidueCountFilter
• packed_residues_ : protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• packer_ : protocols::antibody_legacy::GraftMover , protocols::stepwise::modeler::packer::StepWiseMasterPacker
• packer_pose_ : protocols::stepwise::modeler::packer::StepWiseMasterPacker
• packer_task_ : protocols::simple_moves::CoupledMover
• packing_angle_numbering_ : protocols::antibody::AntibodyInfo
• packing_angle_residues_ : protocols::antibody::AntibodyInfo
• packing_angle_to_enum_ : protocols::antibody::AntibodyEnumManager
• packing_angle_to_string_ : protocols::antibody::AntibodyEnumManager
• packing_isolated_to_active_loops_ : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• packing_shell_ : protocols::simple_filters::RelativePoseFilter
• packonly_after_graft_ : protocols::antibody::AntibodyModelerProtocol , protocols::antibody::GraftCDRLoopsProtocol
• packstat : protocols::analysis::InterfaceData
• packstat_pdb_ : protocols::analysis::PackStatMover
• packtask_ : protocols::seeded_abinitio::SeedSetupMover
• pair_dis_ : protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD
• pair_list_ : protocols::scoring::Interface
• pair_permit_overlap_ : protocols::match::BumpGrid
• pair_vector_ : protocols::toolbox::task_operations::RestrictInterGroupVectorOperation
• paired_ : protocols::dna::DnaPosition
• pairing_dists_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• pairings_ : 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 , protocols::hybridization::HybridizeSetup
• pairings_size_ : protocols::jumping::MembraneJump
• parallel_ : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator
• param1 : protocols::relax::RelaxScriptCommand
• param2 : protocols::relax::RelaxScriptCommand
• param3 : protocols::relax::RelaxScriptCommand
• param4 : protocols::relax::RelaxScriptCommand
• param_cache_ : protocols::toolbox::match_enzdes_util::EnzdesCstCache
• param_index_ : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• param_type_ : protocols::simple_filters::RepeatParameterFilter
• parameter_tag_ : protocols::qsar::scoring_grid::LigandPropertyScore
• parameters_index_ : protocols::helical_bundle::PerturbBundleHelix
• parameters_set_index_ : protocols::helical_bundle::PerturbBundleHelix
• params_ : protocols::mpi_refinement::Scheduler
• params_file : protocols::flexpep_docking::FlexPepDockingFlags
• paratope : protocols::antibody::ParatopeMetric< T >
• paratope_cdrs_ : protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover , protocols::antibody::design::AntibodyDesignMover , protocols::antibody::design::AntibodyGraftDesignMover , protocols::antibody::design::AntibodySeqDesignMover
• paratope_charge_ : protocols::antibody::AntibodyFeatures
• paratope_cst_mover_ : protocols::antibody::design::AntibodyGraftDesignMover , protocols::antibody::design::AntibodySeqDesignMover
• paratope_epitope_cst_mover_ : protocols::antibody::design::AntibodyGraftDesignMover , protocols::antibody::design::AntibodySeqDesignMover
• paratope_heavy : protocols::antibody::ParatopeMetric< T >
• paratope_light : protocols::antibody::ParatopeMetric< T >
• paratope_residues_ : protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover , protocols::antibody::constraints::ParatopeSiteConstraintMover
• paratope_sasa_ : protocols::antibody::AntibodyFeatures
• parent : protocols::pockets::SmallMol
• parent_entities_ : protocols::genetic_algorithm::GeneticAlgorithmBase
• parent_name_ : protocols::loop_modeling::LoopMover
• parent_node_ : protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase
• parent_tags_map_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• parin_favorite_output_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• parse_error_ : protocols::metal_interface::ZincSiteFinder
• parsed_json_ : protocols::rpc::JSON_RPC
• parsed_string_for_resfile : protocols::forge::remodel::RemodelData
• parser_ : protocols::jd2::JobDistributor
• partition_ : protocols::hotspot_hashing::PartitionedSearchPattern
• partition_definition_ : protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::stepwise::modeler::rna::o2prime::O2PrimePacker , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• partner1_ : protocols::contact_map::Contact
• partner2_ : protocols::contact_map::Contact
• partner_ : protocols::docking::DockingEnsemble , protocols::farna::MultipleDomainMover , protocols::rigid::RigidBodyPerturbMover , protocols::rigid::RigidBodyRandomizeMover , protocols::scoring::Interface
• partner_ids_ : protocols::noesy_assign::FloatingResonance
• partners_ : protocols::dna::DNAParameters , protocols::docking::DockingHighRes , protocols::docking::DockingProtocol , protocols::docking::DockSetupMover , protocols::docking::EllipsoidalRandomizationMover , protocols::docking::TemperedDocking , protocols::protein_interface_design::filters::HbondsToAtomFilter , protocols::protein_interface_design::filters::HbondsToResidueFilter
• pass_ : protocols::environment::DofUnlock
• pass_base_centroid_screen : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• pass_count_ : protocols::stepwise::screener::NativeRMSD_Screener
• pass_screen_struct_pair_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• 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
• passports_ : protocols::environment::ClientMover
• patch_scores_ : protocols::toolbox::pose_metric_calculators::HPatchCalculator
• patchdock_entry_num_ : protocols::protein_interface_design::PatchdockReader
• patchdock_fname_ : protocols::protein_interface_design::PatchdockReader
• path : protocols::hybridization::TMalign
• path_ : protocols::jd2::FileSystemJobDistributor , protocols::jd2::PDBJobOutputter , protocols::motifs::Motif
• path_tightness_ : protocols::simple_filters::AveragePathLengthFilter
• pattern_ : protocols::hotspot_hashing::AddSearchPatternRotSetOp
• pb_cached_data_ : protocols::simple_moves::ddG
• pb_enabled_ : protocols::simple_filters::DdgFilter , protocols::simple_moves::ddG
• 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
• 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_all_ : protocols::scoring::methods::pcs2::PcsDataCenterManager , protocols::scoring::methods::pcs2::PcsDataCenterManagerSingleton
• 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_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_e_p_all_ : protocols::scoring::methods::pcs2::PcsEnergyParameterManager
• 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_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_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
• PcsInputCenter_all_ : protocols::scoring::methods::pcs2::PcsInputCenterManager
• PcsInputFile_all_ : protocols::scoring::methods::pcs2::PcsInputCenter
• PcsInputLine_all_ : protocols::scoring::methods::pcs2::PcsInputFile
• pcut_ : protocols::hybridization::DDomainParse , protocols::hybridization::HybridizeProtocol , protocols::hybridization::HybridizeSetup
• pd_reader_ : protocols::protein_interface_design::movers::PatchdockTransform
• pdb : protocols::antibody::CDRPose
• 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_insertion_code_ : protocols::antibody::clusters::CDRCluster
• pdb_file_names_ : protocols::pmut_scan::PointMutScanDriver
• pdb_filenames_ : protocols::docking::DockingEnsemble
• pdb_hash_ : protocols::frag_picker::PdbIdChunkFilter
• pdb_id : protocols::loophash::BBExtraData
• pdb_name_ : protocols::pack_daemon::StructureFileNames
• 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_pose_map_ : protocols::pack_daemon::EntityCorrespondence
• pdb_prefix_ : protocols::helical_bundle::BundleGridSampler
• pdb_resnum_ : protocols::pmut_scan::MutationData
• 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::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
• PDBfileName : protocols::sparta::PDB
• pdbListName : protocols::sparta::Sparta::SpartaLib
• pdbname_ : protocols::dna::DnaInterfacePacker , protocols::metal_interface::AddZincSiteConstraints , protocols::simple_filters::SSMotifFinder
• pdbno_ : protocols::pockets::PocketGrid
• pdboutput_ : protocols::dna::DnaInterfacePacker , protocols::motifs::MotifDnaPacker
• pdbpos : protocols::dna::DnaDesignDef
• pdbs_this_round_ : protocols::optimize_weights::IterativeOptEDriver
• pdf_ : protocols::nonlocal::BiasedFragmentMover
• peak_id_ : protocols::noesy_assign::CrossPeak
• peak_violation_counts_ : protocols::noesy_assign::DistanceScoreMover
• peaks_ : protocols::noesy_assign::CrossPeakList , protocols::noesy_assign::PeakCalibrator
• PENALTY : protocols::frag_picker::scores::ProlinePhiScore , protocols::frag_picker::scores::SecondaryIdentity , protocols::frag_picker::scores::SequenceIdentity
• penalty_ : protocols::simple_moves::FavorSymmetricSequence
• penalty_factor_ : protocols::simple_filters::ResidueIEFilter
• penalty_res_ : protocols::rbsegment_relax::SequenceShiftMover
• pending_notifications_ : protocols::jd2::archive::MPIArchiveJobDistributor
• pep_fold_only : protocols::flexpep_docking::FlexPepDockingFlags
• pep_lengths_ : protocols::analysis::PeptideDeriverFilter
• pep_refine : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_anchors : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_chain_ : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_chain_num_ : protocols::simple_moves::DisulfideInsertionMover
• peptide_cuts : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_first_res_ : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_loop_model : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_nres_ : protocols::flexpep_docking::FlexPepDockingFlags
• 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_res_atom_ind_ : protocols::match::output::UpstreamDownstreamCollisionFilter
• per_residue_data_ : protocols::analysis::InterfaceAnalyzerMover
• per_residue_ddg_ : protocols::simple_moves::ddG
• perform_electron_density_screen_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer
• perform_filters_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• perform_minimizer_run_ : protocols::farna::RNA_Minimizer
• perform_score_diff_cut_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• perform_VDW_rep_screen_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• periodicity_ : protocols::match::downstream::AtomDihedralSecMatchRPE , protocols::toolbox::match_enzdes_util::GeomSampleInfo
• permanent_ : protocols::topology_broker::claims::JumpClaim
• permitted_overlap_ : protocols::match::MatcherTask
• 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
• 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_CCD_off_ : protocols::anchored_design::AnchoredPerturbMover
• perturb_cycles_ : protocols::anchored_design::AnchoredPerturbMover
• perturb_KIC_off_ : protocols::anchored_design::AnchoredPerturbMover
• perturb_show_ : protocols::anchored_design::AnchoredPerturbMover
• perturb_start_structures_ : protocols::abinitio::IterativeFullatom
• perturb_temp_ : protocols::anchored_design::AnchoredPerturbMover
• perturb_torsion_ : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger
• perturbable_ : protocols::helical_bundle::PerturbBundleOptions
• perturbation_magnitude_ : protocols::helical_bundle::PerturbBundleOptions
• perturbation_type_ : protocols::helical_bundle::PerturbBundleOptions
• 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
• perturber_ : protocols::docking::DockingProtocol , protocols::loops::loop_closure::kinematic_closure::KinematicMover
• perturberlist_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• perturbers_ : protocols::kinematic_closure::BalancedKicMover , protocols::kinematic_closure::KicMover , protocols::kinematic_closure::perturbers::PerturberSet
• 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
• phi : protocols::jumping::DisulfTemplate , protocols::jumping::PairingTemplate , protocols::pockets::spherical_coor_triplet , protocols::pockets::triplet_and_originnum , protocols::simple_moves::MinimalRotamer
• phi_ : 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::optimize_weights::PNatRotOptEPositionData , protocols::stepwise::modeler::protein::MainChainTorsionSet
• phi_angle_ : protocols::rigid::RigidBodyRandomizeMover , protocols::simple_moves::oop::OopMover
• phi_bin_width_ : protocols::qsar::scoring_grid::ShapeGrid
• phi_offsets_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger
• phis : protocols::antibody::clusters::ClusterData
• 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_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
• physical_cut_ : protocols::environment::claims::JumpClaim
• physical_pose_clash_dist_cutoff_ : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• pi_pi_total_ : protocols::toolbox::pose_metric_calculators::PiPiCalculator
• pick_boundary_ : protocols::toolbox::SelectResiduesByLayer
• pick_core_ : protocols::toolbox::SelectResiduesByLayer
• pick_objfunction_ : protocols::mpi_refinement::Scheduler
• pick_strategy_ : protocols::mpi_refinement::Scheduler
• pick_surface_ : protocols::toolbox::SelectResiduesByLayer
• picking_rounds_ : protocols::antibody::design::ResidueProbDesignOperation
• piece_ : protocols::grafting::GraftMoverBase
• pipemap_ : protocols::wum2::WorkUnit_ElScripts
• 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
• pivot_picker_ : protocols::kinematic_closure::BalancedKicMover , protocols::kinematic_closure::KicMover
• pivot_res_ : protocols::coarse_rna::CoarseRNA_LoopCloser
• pivot_residues_ : protocols::backrub::BackrubMover
• pivot_to_scratch_res_ : protocols::coarse_rna::CoarseRNA_LoopCloser
• pivots_ : protocols::kinematic_closure::ClosureProblem
• place_peptide : protocols::flexpep_docking::FlexPepDockingFlags
• place_scaffold_ : protocols::protein_interface_design::movers::PlaceStubMover
• placed_stubs_ : protocols::protein_interface_design::movers::PlaceStubMover
• plain_text : protocols::sparta::GDB
• plane_tolerance_ : protocols::simple_moves::symmetry::DetectSymmetry
• pleats1_ : protocols::fldsgn::topology::StrandPairing
• pleats2_ : protocols::fldsgn::topology::StrandPairing
• pocket_CoM_ : protocols::pockets::NonPlaidFingerprint
• pocketgrid_ : protocols::pockets::PocketConstraint
• pocketGrid_dim_ : protocols::pockets::FingerprintBase
• pocketGrid_mid_ : protocols::pockets::FingerprintBase
• pocketGrid_spacing_ : protocols::pockets::FingerprintBase
• pockets_ : protocols::pockets::PocketGrid
• point_ : protocols::match::VoxelSetIterator
• points_ : protocols::pockets::CCluster , protocols::pockets::PCluster , protocols::scoring::ImplicitFastClashCheck , protocols::sic_dock::CBScore
• 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
• polar_ : protocols::simple_filters::InterfaceSasaFilter , protocols::simple_filters::TotalSasaFilter
• polar_gap_ : protocols::toolbox::task_operations::CrystalContactsOperation
• polar_max : protocols::hotspot_hashing::SphericalRotationSearchPattern
• polar_min : protocols::hotspot_hashing::SphericalRotationSearchPattern
• polar_rotation_sampling : protocols::hotspot_hashing::SphericalRotationSearchPattern
• polars : protocols::sic_dock::BuriedPolarScore
• policy_ : protocols::nonlocal::BiasedFragmentMover , protocols::nonlocal::SingleFragmentMover
• poly_A_seq_ : protocols::frag_picker::VallProvider
• polymer_type_ : protocols::make_rot_lib::MakeRotLibOptionsData
• 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_defs_ : protocols::frag_picker::quota::ABEGO_SS_Config
• 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_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
• pop_from_ss_ : protocols::dna::DnaInterfaceMultiStateDesign , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• pop_size_ : protocols::dna::DnaInterfaceMultiStateDesign , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• population_weight_ : protocols::cluster::ClusterBase
• pore_radius_ : protocols::toolbox::SelectResiduesByLayer
• pos : protocols::environment::EnvClaimBroker::BrokeredJumpData
• pos1 : protocols::farna::RNA_Pairing , protocols::jumping::DisulfPairing
• pos1_ : protocols::environment::claims::JumpClaim , protocols::topology_broker::claims::LegacyRootClaim
• pos2 : protocols::farna::RNA_Pairing , protocols::jumping::DisulfPairing
• pos2_ : protocols::environment::claims::JumpClaim
• pos_ : protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::kinmatch::FunGroupTK
• pos_list_ : protocols::idealize::IdealizeMover , protocols::simple_moves::BackboneMover
• pose : protocols::antibody::CDRPose , protocols::canonical_sampling::DbTrajectoryRecorder::Frame , protocols::cartesian::MolecularDynamics , protocols::environment::EnvClaimBroker::BrokerResult , protocols::trajectory::DbTrajectoryWriter::Frame
• pose0_ : protocols::md::MDBase , protocols::mpi_refinement::MPI_Refinement , protocols::normalmode::NormalModeMultifunc
• pose1_ : protocols::hybridization::DomainAssembly , protocols::sic_dock::LinkerScore , protocols::sic_dock::scores::MotifHashRigidScore
• pose2_ : protocols::hybridization::DomainAssembly , protocols::sic_dock::LinkerScore , protocols::sic_dock::scores::MotifHashRigidScore
• pose_ : protocols::abinitio::Template , protocols::electron_density::BfactorMultifunc , 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::kinmatch::FunGroupTK , protocols::ligand_docking::rdf::RDFBinaryOrbitalFunction , protocols::ligand_docking::rdf::RDFOrbitalFunction , protocols::LoopRebuild , protocols::match::output::PoseInserter , protocols::normalmode::NormalModeMultifunc , protocols::pack_daemon::BasicSimAnnealerRepacker , protocols::pack_daemon::EntityCorrespondence , protocols::pack_daemon::PackDaemon , protocols::pack_daemon::QuickRepacker , protocols::pockets::PlaidFingerprint , 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::NativeRMSD_Screener
• pose_at_origin_ : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler
• pose_build_resids_ : protocols::match::Matcher
• pose_comments_features_ : protocols::features::ProteinSilentReport
• pose_conformation_features_ : protocols::features::ProteinSilentReport
• 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_frag_moves_ : protocols::forge::remodel::RemodelMover::instruction_flags
• pose_free_ : protocols::stepwise::modeler::rna::phosphate::PhosphateMover
• pose_has_resolved_loop_indices_ : protocols::loops::GuardedLoopsFromFile
• pose_index_ : protocols::loops::ResidueIndexDescription
• pose_init_ : protocols::stepwise::modeler::packer::StepWisePacker
• pose_input_cache_ : protocols::rosetta_scripts::MultiplePoseMover
• pose_input_stream_ : protocols::stepwise::modeler::protein::InputStreamWithResidueInfo
• pose_list : protocols::stepwise::modeler::rna::sugar::SugarModeling
• pose_list_ : 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_minobj_ : protocols::md::MDBase
• pose_name : protocols::stepwise::modeler::rna::checker::VDW_RepScreeninfo
• pose_numb_ : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• pose_numbered_ : protocols::loops::ResidueIndexDescription
• pose_output_cache_ : protocols::rosetta_scripts::MultiplePoseMover
• pose_output_list_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• pose_p_ : protocols::multistate_design::SingleState
• pose_pddf_ : protocols::scoring::methods::saxs::PDDFEnergy
• pose_ref_ : protocols::simple_moves::CombinePoseMover
• pose_relax_ : protocols::forge::remodel::RemodelMover::instruction_flags
• pose_resnum_ : protocols::pmut_scan::MutationData
• pose_right_ : protocols::forge::build::ConnectRight
• pose_sequence_ : protocols::antibody::design::ConservativeDesignOperation
• pose_start_ : protocols::protein_interface_design::filters::ClashWithTargetFilter
• pose_store_ : protocols::forge::remodel::RemodelAccumulator
• pose_string_ : protocols::simple_moves::CopyDofMover
• pose_tag_ : protocols::simple_moves::CombinePoseMover
• pose_to_native_map_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer
• 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::StepWiseRNA_VirtualSugarSampler
• poselist : protocols::cluster::GatherPosesMover
• posename_ : protocols::analysis::InterfaceAnalyzerMover
• posename_base_ : protocols::analysis::InterfaceAnalyzerMover
• poses_ : protocols::abinitio::StructureStore , protocols::docking::membrane::MPDockingSetupMover , protocols::hybridization::DomainAssembly , protocols::moves::VectorPoseMover , protocols::mpi_refinement::StructAvrgMover , protocols::simple_filters::StructuralSimilarityEvaluator
• poses_input_ : protocols::rosetta_scripts::MultiplePoseMover
• poses_output_ : protocols::rosetta_scripts::MultiplePoseMover
• poseselector_creator_map_ : protocols::rosetta_scripts::PoseSelectorFactory
• position : protocols::cartesian::CartesianAtom , protocols::dna::PositionType , protocols::hotspot_hashing::VectorPair
• position_ : protocols::optimize_weights::PNatAAOptEPositionData , protocols::topology_broker::claims::CutClaim
• position_above_surface_ : protocols::surface_docking::SurfaceDockingProtocol
• position_ddGs_ : protocols::toolbox::task_operations::RestrictConservedLowDdgOperation
• position_index_ : protocols::frag_picker::VallResidue
• positions_ : protocols::analysis::LoopAnalyzerMover , protocols::antibody::design::ConservativeDesignOperation , protocols::dna::DnaChains , protocols::environment::claims::EnvLabelSelector , protocols::enzdes::EnzdesFlexibleRegion , protocols::simple_filters::ScoreCutoffFilter
• positions_to_replace_ : protocols::enzdes::PredesignPerturbMover
• positive_filters_ : protocols::protein_interface_design::filters::BoltzmannFilter
• positive_scores_ : protocols::jd2::archive::NormalizedEvaluatedArchive
• possible_hbond_acceptors_ : protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker
• possible_working_res_1 : protocols::stepwise::modeler::rna::InternalWorkingResidueParameter
• possible_working_res_2 : protocols::stepwise::modeler::rna::InternalWorkingResidueParameter
• post_graft_ensemble_output_ : protocols::antibody::design::AntibodyDesignMover
• post_graft_modeling_cycles_ : protocols::antibody::design::AntibodyGraftDesignMover
• post_loop_closure_protocol_ : protocols::abinitio::AbrelaxMover
• post_placement_sdev_ : protocols::protein_interface_design::movers::PlaceStubMover
• potential_ : protocols::protein_interface_design::filters::DisulfideFilter , protocols::protein_interface_design::movers::DisulfideMover
• potential_energy_ : protocols::md::MDBase
• potential_starting_positions_ : protocols::ligand_docking::StartFrom
• ppk_only : protocols::flexpep_docking::FlexPepDockingFlags
• pre_ligand_atom_id_ : protocols::metal_interface::MetalSiteResidue
• pre_loop_closure_protocol_ : protocols::abinitio::AbrelaxMover
• pre_minimization_ : protocols::antibody::SnugDock
• pre_pre_ligand_atom_id_ : protocols::metal_interface::MetalSiteResidue
• 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
• preapply_ : protocols::simple_moves::GenericMonteCarloMover
• precision_ : protocols::frag_picker::scores::FragmentScoreManager , protocols::rotamer_recovery::RRReporterHuman
• precomputed_library_mover_ : protocols::stepwise::modeler::StepWiseModeler
• PRED_DIR : protocols::sparta::Sparta::SpartaLib
• pred_ss_ : protocols::medal::MedalExchangeMover , protocols::star::Extender , protocols::star::StarAbinitio
• predefined_torsions_ : protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber
• predefined_window_start_ : protocols::simple_moves::ClassicFragmentMover
• predicted_burial_ : protocols::simple_filters::PredictedBurialEvaluator
• predicted_H3_base_type_ : protocols::antibody::AntibodyInfo
• predicted_sa_norm_ : protocols::frag_picker::scores::SolventAccessibility
• 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
• prefilter_scorefxn_ : protocols::loophash::LoopHashMoverWrapper
• 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
• PREFIX_FINAL : protocols::nonlocal::StarTreeBuilder
• PREFIX_INITIAL : protocols::nonlocal::StarTreeBuilder
• prepack_ : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• prepack_full_repack_ : protocols::docking::DockingEnsemblePrepackProtocol , protocols::docking::DockingPrepackProtocol
• prepack_only_ : protocols::docking::DockTaskFactory
• prepack_res_was_inputted_ : protocols::stepwise::modeler::StepWiseModeler
• prepacked_ : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• prepare_for_centroid_ : protocols::loop_modeling::LoopModeler
• prepare_for_fullatom_ : protocols::loop_modeling::LoopModeler
• preparers_ : protocols::abinitio::abscript::AbscriptStageMover
• prepend_n_residues_ : protocols::ncbb::oop::OopCreatorMover
• prepend_output_name_ : protocols::canonical_sampling::MetricRecorder
• preprocessing_script_version_ : protocols::antibody::GraftOneCDRLoop
• presample_added_residue_ : protocols::stepwise::monte_carlo::mover::AddMover
• presample_by_swa_ : protocols::stepwise::monte_carlo::mover::AddMover
• preserve_buried_contacts_ : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• 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_whole_input_tag_ : protocols::jobdist::BasicJob
• prev_state_hash_ : protocols::pack_daemon::PackDaemon
• PREV_Tab : protocols::sparta::Sparta::SpartaLib
• prevent_repacking_ : protocols::simple_moves::DesignRepackMover , protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation , protocols::toolbox::task_operations::RestrictIdentitiesOperation , protocols::toolbox::task_operations::RestrictNativeResiduesOperation
• prevFileName : protocols::sparta::Sparta::SpartaLib
• previous_ : protocols::simple_moves::sidechain_moves::SidechainMCMover
• previous_coordinate_constraints_ : protocols::protein_interface_design::movers::PlaceStubMover
• previous_mover_ : protocols::rosetta_scripts::MultiplePoseMover
• previous_sequence_ : protocols::docking::DockingProtocol , protocols::docking::TemperedDocking
• 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
• previously_grown_ : protocols::seeded_abinitio::SwapSegment
• 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
• principal_component_ : protocols::features::helixAssembly::HelicalFragment
• print_statw_interval_ : protocols::wum::MPI_WorkUnitManager
• print_tracer_info_ : protocols::antibody::design::AntibodyGraftDesignMover
• prioritize_ : protocols::wum2::WorkUnit
• priority_ : protocols::frag_picker::scores::FragmentScoringMethod , protocols::topology_broker::claims::SequenceClaim , protocols::topology_broker::SequenceClaimer
• prob_cutoff_ : protocols::antibody::design::AntibodySeqDesignTFCreator
• prob_larger_current_ : protocols::toolbox::task_operations::SeqprofConsensusOperation
• prob_level_ : protocols::noesy_assign::PeakAssignmentParameters
• prob_random_pert_to_current_ : protocols::simple_moves::sidechain_moves::SidechainMover
• prob_set_ : protocols::antibody::design::ResidueProbDesignOperation
• prob_sigmoid_m_ : protocols::noesy_assign::PeakAssignmentParameters
• prob_sigmoid_tau_ : protocols::noesy_assign::PeakAssignmentParameters
• prob_sigmoid_w_ : protocols::noesy_assign::PeakAssignmentParameters
• prob_table_ : protocols::docking::ConformerSwitchMover
• prob_terminus_ramapert_ : protocols::mpi_refinement::MPI_Refine_Master
• prob_uniform_ : protocols::simple_moves::sidechain_moves::SidechainMover
• prob_withinrot_ : protocols::simple_moves::sidechain_moves::SidechainMover
• probability_ : protocols::make_rot_lib::RotData
• probe_atom_type_ : protocols::qsar::scoring_grid::SolvationGrid
• probe_rad_ : protocols::pockets::PocketGrid
• probe_radius_ : protocols::simple_filters::TaskAwareSASAFilter , protocols::toolbox::task_operations::SelectBySASAOperation
• probe_specificity_ : protocols::dna::DnaInterfacePacker
• 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
• process_termination_ : protocols::mpi_refinement::MPI_Refine_Emperor
• processed_ : protocols::cluster::AssignToClustersMover , protocols::cluster::GatherPosesMover
• procorr_alt_conf_ : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• procorr_curr_conf_ : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• procorr_energies_ : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• profile_ : protocols::frag_picker::VallResidue
• profile_scoring_ : protocols::frag_picker::scores::ProfileScore
• profile_struct_ : protocols::frag_picker::VallResidue
• profile_wgt_ : protocols::simple_moves::SequenceProfileMover
• progress_ : protocols::canonical_sampling::ProgressBarObserver
• progress_file_ : protocols::simple_moves::GenericMonteCarloMover
• prohibit_single_residue_loops_ : protocols::loops::LoopFromFileData , protocols::loops::LoopsFileOptions
• 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
• propeller_ : protocols::dna::DNABasepair
• proposal_hists_ : protocols::backrub::BackrubSidechainMover
• proposed_since_last_batch_ : protocols::jd2::archive::ArchiveBase
• 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_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_interface_design_ : protocols::toolbox::task_operations::SeqprofConsensusOperation
• protein_neighbors_ : protocols::dna::DnaInterfaceFinder
• protein_positions_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• protein_prepack_ : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• protein_residue_conformation_features_ : protocols::features::ProteinSilentReport
• protein_scan_ : protocols::dna::DnaInterfacePacker
• protein_silent_report_ : protocols::features::DatabaseJobInputter , protocols::features::DatabaseJobOutputter
• 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
• proton1_ : protocols::noesy_assign::CrossPeak
• proton2_ : protocols::noesy_assign::CrossPeak
• proton_atom_name_ : protocols::noesy_assign::CrossPeakInfo
• proton_tolerance_ : protocols::noesy_assign::CrossPeakInfo
• protonated_H1_adenosine_list_ : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• protons_ : protocols::simple_filters::AtomicContactFilter
• prv_eqxyz_ : protocols::md::MDBase
• pSer2Asp_centroid : protocols::flexpep_docking::FlexPepDockingFlags
• pSer2Glu_centroid : protocols::flexpep_docking::FlexPepDockingFlags
• pseudorotation_ : protocols::dna::DNABase
• psi : protocols::jumping::DisulfTemplate , protocols::jumping::PairingTemplate , protocols::pockets::spherical_coor_triplet , protocols::pockets::triplet_and_originnum
• psi_ : protocols::frag_picker::DiversifyDihedralsSelector , protocols::frag_picker::VallResidue , protocols::frags::RMSVallData , protocols::frags::VallData , protocols::loophash::BackboneSegment , protocols::match::upstream::ProteinBackboneBuildPoint , protocols::optimize_weights::PNatRotOptEPositionData , protocols::stepwise::modeler::protein::MainChainTorsionSet
• psi_angle_ : protocols::rigid::RigidBodyRandomizeMover , protocols::simple_moves::oop::OopMover
• psi_offsets_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger
• psis : protocols::antibody::clusters::ClusterData
• pssm_ : protocols::protein_interface_design::movers::InterfaceRecapitulationMover
• pssm_data_ : protocols::optimize_weights::IterativeOptEDriver , protocols::protein_interface_design::ReportPSSMDifferences
• pssm_probabilities_ : protocols::optimize_weights::PSSMOptEPositionData
• ptask_ : protocols::enzdes::RepackLigandSiteWithoutLigandMover , protocols::simple_moves::ConsensusDesignMover
• ptask_p_ : protocols::multistate_design::PackingState
• pts_ : protocols::cluster::APCluster
• pucker_flip_rate_ : protocols::stepwise::sampler::rna::RNA_MC_Suite
• 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
• put_jump_stub_intra_residue : protocols::environment::EnvClaimBroker::BrokeredJumpData
• pymol_ : protocols::moves::PyMolObserver , protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• pymol_name_ : protocols::moves::PyMolMover
• pymol_sel_hbond_unsat : protocols::analysis::InterfaceData
• pymol_sel_interface : protocols::analysis::InterfaceData
• pymol_sel_packing : protocols::analysis::InterfaceData