Here is a list of all namespace members with links to the namespace documentation for each member:

- p -

• PACK : protocols::stepwise::screener
• pack_polar_hydrogens() : protocols::stepwise::modeler::polar_hydrogens
• PackDaemonCOP : protocols::pack_daemon
• PackDaemonOP : protocols::pack_daemon
• PackerEnergy : protocols::flexpack
• PackerNeighborGraphFilterCOP : protocols::simple_filters
• PackerNeighborGraphFilterOP : protocols::simple_filters
• packing_helper() : protocols::loop_modeling::refiners
• PackingAngleEnum : protocols::antibody
• PackingAngleEnum_start : protocols::antibody
• PackingAngleEnum_total : protocols::antibody
• PackingStateCOP : protocols::multistate_design
• PackingStateOP : protocols::multistate_design
• PackRotamersMoverCOP : protocols::simple_moves
• PackRotamersMoverLazyCOP : protocols::simple_moves
• PackRotamersMoverLazyOP : protocols::simple_moves
• PackRotamersMoverOP : protocols::simple_moves
• PackScreenerCOP : protocols::stepwise::screener
• PackScreenerOP : protocols::stepwise::screener
• PackStatFilterCOP : protocols::simple_filters
• PackStatFilterOP : protocols::simple_filters
• PackStatMoverOP : protocols::analysis
• pair_first_sort_helper() : protocols::toolbox::rotamer_set_operations
• pair_sort_criterion() : protocols::stepwise::legacy::modeler::rna
• PairFeaturesCOP : protocols::features
• PairFeaturesOP : protocols::features
• PairingLibraryCOP : protocols::jumping
• PairingLibraryOP : protocols::jumping
• PairingStatisticsCOP : protocols::abinitio
• PairingStatisticsOP : protocols::abinitio
• PairMap : protocols::features::helixAssembly
• parallel_base_test() : protocols::motifs
• ParallelBetaPairingPreferenceFilterCOP : protocols::fldsgn::filters
• ParallelBetaPairingPreferenceFilterOP : protocols::fldsgn::filters
• ParallelTemperingCOP : protocols::canonical_sampling
• ParallelTemperingOP : protocols::canonical_sampling
• paratope_charge() : protocols::antibody
• paratope_sasa() : protocols::antibody
• ParatopeEpitopeSiteConstraintMoverCOP : protocols::antibody::constraints
• ParatopeEpitopeSiteConstraintMoverOP : protocols::antibody::constraints
• ParatopeSiteConstraintMoverCOP : protocols::antibody::constraints
• ParatopeSiteConstraintMoverOP : protocols::antibody::constraints
• PARENT_LABEL_OPTION : protocols::environment::claims
• ParetoOptMutationMoverCOP : protocols::design_opt
• ParetoOptMutationMoverOP : protocols::design_opt
• parse_bogus_res_tag() : protocols::rosetta_scripts
• parse_filter() : protocols::rosetta_scripts
• parse_movemap() : protocols::rosetta_scripts
• parse_movemapdef() : protocols::elscripts
• parse_mover() : protocols::rosetta_scripts
• parse_mover_subtag() : protocols::rosetta_scripts
• parse_out_non_standard_residues() : protocols::stepwise::setup
• parse_res() : protocols::hybridization
• parse_resfile_string_with_no_lockdown() : protocols::forge::methods
• parse_score_function() : protocols::rosetta_scripts
• parse_scoredef() : protocols::elscripts
• parse_seeds() : protocols::seeded_abinitio
• parse_spans() : protocols::seeded_abinitio
• parse_stub_sets() : protocols::protein_interface_design::movers
• parse_task_operations() : protocols::rosetta_scripts
• parse_taskdef() : protocols::elscripts
• parse_xyz_vector() : protocols::rosetta_scripts
• ParsedProtocolAP : protocols::rosetta_scripts
• ParsedProtocolCAP : protocols::rosetta_scripts
• ParsedProtocolCOP : protocols::rosetta_scripts
• ParsedProtocolOP : protocols::rosetta_scripts
• ParserCOP : protocols::jd2
• ParserOP : protocols::jd2
• part_complex() : protocols::protein_interface_design::movers
• partial_align() : protocols::hybridization
• PARTITION_CONTACT : protocols::stepwise::screener
• PartitionContactScreenerCOP : protocols::stepwise::screener
• PartitionContactScreenerOP : protocols::stepwise::screener
• Partner : protocols::rigid
• partner_downstream : protocols::rigid
• partner_upstream : protocols::rigid
• passes_filters() : protocols::ligand_docking
• PatchdockJobInputterCOP : protocols::protein_interface_design
• PatchdockJobInputterOP : protocols::protein_interface_design
• PatchdockReaderCOP : protocols::protein_interface_design
• PatchdockReaderOP : protocols::protein_interface_design
• PatchdockTransformCOP : protocols::protein_interface_design::movers
• PatchdockTransformOP : protocols::protein_interface_design::movers
• path_basename() : protocols::stepwise::legacy::modeler::rna
• PCA_OP : protocols::evaluation
• PCS_data_Ts1OP : protocols::scoring::methods::pcsTs1
• PCS_data_Ts2OP : protocols::scoring::methods::pcsTs2
• PCS_data_Ts3OP : protocols::scoring::methods::pcsTs3
• PCS_data_Ts4OP : protocols::scoring::methods::pcsTs4
• PCS_dataOP : protocols::scoring::methods::pcs
• PCS_Energy_Ts1COP : protocols::scoring::methods::pcsTs1
• PCS_Energy_Ts1OP : protocols::scoring::methods::pcsTs1
• PCS_Energy_Ts2COP : protocols::scoring::methods::pcsTs2
• PCS_Energy_Ts2OP : protocols::scoring::methods::pcsTs2
• PCS_Energy_Ts3COP : protocols::scoring::methods::pcsTs3
• PCS_Energy_Ts3OP : protocols::scoring::methods::pcsTs3
• PCS_Energy_Ts4COP : protocols::scoring::methods::pcsTs4
• PCS_Energy_Ts4OP : protocols::scoring::methods::pcsTs4
• PCS_EnergyCOP : protocols::scoring::methods::pcs
• PCS_EnergyOP : protocols::scoring::methods::pcs
• PcsDataCenterCOP : protocols::scoring::methods::pcs2
• PcsDataCenterManagerOP : protocols::scoring::methods::pcs2
• PcsDataCenterOP : protocols::scoring::methods::pcs2
• PcsEnergyControllerAP : protocols::topology_broker
• PcsEnergyControllerCAP : protocols::topology_broker
• PcsEnergyControllerCOP : protocols::topology_broker
• PcsEnergyControllerOP : protocols::topology_broker
• PcsEnergyCOP : protocols::scoring::methods::pcs2
• PcsEnergyOP : protocols::scoring::methods::pcs2
• PcsInputCenterCOP : protocols::scoring::methods::pcs2
• PcsInputCenterOP : protocols::scoring::methods::pcs2
• pct_features_in_common() : protocols::simple_filters
• PDB_Entry : protocols::sparta
• PDB_FILE : protocols::jd2::JobInputterInputSource
• PdbDataFeaturesOP : protocols::features
• PDBDumpMoverCOP : protocols::moves
• PDBDumpMoverOP : protocols::moves
• PdbIdChunkFilterCOP : protocols::frag_picker
• PdbIdChunkFilterOP : protocols::frag_picker
• PDBInputterSP : protocols::inputter
• PDBJobInputterOP : protocols::jd2
• PDBJobOutputterOP : protocols::jd2
• PDBLandmarkCOP : protocols::antibody
• PDBLandmarkOP : protocols::antibody
• PDBOutputCOP : protocols::dna
• PDBOutputOP : protocols::dna
• PDBOutputterSP : protocols::outputter
• PDBReloadMoverCOP : protocols::simple_moves
• PDBReloadMoverOP : protocols::simple_moves
• PDBWriterCOP : protocols::match::output
• PDBWriterOP : protocols::match::output
• PDDFEnergyCOP : protocols::scoring::methods::saxs
• PDDFEnergyOP : protocols::scoring::methods::saxs
• PDDFScoreFilterCOP : protocols::simple_filters
• PDDFScoreFilterOP : protocols::simple_filters
• PeakAssignmentAP : protocols::noesy_assign
• PeakAssignmentCAP : protocols::noesy_assign
• PeakAssignmentCOP : protocols::noesy_assign
• PeakAssignmentOP : protocols::noesy_assign
• PeakAssignmentResidueMapAP : protocols::noesy_assign
• PeakAssignmentResidueMapCAP : protocols::noesy_assign
• PeakAssignmentResidueMapCOP : protocols::noesy_assign
• PeakAssignmentResidueMapOP : protocols::noesy_assign
• PeakAssignments : protocols::noesy_assign
• PeakCalibratorAP : protocols::noesy_assign
• PeakCalibratorCAP : protocols::noesy_assign
• PeakCalibratorCOP : protocols::noesy_assign
• PeakCalibratorOP : protocols::noesy_assign
• PeakFileFormatCOP : protocols::noesy_assign
• PeakFileFormatOP : protocols::noesy_assign
• PEPTIDE : protocols::make_rot_lib
• PeptideDeriverEntryType : protocols::analysis
• PeptideDeriverFilterCOP : protocols::analysis
• PeptideDeriverFilterCreatorCOP : protocols::analysis
• PeptideDeriverFilterCreatorOP : protocols::analysis
• PeptideDeriverFilterOP : protocols::analysis
• PeptideDeriverOutputterCOP : protocols::analysis
• PeptideDeriverOutputterOP : protocols::analysis
• PeptideDeriverReportFormat : protocols::analysis
• PeptideStapleMoverCOP : protocols::simple_moves
• PeptideStapleMoverOP : protocols::simple_moves
• PEPTOID : protocols::make_rot_lib
• PerNativeRRReporterHumanCOP : protocols::rotamer_recovery
• PerNativeRRReporterHumanOP : protocols::rotamer_recovery
• PerResidueAAProbSet : protocols::antibody::design
• PertType : protocols::helical_bundle
• PERTURB() : protocols::loops::loop_mover
• perturb_backbone_by_bins : protocols::generalized_kinematic_closure::perturber
• perturb_backbone_for_test() : protocols::grafting
• perturb_dihedral : protocols::generalized_kinematic_closure::perturber
• perturb_dihedral_bbg : protocols::generalized_kinematic_closure::perturber
• PerturbBundleCOP : protocols::helical_bundle
• PerturbBundleCOPs : protocols::helical_bundle
• PerturbBundleHelixCOP : protocols::helical_bundle
• PerturbBundleHelixCOPs : protocols::helical_bundle
• PerturbBundleHelixOP : protocols::helical_bundle
• PerturbBundleHelixOPs : protocols::helical_bundle
• PerturbBundleOP : protocols::helical_bundle
• PerturbBundleOPs : protocols::helical_bundle
• PerturbBundleOptionsAP : protocols::helical_bundle
• PerturbBundleOptionsCAP : protocols::helical_bundle
• PerturbBundleOptionsCAPs : protocols::helical_bundle
• PerturbBundleOptionsCOP : protocols::helical_bundle
• PerturbBundleOptionsCOPs : protocols::helical_bundle
• PerturbBundleOptionsOP : protocols::helical_bundle
• PerturbBundleOptionsOPs : protocols::helical_bundle
• PerturbByBinsCOP : protocols::simple_moves::bin_transitions
• PerturbByBinsCOPs : protocols::simple_moves::bin_transitions
• PerturbByBinsOP : protocols::simple_moves::bin_transitions
• PerturbByBinsOPs : protocols::simple_moves::bin_transitions
• PerturbChiSidechainMoverCOP : protocols::simple_moves::sidechain_moves
• PerturbChiSidechainMoverOP : protocols::simple_moves::sidechain_moves
• perturber_effect : protocols::generalized_kinematic_closure::perturber
• PerturberCOP : protocols::kinematic_closure::perturbers
• PerturberOP : protocols::kinematic_closure::perturbers
• PerturberSetCOP : protocols::kinematic_closure::perturbers
• PerturberSetOP : protocols::kinematic_closure::perturbers
• PerturbRotamerSidechainMoverCOP : protocols::simple_moves::sidechain_moves
• PerturbRotamerSidechainMoverOP : protocols::simple_moves::sidechain_moves
• PG_like : protocols::fldsgn::topology
• phe_tyr_corrections() : protocols::make_rot_lib
• PHIPSI_ERR_SURF : protocols::sparta
• phosphate_base_phosphate_rmsd() : protocols::stepwise::modeler::rna
• phosphate_base_phosphate_square_deviation() : protocols::stepwise::modeler::rna
• PHOSPHATE_PACK : protocols::stepwise::screener
• phosphate_square_deviation() : protocols::stepwise::modeler::rna
• PhosphateMoveCOP : protocols::stepwise::modeler::rna::phosphate
• PhosphateMoveOP : protocols::stepwise::modeler::rna::phosphate
• PhosphateMoverCOP : protocols::stepwise::modeler::rna::phosphate
• PhosphateMoverOP : protocols::stepwise::modeler::rna::phosphate
• PhosphateScreenerCOP : protocols::stepwise::screener
• PhosphateScreenerOP : protocols::stepwise::screener
• PhosphateTerminus : protocols::stepwise::modeler::rna::phosphate
• pick_loops_chainbreak() : protocols::comparative_modeling
• pick_loops_unaligned() : protocols::comparative_modeling
• pick_pivots() : protocols::hybridization
• PivotBasedKinematicPerturberCOP : protocols::loops::loop_closure::kinematic_closure
• PivotBasedKinematicPerturberOP : protocols::loops::loop_closure::kinematic_closure
• PivotPickerCOP : protocols::kinematic_closure::pivot_pickers
• PivotPickerOP : protocols::kinematic_closure::pivot_pickers
• place_atom_positions() : protocols::helical_bundle
• PlacementAuctionMoverCOP : protocols::protein_interface_design::movers
• PlacementAuctionMoverOP : protocols::protein_interface_design::movers
• PlacementMinimizationMoverCOP : protocols::protein_interface_design::movers
• PlacementMinimizationMoverOP : protocols::protein_interface_design::movers
• PlaceOnLoopCOP : protocols::protein_interface_design::movers
• PlaceOnLoopOP : protocols::protein_interface_design::movers
• PlaceStubMoverCOP : protocols::protein_interface_design::movers
• PlaceStubMoverOP : protocols::protein_interface_design::movers
• PlaceSurfaceProbeCOP : protocols::hotspot_hashing::movers
• PlaceSurfaceProbeOP : protocols::hotspot_hashing::movers
• PlaidFingerprintCOP : protocols::pockets
• PlaidFingerprintOP : protocols::pockets
• PlainSilentFileJobDistributorOP : protocols::jobdist
• Ploop2x3 : protocols::fldsgn::topology
• Ploop3x3 : protocols::fldsgn::topology
• PNatAAOptEPositionDataOP : protocols::optimize_weights
• PNatAAOptERotamerDataOP : protocols::optimize_weights
• PNatAAOptERotamerDataOPs : protocols::optimize_weights
• PNatLigPoseOptEDataCOP : protocols::optimize_weights
• PNatLigPoseOptEDataOP : protocols::optimize_weights
• PNatRotOptEPositionDataOP : protocols::optimize_weights
• PNatRotOptERotamerDataOP : protocols::optimize_weights
• PNatRotOptERotamerDataOPs : protocols::optimize_weights
• PNatStructureOptEDataOP : protocols::optimize_weights
• PocketConstraintOP : protocols::pockets
• PocketGridCOP : protocols::pockets
• PocketGridOP : protocols::pockets
• point_graph_dme() : protocols::simple_moves
• pointer_sorter() : protocols::fldsgn::topology
• PointList : protocols::jumping
• PointMutationCalculatorCOP : protocols::design_opt
• PointMutationCalculatorOP : protocols::design_opt
• PolarHydrogenPackerCOP : protocols::stepwise::modeler::polar_hydrogens
• PolarHydrogenPackerOP : protocols::stepwise::modeler::polar_hydrogens
• PolicyCOP : protocols::nonlocal
• PolicyOP : protocols::nonlocal
• POLY_CASES : protocols::viewer
• Pool_RMSD_OP : protocols::canonical_sampling::mc_convergence_checks
• PoolDataCOP : protocols::canonical_sampling::mc_convergence_checks
• PoolDataOP : protocols::canonical_sampling::mc_convergence_checks
• Pose : protocols::filters , protocols::fldsgn::potentials::sspot , protocols::flxbb
• POSE : protocols::jd2::JobInputterInputSource
• Pose : protocols::protein_interface_design::movers , protocols::rosetta_scripts , protocols::sic_dock , protocols::sic_dock::scores
• pose1_has_most_CBs() : protocols::sic_dock
• POSE_BUFSIZE : protocols::boinc
• pose_charge() : protocols::antibody
• pose_energies_to_json() : protocols::rpc
• pose_from_binary_silent_file() : protocols::checkpoint
• pose_matches_user_tag() : protocols::jobdist
• POSE_SELECTION : protocols::stepwise::screener
• pose_to_binary_silent_file() : protocols::checkpoint
• pose_with_most_CBs() : protocols::sic_dock
• PoseCommentCOP : protocols::simple_filters
• PoseCommentOP : protocols::simple_filters
• PoseCommentsFeaturesCOP : protocols::features
• PoseCommentsFeaturesOP : protocols::features
• PoseConditionCOP : protocols::moves
• PoseConditionOP : protocols::moves
• PoseConformationFeaturesCOP : protocols::features
• PoseConformationFeaturesOP : protocols::features
• PoseEvaluatorCOP : protocols::evaluation
• PoseEvaluatorOP : protocols::evaluation
• PoseEvaluators : protocols::evaluation
• PoseEvaluatorsCOP : protocols::evaluation
• PoseEvaluatorsOP : protocols::evaluation
• PoseFoundResiduesCombinationOP : protocols::enzdes
• PoseInputStreamJobInputterOP : protocols::jd2
• PoseInserterCOP : protocols::match::output
• PoseInserterOP : protocols::match::output
• PoseList : protocols::stepwise::modeler
• PoseMatchOutputWriterCOP : protocols::match::output
• PoseMatchOutputWriterOP : protocols::match::output
• PosePropertyReporterCOP : protocols::rosetta_scripts
• PosePropertyReporterCreatorCOP : protocols::rosetta_scripts
• PosePropertyReporterCreatorOP : protocols::rosetta_scripts
• PosePropertyReporterFactoryCOP : protocols::rosetta_scripts
• PosePropertyReporterFactoryOP : protocols::rosetta_scripts
• PosePropertyReporterOP : protocols::rosetta_scripts
• poses_from_cmd_line() : protocols::comparative_modeling
• PoseSelectionScreenerCOP : protocols::stepwise::screener
• PoseSelectionScreenerOP : protocols::stepwise::screener
• PoseSelectorCOP : protocols::rosetta_scripts
• PoseSelectorCreatorCOP : protocols::rosetta_scripts
• PoseSelectorCreatorOP : protocols::rosetta_scripts
• PoseSelectorFactoryCOP : protocols::rosetta_scripts
• PoseSelectorFactoryOP : protocols::rosetta_scripts
• PoseSelectorFlags : protocols::rosetta_scripts
• PoseSelectorOP : protocols::rosetta_scripts
• PoseWithScore : protocols::abinitio
• Positions : protocols::dna
• positions_in_secstruct() : protocols::simple_filters
• PositionSpecificRandomizerCOP : protocols::genetic_algorithm
• PositionSpecificRandomizerOP : protocols::genetic_algorithm
• PositionTypes : protocols::dna
• PosPair : protocols::frag_picker::nonlocal , protocols::frag_picker
• possible_root() : protocols::farna
• PostDockAssemblyScorerCOP : protocols::domain_assembly
• PostDockAssemblyScorerOP : protocols::domain_assembly
• PosTypeCOP : protocols::multistate_design
• PosTypeOP : protocols::multistate_design
• PowExpressionCOP : protocols::pack_daemon
• PowExpressionOP : protocols::pack_daemon
• PRECISION : protocols::dna
• PrecomputedFlexbbInteractionGraphCOP : protocols::flexpack::interaction_graph
• PrecomputedFlexbbInteractionGraphOP : protocols::flexpack::interaction_graph
• PrecomputedLibraryMoverCOP : protocols::stepwise::modeler::precomputed
• PrecomputedLibraryMoverOP : protocols::stepwise::modeler::precomputed
• PredesignPerturbMoverOP : protocols::enzdes
• prepare_and_write_number_of_electrostatic_interactions_of_residues_to_files() : protocols::features::strand_assembly
• prepare_silent_struct() : protocols::stepwise::monte_carlo
• prepare_WriteToDB_sandwich() : protocols::features::strand_assembly
• PrepareForCentroidCOP : protocols::loop_modeling::utilities
• PrepareForCentroidOP : protocols::loop_modeling::utilities
• PrepareForFullatomCOP : protocols::loop_modeling::utilities
• PrepareForFullatomOP : protocols::loop_modeling::utilities
• prepend : protocols::cyclic_peptide
• pretty_print_rd() : protocols::make_rot_lib
• PreventChainFromRepackingOperationCOP : protocols::toolbox::task_operations
• PreventChainFromRepackingOperationOP : protocols::toolbox::task_operations
• PreventResiduesFromRepackingOperationCOP : protocols::toolbox::task_operations
• PreventResiduesFromRepackingOperationOP : protocols::toolbox::task_operations
• PREVIOUS_HILL : protocols::simple_moves
• PRF_BASIC : protocols::analysis
• PRF_MARKDOWN : protocols::analysis
• primary_fixed_domain() : protocols::stepwise::modeler
• print_atom_info() : protocols::stepwise::modeler::rna
• print_backbone_torsions() : protocols::stepwise::legacy::modeler::rna
• print_base_state() : protocols::stepwise::modeler::rna
• print_buried_unsat_Hbonds() : protocols::ligand_docking
• print_ddgs() : protocols
• print_hbonds() : protocols::farna
• print_heavy_atoms() : protocols::stepwise::modeler::rna
• print_individual_atom_info() : protocols::stepwise::modeler::rna
• print_internal_coords() : protocols::farna
• print_interres_bond() : protocols::viewer
• print_nmer_svm_energy_data() : protocols::simple_filters
• print_node() : protocols::match::output , protocols::viewer
• print_sequence_pdb_nums() : protocols::dna
• print_sequences_pdb_nums() : protocols::dna
• print_sugar_pucker_state() : protocols::stepwise::modeler::rna
• print_torsion_info() : protocols::stepwise::modeler::rna
• print_WorkingParameters_info() : protocols::stepwise::legacy::modeler::rna
• printbpy() : protocols::sic_dock::scores
• prob_native_amino_acid : protocols::optimize_weights
• prob_native_amino_acid_with_unfolded_energy : protocols::optimize_weights
• prob_native_ligand_pose : protocols::optimize_weights
• prob_native_rotamer : protocols::optimize_weights
• prob_native_structure : protocols::optimize_weights
• Probabilities : protocols::medal , protocols::nonlocal , protocols::star
• probe_radius_for_atom_type() : protocols::match
• ProbeRadius : protocols::match
• process_input_file() : protocols::farna
• process_last_resonances() : protocols::noesy_assign
• ProcessorFactoryCOP : protocols::match::output
• ProcessorFactoryOP : protocols::match::output
• PRODUCT : protocols::simple_filters
• ProfilerMoverCOP : protocols::moves
• ProfilerMoverOP : protocols::moves
• ProfileScoreCOP : protocols::frag_picker::scores
• ProfileScoreL1COP : protocols::frag_picker::scores
• ProfileScoreL1OP : protocols::frag_picker::scores
• ProfileScoreOP : protocols::frag_picker::scores
• ProgressBarObserverCOP : protocols::canonical_sampling
• ProgressBarObserverOP : protocols::canonical_sampling
• projperp() : protocols::sic_dock
• ProlineFixMoverCOP : protocols::simple_moves
• ProlineFixMoverOP : protocols::simple_moves
• ProtectedConformationAP : protocols::environment
• ProtectedConformationCAP : protocols::environment
• ProtectedConformationCOP : protocols::environment
• ProtectedConformationOP : protocols::environment
• PROTEIN_ATR_REP : protocols::stepwise::screener
• PROTEIN_BETA_ANTIPARALLEL : protocols::stepwise::sampler
• PROTEIN_CCD_CLOSURE : protocols::stepwise::screener
• PROTEIN_FRAGMENT : protocols::stepwise::sampler
• PROTEIN_MAIN_CHAIN : protocols::stepwise::sampler
• ProteinAtrRepCheckerCOP : protocols::stepwise::modeler::protein::checker
• ProteinAtrRepCheckerOP : protocols::stepwise::modeler::protein::checker
• ProteinAtrRepScreenerCOP : protocols::stepwise::legacy::screener
• ProteinAtrRepScreenerOP : protocols::stepwise::legacy::screener
• ProteinBackboneAtomAtomPairFeaturesCOP : protocols::features
• ProteinBackboneAtomAtomPairFeaturesOP : protocols::features
• ProteinBackboneBuildPointCOP : protocols::match::upstream
• ProteinBackboneBuildPointOP : protocols::match::upstream
• ProteinBackboneTorsionAngleFeaturesCOP : protocols::features
• ProteinBackboneTorsionAngleFeaturesOP : protocols::features
• ProteinBetaAntiParallelStepWiseSamplerCOP : protocols::stepwise::sampler::protein
• ProteinBetaAntiParallelStepWiseSamplerOP : protocols::stepwise::sampler::protein
• ProteinBondGeometryFeaturesCOP : protocols::features
• ProteinBondGeometryFeaturesOP : protocols::features
• ProteinCCD_ClosureScreenerCOP : protocols::stepwise::screener
• ProteinCCD_ClosureScreenerOP : protocols::stepwise::screener
• ProteinFragmentStepWiseSamplerCOP : protocols::stepwise::sampler::protein
• ProteinFragmentStepWiseSamplerOP : protocols::stepwise::sampler::protein
• ProteinInterfaceDesignOperationCOP : protocols::toolbox::task_operations
• ProteinInterfaceDesignOperationOP : protocols::toolbox::task_operations
• ProteinInterfaceMultiStateDesignMoverCOP : protocols::dna
• ProteinInterfaceMultiStateDesignMoverOP : protocols::dna
• ProteinLigandInterfaceUpweighterCOP : protocols::enzdes
• ProteinLigandInterfaceUpweighterOP : protocols::enzdes
• ProteinMainChainStepWiseSamplerCOP : protocols::stepwise::sampler::protein
• ProteinMainChainStepWiseSamplerOP : protocols::stepwise::sampler::protein
• ProteinResidueConformationFeaturesCOP : protocols::features
• ProteinResidueConformationFeaturesOP : protocols::features
• ProteinRMSDFeaturesCOP : protocols::features
• ProteinRMSDFeaturesOP : protocols::features
• ProteinRMSDNoSuperpositionFeaturesCOP : protocols::features
• ProteinRMSDNoSuperpositionFeaturesOP : protocols::features
• ProteinSCSamplerCOP : protocols::match::upstream
• ProteinSCSamplerOP : protocols::match::upstream
• ProteinSilentReportCOP : protocols::features
• ProteinSilentReportOP : protocols::features
• ProteinUpstreamBuilderCOP : protocols::match::upstream
• ProteinUpstreamBuilderOP : protocols::match::upstream
• protocol_table_initialized_ : protocols::features
• ProtocolCOP : protocols::abinitio
• ProtocolFeaturesCOP : protocols::features
• ProtocolFeaturesOP : protocols::features
• ProtocolOP : protocols::abinitio
• ProtonResonanceAP : protocols::noesy_assign
• ProtonResonanceCAP : protocols::noesy_assign
• ProtonResonanceCOP : protocols::noesy_assign
• ProtonResonanceOP : protocols::noesy_assign
• PseudocontactShiftEnergyController_Ts1AP : protocols::topology_broker
• PseudocontactShiftEnergyController_Ts1CAP : protocols::topology_broker
• PseudocontactShiftEnergyController_Ts1COP : protocols::topology_broker
• PseudocontactShiftEnergyController_Ts1OP : protocols::topology_broker
• PseudocontactShiftEnergyController_Ts2AP : protocols::topology_broker
• PseudocontactShiftEnergyController_Ts2CAP : protocols::topology_broker
• PseudocontactShiftEnergyController_Ts2COP : protocols::topology_broker
• PseudocontactShiftEnergyController_Ts2OP : protocols::topology_broker
• PseudocontactShiftEnergyController_Ts3AP : protocols::topology_broker
• PseudocontactShiftEnergyController_Ts3CAP : protocols::topology_broker
• PseudocontactShiftEnergyController_Ts3COP : protocols::topology_broker
• PseudocontactShiftEnergyController_Ts3OP : protocols::topology_broker
• PseudocontactShiftEnergyController_Ts4AP : protocols::topology_broker
• PseudocontactShiftEnergyController_Ts4CAP : protocols::topology_broker
• PseudocontactShiftEnergyController_Ts4COP : protocols::topology_broker
• PseudocontactShiftEnergyController_Ts4OP : protocols::topology_broker
• PseudocontactShiftEnergyControllerAP : protocols::topology_broker
• PseudocontactShiftEnergyControllerCAP : protocols::topology_broker
• PseudocontactShiftEnergyControllerCOP : protocols::topology_broker
• PseudocontactShiftEnergyControllerOP : protocols::topology_broker
• PSF_NEED_FULL_POSE_SET : protocols::rosetta_scripts
• PSF_NONE : protocols::rosetta_scripts
• PSSM2BfactorMoverCOP : protocols::simple_moves
• PSSM2BfactorMoverOP : protocols::simple_moves
• pssm_data : protocols::optimize_weights
• PSSMOptEPositionDataOP : protocols::optimize_weights
• pt_gaussian : protocols::helical_bundle
• pt_registrator : protocols::multistate_design
• pt_undefined_perturbation : protocols::helical_bundle
• pt_uniform : protocols::helical_bundle
• put_in_cutpoint() : protocols::stepwise::setup
• PyMolMoverCOP : protocols::moves
• PyMolMoverOP : protocols::moves
• PyMolObserverCOP : protocols::moves
• PyMolObserverOP : protocols::moves
• PyReturnValuePolicyTest_DummyClassCOP() : protocols::toolbox
• PyReturnValuePolicyTest_DummyClassOP() : protocols::toolbox
• PyReturnValuePolicyTest_PoseCOP() : protocols::toolbox
• PyReturnValuePolicyTest_PoseOP() : protocols::toolbox
• PyReturnValuePolicyTest_ScoreFunctionCOP() : protocols::toolbox
• PyReturnValuePolicyTest_ScoreFunctionCOP2() : protocols::toolbox
• PyReturnValuePolicyTest_ScoreFunctionOP() : protocols::toolbox
• PyReturnValuePolicyTest_SF_ReplicaCOP() : protocols::toolbox
• PyReturnValuePolicyTest_SF_ReplicaOP() : protocols::toolbox