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

- p -

• P : core::chemical::element , core::scoring::packstat
• p_aa : core::scoring
• P_AA_ABEGO3_COP : core::scoring
• P_AA_ABEGO3_OP : core::scoring
• P_AA_EnergyCreator_registrator : core::init
• P_AA_EnergyOP : core::scoring::methods
• p_aa_pp : core::scoring
• P_AA_pp_EnergyCreator_registrator : core::init
• P_AA_pp_EnergyOP : core::scoring::methods
• p_aa_pp_ref : core::scoring
• p_aa_ss : core::scoring
• P_AA_ss_EnergyCreator_registrator : core::init
• P_AA_ss_EnergyOP : core::scoring::methods
• P_AA_ssCOP : core::scoring
• P_AA_ssOP : core::scoring
• P_AACOP : core::scoring
• P_AAOP : core::scoring
• Pa : core::chemical::element
• paa_abego3 : core::scoring
• PACK : protocols::stepwise::screener
• pack_extra_bodies() : protocols::chemically_conjugated_docking
• pack_missing_sidechains() : core::pack
• pack_polar_hydrogens() : protocols::stepwise::modeler::polar_hydrogens
• pack_rotamers() : core::pack
• pack_rotamers_cleanup() : core::pack
• pack_rotamers_loop() : core::pack
• pack_rotamers_run() : core::pack
• pack_rotamers_setup() : core::pack
• pack_scorefxn_pose_handshake() : core::pack
• pack_stat : core::scoring
• PackDaemonCOP : protocols::pack_daemon
• PackDaemonOP : protocols::pack_daemon
• PACKER_PALETTE_TAG() : core::pack::task
• PackerEnergy : core , protocols::flexpack
• PackerNeighborGraphFilterCOP : protocols::simple_filters
• PackerNeighborGraphFilterOP : protocols::simple_filters
• PackerPaletteCOP : core::pack::palette
• PackerPaletteCreatorCOP : core::pack::palette
• PackerPaletteCreatorOP : core::pack::palette
• PackerPaletteFactoryCOP : core::pack::palette
• PackerPaletteFactoryOP : core::pack::palette
• PackerPaletteOP : core::pack::palette
• PackerTask_COP : core::pack::task
• PackerTask_OP : core::pack::task
• PackerTaskCOP : core::pack::task
• PackerTaskOP : core::pack::task
• PackerTaskSymmetryStatus : core::pack::task
• packing_helper() : protocols::loop_modeling::refiners
• PackingAngleEnum : protocols::antibody
• PackingAngleEnum_start : protocols::antibody
• PackingAngleEnum_total : protocols::antibody
• PackingScoreCOP : core::scoring::packstat
• PackingScoreOP : core::scoring::packstat
• PackingScoreResDataCOP : core::scoring::packstat
• PackingScoreResDataOP : core::scoring::packstat
• PackingStateCOP : protocols::multistate_design
• PackingStateOP : protocols::multistate_design
• PackRotamersMoverCOP : protocols::minimization_packing
• PackRotamersMoverLazyCOP : protocols::minimization_packing
• PackRotamersMoverLazyOP : protocols::minimization_packing
• PackRotamersMoverOP : protocols::minimization_packing
• PackScreenerCOP : protocols::stepwise::screener
• PackScreenerOP : protocols::stepwise::screener
• PackStatEnergyCreator_registrator : core::init
• PackStatFilterCOP : protocols::simple_filters
• PackStatFilterOP : protocols::simple_filters
• PackStatMoverOP : protocols::analysis
• PackstatReal : core::scoring::packstat
• pad_dash() : core::kinematics
• pad_dash_left() : core::kinematics
• pad_dash_right() : core::kinematics
• pair : core::scoring
• pair_e_method : core::scoring::methods
• pair_first_sort_helper() : protocols::toolbox::rotamer_set_operations
• pair_map_to_comma_strings() : core::conformation::symmetry
• pair_sort_criterion() : protocols::stepwise::legacy::modeler::rna
• PairedSheetResidueSelectorCOP : protocols::denovo_design::residue_selectors
• PairedSheetResidueSelectorOP : protocols::denovo_design::residue_selectors
• PairEnergyCreator_registrator : core::init
• PairEPotentialCOP : core::scoring
• PairEPotentialOP : core::scoring
• PairFeaturesCOP : protocols::features
• PairFeaturesOP : protocols::features
• PairFuncMapCOP : core::scoring::custom_pair_distance
• PairFuncMapOP : core::scoring::custom_pair_distance
• PairingLibraryCOP : protocols::jumping
• PairingLibraryOP : protocols::jumping
• PairingList : core::scoring::dssp
• PairingsList : core::scoring::dssp
• PairingStatisticsCOP : protocols::abinitio
• PairingStatisticsOP : protocols::abinitio
• PairMap : protocols::features::helixAssembly
• PairScoringSchemeOP : core::sequence
• PARA_ARAMID : core::chemical
• ParaIonAP : core::io::nmr
• ParaIonCAP : core::io::nmr
• ParaIonCOP : core::io::nmr
• ParaIonOP : core::io::nmr
• PARALLEL : core::chemical::rna
• parallel_base_test() : protocols::motifs
• ParallelBetaPairingPreferenceFilterCOP : protocols::fldsgn::filters
• ParallelBetaPairingPreferenceFilterOP : protocols::fldsgn::filters
• ParallelTemperingCOP : protocols::canonical_sampling
• ParallelTemperingOP : protocols::canonical_sampling
• PARAMAGNETIC : core::chemical
• ParamagneticDatabaseHandlerCOP : core::io::nmr
• ParamagneticDatabaseHandlerOP : core::io::nmr
• ParameterAP : core::conformation::parametric
• ParameterCAP : core::conformation::parametric
• ParameterCAPs : core::conformation::parametric
• ParameterCOP : core::conformation::parametric
• ParameterCOPs : core::conformation::parametric
• ParameterOP : core::conformation::parametric
• ParameterOPs : core::conformation::parametric
• ParametersAP : core::conformation::parametric
• ParametersCAP : core::conformation::parametric
• ParametersCAPs : core::conformation::parametric
• ParametersCOP : core::conformation::parametric
• ParametersCOPs : core::conformation::parametric
• ParametersOP : core::conformation::parametric
• ParametersOPs : core::conformation::parametric
• ParametersSetAP : core::conformation::parametric
• ParametersSetCAP : core::conformation::parametric
• ParametersSetCAPs : core::conformation::parametric
• ParametersSetCOP : core::conformation::parametric
• ParametersSetCOPs : core::conformation::parametric
• ParametersSetOP : core::conformation::parametric
• ParametersSetOPs : core::conformation::parametric
• ParameterType : core::conformation::parametric
• ParametrizationCalculatorAP : core::conformation::parametric
• ParametrizationCalculatorCAP : core::conformation::parametric
• ParametrizationCalculatorCAPs : core::conformation::parametric
• ParametrizationCalculatorCOP : core::conformation::parametric
• ParametrizationCalculatorCOPs : core::conformation::parametric
• ParametrizationCalculatorOP : core::conformation::parametric
• ParametrizationCalculatorOPs : core::conformation::parametric
• Params : core::scoring::dna
• ParaNMRScoreMoverAP : protocols::nmr
• ParaNMRScoreMoverCAP : protocols::nmr
• ParaNMRScoreMoverCOP : protocols::nmr
• ParaNMRScoreMoverOP : protocols::nmr
• 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 : protocols::pose_metric_calculators
• PARENT_DELIMETER : protocols::denovo_design
• PARENT_LABEL_OPTION : protocols::environment::claims
• ParetoOptMutationMoverCOP : protocols::design_opt
• ParetoOptMutationMoverOP : protocols::design_opt
• parse_adduct_string() : core::chemical
• parse_atom_type_data() : core::chemical::sdf
• parse_bond_type_data() : core::chemical::sdf
• parse_constraint_generators() : protocols::constraint_generator
• parse_custom_torsion() : protocols::constraint_generator
• parse_database_session() : protocols::rosetta_scripts
• parse_enum_set() : core::chemical::gasteiger
• parse_filter() : protocols::rosetta_scripts
• parse_func() : protocols::constraint_generator
• parse_grid_set_from_tag() : protocols::qsar::scoring_grid
• parse_jump_selector() : core::select::jump_selector
• parse_length_str() : protocols::denovo_design::architects
• parse_length_string() : protocols::denovo_design
• parse_lengths() : protocols::denovo_design::components
• parse_loops_from_tag() : protocols::loop_modeling::utilities
• parse_matrix() : protocols::denovo_design::filters
• parse_motif_string() : protocols::denovo_design
• parse_movemap_factory() : core::select::movemap
• parse_movemap_factory_legacy() : protocols::rosetta_scripts
• parse_movemap_tag() : protocols::rosetta_scripts
• parse_mover() : protocols::rosetta_scripts
• parse_mover_subtag() : protocols::rosetta_scripts
• parse_named_movemap_factory_legacy() : protocols::rosetta_scripts
• parse_NMR_name() : core::scoring::constraints
• parse_NMR_name_old() : core::scoring::constraints
• parse_optional_grid_set_from_tag() : protocols::qsar::scoring_grid
• parse_orientations() : protocols::denovo_design::components
• parse_out_non_standard_residues() : core::sequence
• parse_pdb_code() : protocols::splice
• parse_PDBnum_icode() : core::pose
• parse_plain_text_with_columns() : protocols::antibody::grafting
• parse_res() : protocols::hybridization
• parse_res_agnostic_commands() : core::pack::task
• parse_resfile() : core::pack::task
• parse_resfile_string() : core::pack::task
• parse_resfile_string_with_no_lockdown() : protocols::forge::methods
• parse_residue_level_task_operations() : core::pack::task::operation
• parse_residue_selector() : core::select::residue_selector
• parse_residue_selector_logic_string() : core::select::residue_selector
• parse_residue_selectors() : protocols::denovo_design::movers
• parse_resnames() : protocols::helical_bundle
• parse_resnum() : core::pose
• parse_rotamer_sampling_data() : core::pack::task::operation
• parse_score_function() : core::scoring
• parse_seeds() : protocols::seeded_abinitio
• parse_segment_names() : protocols::denovo_design::connection
• parse_selection_block() : core::pose
• parse_sequence() : core::pose
• parse_single_residue_selector() : protocols::jd3
• parse_spans() : protocols::seeded_abinitio
• parse_strand_pair() : protocols::denovo_design
• parse_stub_sets() : protocols::protein_interface_design::movers
• parse_task_operations() : core::pack::task
• parse_torsion_type() : protocols::constraint_generator
• parse_xyz_vector() : protocols::rosetta_scripts
• ParsedProtocolAP : protocols::rosetta_scripts
• ParsedProtocolCAP : protocols::rosetta_scripts
• ParsedProtocolCOP : protocols::rosetta_scripts
• ParsedProtocolOP : protocols::rosetta_scripts
• ParsedTagCacheOP : protocols::multistage_rosetta_scripts
• part_complex() : protocols::protein_interface_design::movers
• partial_align() : protocols::hybridization
• PARTIALLY_SOLVATED : core::scoring::sc::ElectrostaticComplementarityDefaults
• ParticleCOP : core::optimization
• ParticleOP : core::optimization
• ParticleOPs : core::optimization
• ParticleSwarmMinimizerCOP : core::optimization
• ParticleSwarmMinimizerOP : core::optimization
• partition_by_symm_jumps() : core::pose::symmetry
• PARTITION_CONTACT : protocols::stepwise::screener
• partition_pose_by_jump() : core::pose
• PartitionContactScreenerCOP : protocols::stepwise::screener
• PartitionContactScreenerOP : protocols::stepwise::screener
• Partner : protocols::rigid
• partner_downstream : protocols::rigid
• partner_upstream : protocols::rigid
• PartnerMotifScorerCOP : protocols::sewing::scoring
• PartnerMotifScorerCreatorCOP : protocols::sewing::scoring
• PartnerMotifScorerCreatorOP : protocols::sewing::scoring
• PartnerMotifScorerOP : protocols::sewing::scoring
• pass_metropolis() : core::pack
• passes_filters() : protocols::ligand_docking
• PATCH_LINKER : core::chemical
• patch_operation_from_patch_file_line() : core::chemical
• PatchCaseOP : core::chemical
• PatchCOP : core::chemical
• 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
• PatchOP : core::chemical
• PatchOperationOP : core::chemical
• path : protocols::hybridization
• path_basename() : protocols::stepwise::legacy::modeler::rna
• patterson_corr_energy : core::scoring::methods
• Pb : core::chemical::element
• PB : core::scoring
• PB_elec : core::scoring
• PB_elec_lr : core::scoring::methods
• PBLifetimeCacheAP : core::scoring::methods
• PBLifetimeCacheCAP : core::scoring::methods
• PBLifetimeCacheCOP : core::scoring::methods
• PBLifetimeCacheOP : core::scoring::methods
• PCA_OP : protocols::evaluation
• pci_cation_pi : core::scoring
• pci_hbond : core::scoring
• pci_pi_pi : core::scoring
• pci_salt_bridge : core::scoring
• pcs : core::scoring
• pcs2 : core::scoring
• 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
• pcs_erf() : core::scoring::nmr::pcs
• pcs_func() : core::scoring::nmr
• pcs_lmmin() : protocols::nmr::pcs
• PCSDataAP : core::scoring::nmr::pcs
• PCSDataCAP : core::scoring::nmr::pcs
• PcsDataCenterCOP : protocols::scoring::methods::pcs2
• PcsDataCenterManagerOP : protocols::scoring::methods::pcs2
• PcsDataCenterOP : protocols::scoring::methods::pcs2
• PCSDataCOP : core::scoring::nmr::pcs
• PCSDataOP : core::scoring::nmr::pcs
• PCSEnergyAP : protocols::nmr::pcs
• PCSEnergyCAP : protocols::nmr::pcs
• PcsEnergyControllerAP : protocols::topology_broker
• PcsEnergyControllerCAP : protocols::topology_broker
• PcsEnergyControllerCOP : protocols::topology_broker
• PcsEnergyControllerOP : protocols::topology_broker
• PCSEnergyCOP : protocols::nmr::pcs
• PcsEnergyCOP : protocols::scoring::methods::pcs2
• PCSEnergyOP : protocols::nmr::pcs
• PcsEnergyOP : protocols::scoring::methods::pcs2
• PcsInputCenterCOP : protocols::scoring::methods::pcs2
• PcsInputCenterOP : protocols::scoring::methods::pcs2
• PCSLigandTransformMoverAP : protocols::nmr::pcs
• PCSLigandTransformMoverCAP : protocols::nmr::pcs
• PCSLigandTransformMoverCOP : protocols::nmr::pcs
• PCSLigandTransformMoverOP : protocols::nmr::pcs
• PCSMultiGridCOP : protocols::qsar::scoring_grid
• PCSMultiGridOP : protocols::qsar::scoring_grid
• PCSMultiSetAP : core::scoring::nmr::pcs
• PCSMultiSetCAP : core::scoring::nmr::pcs
• PCSMultiSetCOP : core::scoring::nmr::pcs
• PCSMultiSetOP : core::scoring::nmr::pcs
• PCSSingleAP : core::scoring::nmr::pcs
• PCSSingleCAP : core::scoring::nmr::pcs
• PCSSingleCOP : core::scoring::nmr::pcs
• PCSSingleGridCOP : protocols::qsar::scoring_grid
• PCSSingleGridOP : protocols::qsar::scoring_grid
• PCSSingleOP : core::scoring::nmr::pcs
• PCSSingleSetAP : core::scoring::nmr::pcs
• PCSSingleSetCAP : core::scoring::nmr::pcs
• PCSSingleSetCOP : core::scoring::nmr::pcs
• PCSSingleSetOP : core::scoring::nmr::pcs
• PCSTensorAP : core::scoring::nmr::pcs
• PCSTensorCAP : core::scoring::nmr::pcs
• PCSTensorCOP : core::scoring::nmr::pcs
• PCSTensorOP : core::scoring::nmr::pcs
• PCSTensorOptimizerAP : protocols::nmr::pcs
• PCSTensorOptimizerCAP : protocols::nmr::pcs
• PCSTensorOptimizerCOP : protocols::nmr::pcs
• PCSTensorOptimizerOP : protocols::nmr::pcs
• pcsTs1 : core::scoring
• pcsTs2 : core::scoring
• pcsTs3 : core::scoring
• pcsTs4 : core::scoring
• pct_features_in_common() : protocols::simple_filters
• Pd : core::chemical::element
• PDatomCOP : core::scoring
• PDatomOP : core::scoring
• PDB_file : core::import_pose
• PDB_FILE : protocols::jd2::JobInputterInputSource
• pdb_filename() : protocols::denovo_design::movers
• PDB_LIST : protocols::cluster::calibur
• pdb_to_pose() : core::pose
• PDBChunkLibraryInputterCOP : protocols::jd3::chunk_library_inputters
• PDBChunkLibraryInputterOP : protocols::jd3::chunk_library_inputters
• PdbDataFeaturesOP : protocols::features
• PDBDumpMoverCOP : protocols::moves
• PDBDumpMoverOP : protocols::moves
• PDBFullModelInputterCOP : protocols::jd3::full_model_inputters
• PDBFullModelInputterOP : protocols::jd3::full_model_inputters
• PdbIdChunkFilterCOP : protocols::frag_picker
• PdbIdChunkFilterOP : protocols::frag_picker
• PDBInfoCOP : core::pose
• PDBInfoOP : core::pose
• PDBJobInputterOP : protocols::jd2
• PDBJobOutputterOP : protocols::jd2
• PDBLandmarkCOP : protocols::antibody
• PDBLandmarkOP : protocols::antibody
• PDBOutputCOP : protocols::dna
• PDBOutputOP : protocols::dna
• PDBPoseInputStreamOP : core::import_pose::pose_stream
• PDBPoseInputterCOP : protocols::jd3::pose_inputters
• PDBPoseInputterOP : protocols::jd3::pose_inputters
• PDBPoseMapCOP : core::pose
• PDBPoseMapOP : core::pose
• PDBPoseOutputSpecificationCOP : protocols::jd3::pose_outputters
• PDBPoseOutputSpecificationOP : protocols::jd3::pose_outputters
• PDBPoseOutputterCOP : protocols::jd3::pose_outputters
• PDBPoseOutputterOP : protocols::jd3::pose_outputters
• PDBReloadMoverCOP : protocols::simple_moves
• PDBReloadMoverOP : protocols::simple_moves
• PDBRotamerLibrarySpecificationCOP : core::chemical::rotamers
• PDBRotamerLibrarySpecificationCreator_registrator : core::init
• PDBRotamerLibrarySpecificationOP : core::chemical::rotamers
• PDBSilentStructCreator_registrator : core::init
• pdbslice() : core::pose , protocols::magnesium
• PDBWriterCOP : protocols::match::output
• PDBWriterOP : protocols::match::output
• pddf_score : core::scoring
• PDDFEnergyCOP : protocols::scoring::methods::saxs
• PDDFEnergyOP : protocols::scoring::methods::saxs
• PDDFScoreFilterCOP : protocols::simple_filters
• PDDFScoreFilterOP : protocols::simple_filters
• PDHPatchInteractionGraph : core::pack::interaction_graph
• PDHPatchInteractionGraphOP : core::pack::interaction_graph
• PDInteractionGraphOP : core::pack::interaction_graph
• PDinterCOP : core::scoring , core::scoring::power_diagram
• PDinterOP : core::scoring , core::scoring::power_diagram
• PDsphereCOP : core::scoring::power_diagram
• PDsphereOP : core::scoring::power_diagram
• PDSurfaceInteractionGraph : core::pack::interaction_graph
• PDSurfaceInteractionGraphOP : core::pack::interaction_graph
• PDvertexCOP : core::scoring , core::scoring::power_diagram
• PDvertexOP : core::scoring , core::scoring::power_diagram
• 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
• PENTOSE : core::chemical
• PEPTIDE : protocols::make_rot_lib
• peptide_bond : core::scoring
• PeptideBondEnergyCreator_registrator : core::init
• PeptideCyclizeMoverCOP : protocols::cyclic_peptide
• PeptideCyclizeMoverCOPs : protocols::cyclic_peptide
• PeptideCyclizeMoverOP : protocols::cyclic_peptide
• PeptideCyclizeMoverOPs : protocols::cyclic_peptide
• PeptideDeriverBasicStreamOutputterCOP : protocols::peptide_deriver
• PeptideDeriverBasicStreamOutputterOP : protocols::peptide_deriver
• PeptideDeriverEntryType : protocols::peptide_deriver
• PeptideDeriverFilterCOP : protocols::peptide_deriver
• PeptideDeriverFilterCreatorCOP : protocols::peptide_deriver
• PeptideDeriverFilterCreatorOP : protocols::peptide_deriver
• PeptideDeriverFilterOP : protocols::peptide_deriver
• PeptideDeriverMarkdownStreamOutputterCOP : protocols::peptide_deriver
• PeptideDeriverMarkdownStreamOutputterOP : protocols::peptide_deriver
• PeptideDeriverOutputterContainerCOP : protocols::peptide_deriver
• PeptideDeriverOutputterContainerOP : protocols::peptide_deriver
• PeptideDeriverOutputterCOP : protocols::peptide_deriver
• PeptideDeriverOutputterOP : protocols::peptide_deriver
• PeptideDeriverPoseOutputterCOP : protocols::peptide_deriver
• PeptideDeriverPoseOutputterOP : protocols::peptide_deriver
• PeptideDeriverReportFormat : protocols::peptide_deriver
• PeptideStapleMoverCOP : protocols::simple_moves
• PeptideStapleMoverOP : protocols::simple_moves
• PeptideStubMoverCOP : protocols::cyclic_peptide
• PeptideStubMoverCOPs : protocols::cyclic_peptide
• PeptideStubMoverOP : protocols::cyclic_peptide
• PeptideStubMoverOPs : protocols::cyclic_peptide
• PEPTOID : core::chemical , protocols::make_rot_lib
• per_res_rms_at_corresponding_atoms_no_super() : core::scoring
• per_res_sc_sasa() : core::scoring::sasa
• PERCENT_EDGES : protocols::cluster::calibur
• PeriodicBoxMoverCOP : protocols::simple_moves
• PeriodicBoxMoverOP : protocols::simple_moves
• PerNativeRRReporterHumanCOP : protocols::rotamer_recovery
• PerNativeRRReporterHumanOP : protocols::rotamer_recovery
• PerResidueAAProbSet : protocols::task_operations
• PerResidueClashMetricCOP : core::simple_metrics::per_residue_metrics
• PerResidueClashMetricOP : core::simple_metrics::per_residue_metrics
• PerResidueDensityFitMetricCOP : core::simple_metrics::per_residue_metrics
• PerResidueDensityFitMetricOP : core::simple_metrics::per_residue_metrics
• PerResidueEnergyMetricCOP : core::simple_metrics::per_residue_metrics
• PerResidueEnergyMetricOP : core::simple_metrics::per_residue_metrics
• PerResidueGlycanLayerMetricCOP : core::simple_metrics::per_residue_metrics
• PerResidueGlycanLayerMetricOP : core::simple_metrics::per_residue_metrics
• PerResidueRealMetricCOP : core::simple_metrics
• PerResidueRealMetricCreatorCOP : core::simple_metrics
• PerResidueRealMetricCreatorOP : core::simple_metrics
• PerResidueRealMetricOP : core::simple_metrics
• PerResidueRMSDMetricCOP : core::simple_metrics::per_residue_metrics
• PerResidueRMSDMetricOP : core::simple_metrics::per_residue_metrics
• PerResidueSasaMetricCOP : core::simple_metrics::per_residue_metrics
• PerResidueSasaMetricOP : core::simple_metrics::per_residue_metrics
• PerResidueStringMetricCOP : core::simple_metrics
• PerResidueStringMetricCreatorCOP : core::simple_metrics
• PerResidueStringMetricCreatorOP : core::simple_metrics
• PerResidueStringMetricOP : core::simple_metrics
• PerSphereAccumulatorOP : core::scoring::packstat
• PertMinMoverCOP : protocols::minimization_packing
• PertMinMoverOP : protocols::minimization_packing
• 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
• 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
• perturbtorsion_gaussian : protocols::simple_moves
• perturbtorsion_uniform : protocols::simple_moves
• perturbtorsion_unknown : protocols::simple_moves
• PG_like : protocols::fldsgn::topology
• pH_mode_exceptions() : core::chemical
• pH_MODE_EXCEPTIONS : core::pack::palette
• PH_PO : core::scoring::motif
• pHEnergyCreator_registrator : core::init
• pHEnergyOP : core::scoring::methods
• PHI : core::chemical::rings , core::id , core::scoring
• PHI_ATOM : core::chemical
• phi_dihedral : core::id
• phi_torsion() : core::id
• phi_torsion_beta_aa() : core::id
• phi_torsion_meta_aramid() : core::id
• phi_torsion_oligourea() : core::id
• phi_torsion_ortho_aramid() : core::id
• phi_torsion_para_aramid() : core::id
• phi_torsion_post_methylene_meta_aramid() : core::id
• phi_torsion_post_methylene_ortho_aramid() : core::id
• phi_torsion_post_methylene_para_aramid() : core::id
• phi_torsion_pre_methylene_meta_aramid() : core::id
• phi_torsion_pre_methylene_ortho_aramid() : core::id
• phi_torsion_pre_methylene_para_aramid() : core::id
• PHIPSI_ERR_SURF : protocols::sparta
• PhiSelectorCOP : core::select::residue_selector
• PhiSelectorOP : core::select::residue_selector
• PHOSPHATE : core::chemical , core::chemical::rna
• 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
• PHOSPHONATE : core::chemical
• PHOSPHONATE_UPPER : core::chemical
• PHOSPHONATE_UPPER_VARIANT : core::chemical
• PHOSPHORYLATION : core::chemical
• PI_ATOM : core::chemical
• pick_fragments() : core::fragment::picking_old::vall
• pick_fragments_by_ss() : core::fragment::picking_old::vall
• pick_fragments_by_ss_plus_aa() : core::fragment::picking_old::vall
• pick_loops_chainbreak() : protocols::comparative_modeling
• pick_loops_unaligned() : protocols::comparative_modeling
• pick_loopy_cutpoint() : core::kinematics
• pick_pivots() : protocols::hybridization
• PickerAP : protocols::denovo_design::components
• PickerCAP : protocols::denovo_design::components
• PickerCOP : protocols::denovo_design::components
• PickerOP : protocols::denovo_design::components
• 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
• place_de_novo_wat_at_anchor() : protocols::hydrate
• PlaceableRotamers : protocols::ligand_docking::ga_ligand_dock
• 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
• PlaceProbeMoverCOP : protocols::hotspot_hashing::movers
• PlaceProbeMoverOP : protocols::hotspot_hashing::movers
• PlaceSimultaneously_DesignMovers_subelement_mangler() : protocols::protein_interface_design::movers
• PlaceSimultaneously_NotifyMovers_subelement_mangler() : protocols::protein_interface_design::movers
• PlaceSimultaneously_StubMinimize_subelement_mangler() : protocols::protein_interface_design::movers
• PlaceSimultaneously_StubSets_subelement_mangler() : protocols::protein_interface_design::movers
• PlaceSimultaneously_subelement_mangler() : protocols::protein_interface_design::movers
• PlaceStub_DesignMovers_subelement_mangler() : protocols::protein_interface_design::movers
• PlaceStub_NotifyMovers_subelement_mangler() : protocols::protein_interface_design::movers
• PlaceStub_StubMinimize_subelement_mangler() : protocols::protein_interface_design::movers
• PlaceStub_subelement_mangler() : 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
• PLATFORM : core::scoring::rna
• Ploop2x3 : protocols::fldsgn::topology
• Ploop3x3 : protocols::fldsgn::topology
• Pm : core::chemical::element
• PNA : core::chemical
• 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
• Po : core::chemical::element
• pocket_constraint : core::scoring
• PocketConstraintOP : protocols::pockets
• PocketGridCOP : protocols::pockets
• PocketGridOP : protocols::pockets
• point3d : core::scoring::atomic_depth
• point_graph_dme() : protocols::simple_moves
• point_mutation() : protocols::protein_interface_design
• pointer_equals() : protocols::jd3
• pointer_sorter() : protocols::fldsgn::topology
• PointGraph : core::conformation
• PointGraphOP : core::conformation
• PointList : core::scoring::dssp , protocols::jumping
• PointMutationCalculatorCOP : protocols::design_opt
• PointMutationCalculatorOP : protocols::design_opt
• PointPosition : core::conformation , core
• points_in_triangle() : core::membrane
• pointwater : core::scoring
• PointWaterEnergyCOP : core::scoring::methods
• PointWaterEnergyCreator_registrator : core::init
• PointWaterEnergyOP : core::scoring::methods
• PointWaterPotentialCOP : core::scoring
• PointWaterPotentialOP : core::scoring
• PoissonBoltzmannEnergyAP : core::scoring::methods
• PoissonBoltzmannEnergyCAP : core::scoring::methods
• PoissonBoltzmannEnergyCOP : core::scoring::methods
• PoissonBoltzmannEnergyCreator_registrator : core::init
• PoissonBoltzmannEnergyOP : core::scoring::methods
• PoissonBoltzmannPotentialAP : core::scoring
• PoissonBoltzmannPotentialCAP : core::scoring
• PoissonBoltzmannPotentialCOP : core::scoring
• PoissonBoltzmannPotentialOP : core::scoring
• POLAR : core::chemical
• POLAR_HYDROGEN : core::chemical
• PolarGroupBurialPyMolStringMetricCOP : protocols::analysis::burial_metrics
• PolarGroupBurialPyMolStringMetricOP : protocols::analysis::burial_metrics
• PolarHydrogenEIter : core::chemical
• PolarHydrogenGraph : core::chemical
• PolarHydrogenPackerCOP : protocols::stepwise::modeler::polar_hydrogens
• PolarHydrogenPackerOP : protocols::stepwise::modeler::polar_hydrogens
• PolarHydrogenVIter : core::chemical
• PolarHydrogenVIterPair : core::chemical
• PolicyCOP : protocols::nonlocal
• PolicyOP : protocols::nonlocal
• POLY_CASES : protocols::viewer
• polycubic_interpolation() : core::pack::dunbrack
• POLYMER : core::chemical
• polymer : protocols::sewing::data_storage
• PolymerBondedEnergyContainerCOP : core::scoring
• PolymerBondedEnergyContainerOP : core::scoring
• PolymerBondedNeighborIteratorCOP : core::scoring
• PolymerBondedNeighborIteratorOP : core::scoring
• polymeric_termini_incomplete() : core::scoring
• PolymericType : protocols::sewing::data_storage
• Polynomial_1dCOP : core::scoring::hbonds
• Polynomial_1dOP : core::scoring::hbonds
• Pool_RMSD_OP : protocols::canonical_sampling::mc_convergence_checks
• PoolDataCOP : protocols::canonical_sampling::mc_convergence_checks
• PoolDataOP : protocols::canonical_sampling::mc_convergence_checks
• pos_mod() : core::scoring::electron_density , core::scoring::electron_density_atomwise , core::scoring::fiber_diffraction , protocols::cryst
• Pose : protocols::filters , protocols::fldsgn::potentials::sspot , protocols::flxbb
• POSE : protocols::jd2::JobInputterInputSource
• Pose : protocols::protein_interface_design::movers , protocols::protein_interface_design , 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_data_cache_from_sfr() : core::io
• pose_energies_from_sfr() : core::io
• pose_energies_to_json() : protocols::rpc
• pose_from_atom_tree_diff() : core::import_pose::atom_tree_diffs
• pose_from_binary_silent_file() : protocols::checkpoint
• pose_from_file() : core::import_pose
• pose_from_pdb_stream() : core::import_pose
• pose_from_pdbstring() : core::import_pose
• pose_from_pose() : core::io
• pose_from_saccharide_sequence() : core::pose
• pose_from_store() : protocols::indexed_structure_store
• pose_has_nonzero_Bs() : core::scoring::electron_density
• pose_inputter_xsd_type_definition_w_attributes() : protocols::jd3::pose_inputters
• pose_matches_description() : protocols::denovo_design::components
• pose_matches_user_tag() : protocols::jobdist
• pose_max_nbr_radius() : core::pose
• pose_outputter_xsd_type_definition_w_attributes() : protocols::jd3::pose_outputters
• pose_residue_is_terminal() : core::pose
• POSE_SEGMENT : protocols::legacy_sewing
• POSE_SELECTION : protocols::stepwise::screener
• pose_setup_from_file() : protocols::recces
• pose_setup_turner() : protocols::recces
• pose_tilt_angle_and_center_distance() : protocols::membrane
• pose_tm_com() : protocols::membrane
• pose_to_binary_silent_file() : protocols::checkpoint
• pose_to_pack_data() : core::scoring::packstat
• pose_to_pdb() : core::pose
• pose_to_string() : protocols::network
• pose_with_most_CBs() : protocols::sic_dock
• PoseAP : core::pose
• PoseArchitectCOP : protocols::denovo_design::architects
• PoseArchitectOP : protocols::denovo_design::architects
• PoseCAP : core::pose
• PoseCommentCOP : protocols::evolution , protocols::simple_filters
• PoseCommentOP : protocols::evolution , protocols::simple_filters
• PoseCommentsFeaturesCOP : protocols::features
• PoseCommentsFeaturesOP : protocols::features
• PoseConditionCOP : protocols::moves
• PoseConditionOP : protocols::moves
• PoseConformationFeaturesCOP : protocols::features
• PoseConformationFeaturesOP : protocols::features
• PoseCoordPickMode : core::pose
• PoseCoordPickMode_ALL : core::pose
• PoseCoordPickMode_BB : core::pose
• PoseCoordPickMode_BNP : core::pose
• PoseCoordPickMode_CA : core::pose
• PoseCoordPickMode_CB : core::pose
• PoseCoordPickMode_CB_else_CA : core::pose
• PoseCoordPickMode_CBorCA : core::pose
• PoseCoordPickMode_HVY : core::pose
• PoseCoordPickMode_HVY_IF_NP : core::pose
• PoseCoordPickMode_N_C_O : core::pose
• PoseCoordPickMode_N_CA_C : core::pose
• PoseCoordPickMode_N_CA_C_CB : core::pose
• PoseCoordPickMode_NBR : core::pose
• PoseCoordPickMode_NUL : core::pose
• poseCoords : core::scoring::electron_density
• PoseCOP : core::pose
• PoseCOPs : core::pose
• PoseCR : core::pose::motif
• PoseCUP : core::pose
• PoseEvaluatorCOP : protocols::evaluation
• PoseEvaluatorOP : protocols::evaluation
• PoseEvaluators : protocols::evaluation
• PoseEvaluatorsCOP : protocols::evaluation
• PoseEvaluatorsOP : protocols::evaluation
• PoseFolderCOP : protocols::denovo_design::components
• PoseFolderOP : protocols::denovo_design::components
• PoseFoundResiduesCombinationOP : protocols::enzdes
• PoseFromPoseResourceMoverCOP : protocols::simple_moves
• PoseFromPoseResourceMoverOP : protocols::simple_moves
• PoseInputSourceCOP : protocols::jd3::pose_inputters
• PoseInputSourceOP : protocols::jd3::pose_inputters
• PoseInputSources : protocols::jd3::pose_inputters
• PoseInputSourcesAndInputters : protocols::jd3::pose_inputters
• PoseInputStreamJobInputterOP : protocols::jd2
• PoseInputStreamOP : core::import_pose::pose_stream
• PoseInputterCOP : protocols::jd3::pose_inputters
• PoseInputterCreatorCOP : protocols::jd3::pose_inputters
• PoseInputterCreatorOP : protocols::jd3::pose_inputters
• PoseInputterOP : protocols::jd3::pose_inputters
• PoseInserterCOP : protocols::match::output
• PoseInserterOP : protocols::match::output
• PoseJobResultCOP : protocols::jd3::job_results
• PoseJobResultOP : protocols::jd3::job_results
• PoseList : protocols::stepwise::modeler
• PoseMatchOutputWriterCOP : protocols::match::output
• PoseMatchOutputWriterOP : protocols::match::output
• PoseMetricCalculatorCOP : core::pose::metrics
• PoseMetricCalculatorOP : core::pose::metrics
• PoseMetricContainerCOP : core::pose::metrics
• PoseMetricContainerOP : core::pose::metrics
• PoseMetricCOP : core::pose::metrics
• PoseMetricOP : core::pose::metrics
• PoseOP : core::pose
• PoseOPs : core::pose
• poseOPs_from_files() : core::import_pose
• PoseOutputSpecificationCOP : protocols::jd3::pose_outputters
• PoseOutputSpecificationOP : protocols::jd3::pose_outputters
• PoseOutputterCOP : protocols::jd3::pose_outputters
• PoseOutputterCreatorCOP : protocols::jd3::pose_outputters
• PoseOutputterCreatorOP : protocols::jd3::pose_outputters
• PoseOutputterMap : protocols::jd3::standard
• PoseOutputterOP : protocols::jd3::pose_outputters
• PosePackDataOP : core::scoring::packstat
• PosePropertyReporterCOP : protocols::rosetta_scripts
• PosePropertyReporterCreatorCOP : protocols::rosetta_scripts
• PosePropertyReporterCreatorOP : protocols::rosetta_scripts
• PosePropertyReporterFactoryCOP : protocols::rosetta_scripts
• PosePropertyReporterFactoryOP : protocols::rosetta_scripts
• PosePropertyReporterOP : protocols::rosetta_scripts
• PoseResidueTypeSetCOP : core::chemical
• PoseResidueTypeSetOP : core::chemical
• PoseResourceCOP : core::import_pose
• PoseResourceLoaderCOP : core::import_pose
• PoseResourceLoaderCreator_registrator : core::init
• PoseResourceLoaderOP : core::import_pose
• PoseResourceOP : core::import_pose
• poses_from_cmd_line() : protocols::comparative_modeling
• poses_from_files() : core::import_pose
• 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
• PoseSequenceCOP : core::scoring::electron_density_atomwise
• PoseSequenceOP : core::scoring::electron_density_atomwise
• PoseTag : protocols::stepwise::monte_carlo::submotif
• PoseToStructFileRepConverterCOP : core::io::pose_to_sfr
• PoseToStructFileRepConverterOP : core::io::pose_to_sfr
• PoseUP : core::pose
• PoseWithScore : protocols::abinitio
• position_cutpoint_phosphate_torsions() : core::pose::rna
• position_five_prime_phosphate() : protocols::stepwise::modeler::rna::phosphate
• position_five_prime_phosphate_SLOW() : protocols::stepwise::modeler::rna::phosphate
• position_of_atom_on_ring() : core::conformation
• PositionConservedResiduesStoreCOP : core::pose::datacache
• PositionConservedResiduesStoreOP : core::pose::datacache
• PositionDdGInfoCOP : core::io::PositionDdGInfo
• PositionDdGInfoOP : core::io::PositionDdGInfo
• PositionList : core::fragment
• Positions : protocols::dna
• positions_in_secstruct() : protocols::simple_filters
• positions_incompatible_with_task() : protocols::backrub
• PositionSpecificRandomizerCOP : protocols::genetic_algorithm
• PositionSpecificRandomizerOP : protocols::genetic_algorithm
• PositionTypes : protocols::dna
• POSITIVE_CHARGE : core::chemical
• positive_pow() : core::pack::dunbrack
• PosPair : protocols::frag_picker::nonlocal , protocols::frag_picker
• possible_root() : protocols::rna::denovo
• possible_rts() : protocols::stepwise::modeler::rna
• PossibleLoopCOP : protocols::pose_length_moves
• PossibleLoopOP : protocols::pose_length_moves
• possibly_canonical() : core::chemical::rna
• possibly_canonical_strict() : core::chemical::rna
• post_decoy() : protocols::network
• post_file() : protocols::network
• POST_METHYLENE_META_ARAMID : core::chemical
• POST_METHYLENE_ORTHO_ARAMID : core::chemical
• POST_METHYLENE_PARA_ARAMID : core::chemical
• PostDockAssemblyScorerCOP : protocols::domain_assembly
• PostDockAssemblyScorerOP : protocols::domain_assembly
• PosTypeCOP : protocols::multistate_design
• PosTypeOP : protocols::multistate_design
• power_distance() : core::scoring::power_diagram
• PowerDiagramCOP : core::scoring::power_diagram
• PowerDiagramOP : core::scoring::power_diagram
• PowExpressionCOP : protocols::pack_daemon
• PowExpressionOP : protocols::pack_daemon
• ppo_torbin_a : core::conformation
• ppo_torbin_A : core::conformation
• ppo_torbin_b : core::conformation
• ppo_torbin_B : core::conformation
• ppo_torbin_E : core::conformation
• ppo_torbin_e : core::conformation
• ppo_torbin_G : core::conformation
• ppo_torbin_g : core::conformation
• ppo_torbin_U : core::conformation
• ppo_torbin_X : core::conformation
• ppo_torsion_bin : core::conformation
• PQRAP : core::scoring
• PQRCAP : core::scoring
• PQRCOP : core::scoring
• PQROP : core::scoring
• Pr : core::chemical::element
• pre_and_post_fold_mover_subelements() : protocols::denovo_design::movers
• pre_bump_check() : core::pack::rotamer_set
• pre_erf_opt_tau() : core::scoring::nmr::pre
• pre_erf_opt_tau_xyz() : core::scoring::nmr::pre
• PRE_METHYLENE_META_ARAMID : core::chemical
• PRE_METHYLENE_ORTHO_ARAMID : core::chemical
• PRE_METHYLENE_PARA_ARAMID : core::chemical
• PRE_RATE_TYPE : core::scoring::nmr
• PRE_SPIN_TYPE : core::scoring::nmr
• PRE_SPIN_TYPE_C : core::scoring::nmr
• pre_spin_type_from_atom_name() : core::scoring::nmr
• PRE_SPIN_TYPE_H : core::scoring::nmr
• PRE_SPIN_TYPE_N : core::scoring::nmr
• PRE_TALARIS_2013_STANDARD_WTS() : core::scoring
• precision() : core::io::raw_data
• PRECISION() : protocols::dna
• PrecomputedFlexbbInteractionGraphCOP : protocols::flexpack::interaction_graph
• PrecomputedFlexbbInteractionGraphOP : protocols::flexpack::interaction_graph
• PrecomputedLibraryMoverCOP : protocols::stepwise::modeler::precomputed
• PrecomputedLibraryMoverOP : protocols::stepwise::modeler::precomputed
• PrecomputedPairEnergiesInteractionGraphCOP : core::pack::interaction_graph
• PrecomputedPairEnergiesInteractionGraphOP : core::pack::interaction_graph
• PREDataAP : core::scoring::nmr::pre
• PREDataCAP : core::scoring::nmr::pre
• PREDataCOP : core::scoring::nmr::pre
• PREDataOP : core::scoring::nmr::pre
• PredesignPerturbMoverOP : protocols::enzdes
• PredicateCOP : core::scoring
• PredicateOP : core::scoring
• PREDistanceRecordAP : protocols::nmr::pre
• PREDistanceRecordCAP : protocols::nmr::pre
• PREDistanceRecordCOP : protocols::nmr::pre
• PREDistanceRecordOP : protocols::nmr::pre
• PREEnergyAP : protocols::nmr::pre
• PREEnergyCAP : protocols::nmr::pre
• PREEnergyCOP : protocols::nmr::pre
• PREEnergyOP : protocols::nmr::pre
• PREFERENCE_NA : core::scoring::carbohydrates
• PREFERRED_ROOT : core::pose::full_model_info
• PreliminaryLarvalJobCOP : protocols::jd3::chunk_library , protocols::jd3::full_model
• PreliminaryLarvalJobOP : protocols::jd3::chunk_library , protocols::jd3::full_model
• PreliminaryLarvalJobs : protocols::jd3::standard
• PreliminaryLarvalJobTrackerCOP : protocols::jd3::standard
• PreliminaryLarvalJobTrackerOP : protocols::jd3::standard
• preload_motif_data() : core::scoring::motif
• preload_motif_data_pthread_wrapper() : core::scoring::motif
• PreloadedPDBOP : protocols::cluster::calibur
• PREMoverAP : protocols::nmr::pre
• PREMoverCAP : protocols::nmr::pre
• PREMoverCOP : protocols::nmr::pre
• PREMoverOP : protocols::nmr::pre
• PREMultiSetAP : core::scoring::nmr::pre
• PREMultiSetCAP : core::scoring::nmr::pre
• PREMultiSetCOP : core::scoring::nmr::pre
• PREMultiSetOP : core::scoring::nmr::pre
• prepare_and_write_number_of_electrostatic_interactions_of_residues_to_files() : protocols::features::strand_assembly
• prepare_scratch_residue() : core::pose::rna
• 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_new_residues() : protocols::denovo_design::components
• PreProlineFilterAP : protocols::denovo_design::filters
• PreProlineFilterCAP : protocols::denovo_design::filters
• PreProlineFilterCOP : protocols::denovo_design::filters
• PreProlineFilterOP : protocols::denovo_design::filters
• PreserveCBetaCreator_registrator : core::init
• PreserveCBetaOP : core::pack::task::operation
• PreserveCBetaRLTCreator_registrator : core::init
• PRESingleAP : core::scoring::nmr::pre
• PRESingleCAP : core::scoring::nmr::pre
• PRESingleCOP : core::scoring::nmr::pre
• PRESingleOP : core::scoring::nmr::pre
• PRESingleSetAP : core::scoring::nmr::pre
• PRESingleSetCAP : core::scoring::nmr::pre
• PRESingleSetCOP : core::scoring::nmr::pre
• PRESingleSetOP : core::scoring::nmr::pre
• prestore_sc_oversat() : core::pack::guidance_scoreterms::approximate_buried_unsat_penalty
• pretty_print_atomicoor() : core::chemical
• PreventChainFromRepackingOperationCOP : protocols::task_operations
• PreventChainFromRepackingOperationOP : protocols::task_operations
• PreventRepackingCreator_registrator : core::init
• PreventRepackingOP : core::pack::task::operation
• PreventRepackingRLTCreator_registrator : core::init
• PreventRepackingRLTOP : core::pack::task::operation
• PreventResiduesFromRepackingOperationCOP : protocols::task_operations
• PreventResiduesFromRepackingOperationOP : protocols::task_operations
• PREVIOUS_HILL : protocols::simple_moves
• PRF_BASIC : protocols::peptide_deriver
• PRF_MARKDOWN : protocols::peptide_deriver
• PRIMARY_ATOM : core::chemical
• primary_fixed_domain() : protocols::stepwise::modeler
• PrimarySequenceNeighborhoodSelectorCOP : core::select::residue_selector
• PrimarySequenceNeighborhoodSelectorOP : core::select::residue_selector
• print_atom() : core::conformation
• print_atom_info() : protocols::stepwise::modeler::rna
• print_atom_pair_constraints() : core::scoring::constraints
• print_backbone_torsions() : protocols::stepwise::legacy::modeler::rna
• print_base_centroid_atoms_for_rb_entropy() : protocols::recces
• print_base_state() : protocols::stepwise::modeler::rna
• print_buried_unsat_Hbonds() : protocols::ligand_docking
• print_chemical_shift_data() : core::scoring::rna::chemical_shift
• print_chis() : core::chemical
• print_ddgs() : protocols
• print_generators() : core::scoring::power_diagram
• print_hbonds() : protocols::rna::denovo
• print_headers() : protocols::hbnet
• print_heavy_atoms() : protocols::stepwise::modeler::rna
• print_individual_atom_info() : protocols::stepwise::modeler::rna
• print_information() : protocols::rosetta_scripts
• print_internal_coords() : protocols::rna::denovo
• print_interres_bond() : protocols::viewer
• print_job_template() : protocols::jd3
• print_list_to_string() : protocols::hbnet
• print_matrix() : protocols::cluster::calibur
• print_network() : protocols::hbnet
• print_network_w_pdb_numbering() : protocols::hbnet
• print_nmer_svm_energy_data() : protocols::simple_filters
• print_node() : core::conformation , protocols::match::output , protocols::viewer
• print_partners() : core::scoring::power_diagram
• print_points() : core::scoring::power_diagram
• print_residues_near_water() : protocols::hydrate
• print_sequence_pdb_nums() : protocols::dna
• print_sequences_pdb_nums() : protocols::dna
• print_string_vector() : protocols::flxbb
• print_sugar_pucker_state() : protocols::stepwise::modeler::rna
• print_template_script() : protocols::rosetta_scripts
• print_torsion_info() : core::pose::rna , protocols::stepwise::modeler::rna
• print_vertices() : core::scoring::power_diagram
• print_WorkingParameters_info() : protocols::stepwise::legacy::modeler::rna
• printbpy() : protocols::sic_dock::scores
• printChi() : protocols::splice
• printxyz() : protocols::loop_grower
• pro_close : core::scoring
• pro_close_ref : core::scoring
• 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
• Probability : core , core::scoring
• probability : protocols::simple_moves::bb_sampler
• Probability : protocols::simple_moves
• PROBE : core::scoring::sc
• probe_radius_for_atom_type() : protocols::match
• ProbeRadius : protocols::match
• process_decoy() : protocols::features::strand_assembly
• process_input_file() : core::import_pose
• process_last_resonances() : protocols::noesy_assign
• process_line() : protocols::ligand_docking
• process_residue_request() : core::conformation::symmetry
• ProcessorFactoryCOP : protocols::match::output
• ProcessorFactoryOP : protocols::match::output
• ProClosureEnergyCOP : core::scoring::methods
• ProClosureEnergyCreator_registrator : core::init
• ProClosureEnergyOP : core::scoring::methods
• product() : core::pack::dunbrack
• PRODUCT : protocols::calc_taskop_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
• ProhibitResiduePropertiesCreator_registrator : core::init
• ProhibitResiduePropertiesOP : core::pack::task::operation
• ProhibitSpecifiedBaseResidueTypesCreator_registrator : core::init
• ProhibitSpecifiedBaseResidueTypesOP : core::pack::task::operation
• projperp() : protocols::sic_dock
• ProlineFixMoverCOP : protocols::simple_moves
• ProlineFixMoverOP : protocols::simple_moves
• promote_sameresidue_child_of_jump_atom() : core::conformation
• PropagateClashCheckFilterCOP : protocols::dna_dock
• PropagateClashCheckFilterOP : protocols::dna_dock
• properties : update_ResidueType_enum_files
• PROPERTY_MAP() : core::chemical
• ProQ : core::scoring
• ProQ_EnergyCreator_registrator : core::init
• ProQM : core::scoring
• ProQPotentialOP : core::scoring
• ProtectedConformationAP : protocols::environment
• ProtectedConformationCAP : protocols::environment
• ProtectedConformationCOP : protocols::environment
• ProtectedConformationOP : protocols::environment
• PROTEIN : core::chemical
• protein_atom_name_to_num() : core::scoring::rna
• PROTEIN_ATR_REP : protocols::stepwise::screener
• PROTEIN_BETA_ANTIPARALLEL : protocols::toolbox
• PROTEIN_CCD_CLOSURE : protocols::stepwise::screener
• PROTEIN_FRAGMENT : protocols::toolbox
• PROTEIN_MAIN_CHAIN : protocols::toolbox
• protein_torsion_end : core::scoring
• 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::task_operations
• ProteinInterfaceDesignOperationOP : protocols::task_operations
• ProteinInterfaceMultiStateDesignMoverCOP : protocols::dna
• ProteinInterfaceMultiStateDesignMoverOP : protocols::dna
• ProteinLigandInterfaceUpweighterCOP : protocols::enzdes
• ProteinLigandInterfaceUpweighterOP : protocols::enzdes
• ProteinMainChainStepWiseSamplerCOP : protocols::stepwise::sampler::protein
• ProteinMainChainStepWiseSamplerOP : protocols::stepwise::sampler::protein
• ProteinProteinInterfaceUpweighterCOP : protocols::pack_interface
• ProteinProteinInterfaceUpweighterOP : protocols::pack_interface
• ProteinResidueConformationFeaturesCOP : protocols::features
• ProteinResidueConformationFeaturesOP : protocols::features
• ProteinResidueSelectorCOP : protocols::fold_from_loops::selectors
• ProteinResidueSelectorOP : protocols::fold_from_loops::selectors
• 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
• ProteinSilentStruct : core::io::silent
• ProteinSilentStruct_SinglePrec : core::io::silent
• ProteinSilentStruct_SinglePrecCreator_registrator : core::init
• ProteinSilentStructCreator_registrator : core::init
• ProteinSilentStructOP : core::io::silent
• ProteinTorsion : core::scoring
• ProteinUpstreamBuilderCOP : protocols::match::upstream
• ProteinUpstreamBuilderOP : protocols::match::upstream
• ProtLigEnsembleCOP : protocols::ligand_docking
• ProtLigEnsembleCOPs : protocols::ligand_docking
• ProtLigEnsembleOP : protocols::ligand_docking
• ProtLigEnsembleOPs : protocols::ligand_docking
• proto_h4 : protocols::antibody
• proto_l4 : protocols::antibody
• protocol_table_initialized_ : protocols::features
• ProtocolCOP : protocols::abinitio
• ProtocolFeaturesCOP : protocols::features
• ProtocolFeaturesOP : protocols::features
• ProtocolOP : protocols::abinitio
• ProtocolSettingsMetricCOP : core::simple_metrics::composite_metrics
• ProtocolSettingsMetricOP : core::simple_metrics::composite_metrics
• PROTONATED : core::chemical
• PROTONATED_N1 : core::chemical
• PROTONATED_N3 : core::chemical
• ProtonResonanceAP : protocols::noesy_assign
• ProtonResonanceCAP : protocols::noesy_assign
• ProtonResonanceCOP : protocols::noesy_assign
• ProtonResonanceOP : protocols::noesy_assign
• prune_1pass() : core::scoring::packstat
• prune_cavity_balls() : core::scoring::packstat
• prune_hidden_cavity_balls() : core::scoring::packstat
• prune_unpaired_residues() : protocols::denovo_design::components
• PruneBuriedUnsats_RotamerSetsOperationCOP : protocols::task_operations
• PruneBuriedUnsats_RotamerSetsOperationOP : protocols::task_operations
• PruneBuriedUnsatsOperationCOP : protocols::task_operations
• PruneBuriedUnsatsOperationOP : protocols::task_operations
• psc_compare() : core::pack::dunbrack
• PseudoBond : core::chemical
• PseudoBondCollectionCOP : core::conformation
• PseudoBondCollectionOP : core::conformation
• PseudoBondOrder : core::chemical
• 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
• PSI : core::scoring
• PSI_ATOM : core::chemical
• psi_dihedral : core::id
• psi_torsion() : core::id
• psi_torsion_beta_aa() : core::id
• psi_torsion_meta_aramid() : core::id
• psi_torsion_oligourea() : core::id
• psi_torsion_ortho_aramid() : core::id
• psi_torsion_para_aramid() : core::id
• psi_torsion_post_methylene_meta_aramid() : core::id
• psi_torsion_post_methylene_ortho_aramid() : core::id
• psi_torsion_post_methylene_para_aramid() : core::id
• psi_torsion_pre_methylene_meta_aramid() : core::id
• psi_torsion_pre_methylene_ortho_aramid() : core::id
• psi_torsion_pre_methylene_para_aramid() : core::id
• PsiPredInterfaceCOP : core::io::external
• PsiPredInterfaceOP : core::io::external
• PsiPredResultMap : core::io::external
• PSM_append : protocols::cyclic_peptide
• PSM_insert : protocols::cyclic_peptide
• PSM_prepend : protocols::cyclic_peptide
• PSM_StubMode : protocols::cyclic_peptide
• pss_tr() : core::io::silent
• PSSM2BfactorMoverCOP : protocols::simple_moves
• PSSM2BfactorMoverOP : protocols::simple_moves
• pssm_data : protocols::optimize_weights
• PSSMOptEPositionDataOP : protocols::optimize_weights
• Pt : core::chemical::element
• PT_angle : core::conformation::parametric
• PT_angle_vector : core::conformation::parametric
• PT_boolean : core::conformation::parametric
• PT_end_of_list : core::conformation::parametric
• PT_generic_integer : core::conformation::parametric
• PT_generic_integer_vector : core::conformation::parametric
• PT_generic_natural_number : core::conformation::parametric
• PT_generic_natural_number_vector : core::conformation::parametric
• PT_generic_nonnegative_valued_real : core::conformation::parametric
• PT_generic_nonnegative_valued_real_vector : core::conformation::parametric
• PT_generic_positive_valued_real : core::conformation::parametric
• PT_generic_positive_valued_real_vector : core::conformation::parametric
• PT_generic_real : core::conformation::parametric
• PT_generic_real_vector : core::conformation::parametric
• PT_generic_whole_number : core::conformation::parametric
• PT_generic_whole_number_vector : core::conformation::parametric
• PT_invalid_type : core::conformation::parametric
• pt_registrator : protocols::multistate_design
• Pu : core::chemical::element
• PuckerState : core::chemical::rna
• PURINE : core::chemical
• put_angle_in_0to360() : core::scoring::dna
• put_in_cutpoint() : core::import_pose
• put_line3() : core::scoring::electron_density::SplineInterp
• put_line4() : core::scoring::electron_density::SplineInterp
• PWatRotamerCloud : protocols::simple_moves
• PYMOL_OBSERVER : core::pose::datacache
• PyMOLMoverCOP : protocols::moves
• PyMOLMoverOP : protocols::moves
• PyMOLObserverCOP : protocols::moves
• PyMOLObserverOP : protocols::moves
• PYRANOSE : core::chemical
• 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
• PYRIMIDINE : core::chemical
• python : core::scoring