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• pack_residue() : app.pyrosetta_toolkit.modules.protocols.DesignProtocols.DesignProtocols
• packDesign() : app.pyrosetta_toolkit.modules.protocols.DesignProtocols.DesignProtocols
• PackingAngle() : PackingAngle
• packRes() : app.pyrosetta_toolkit.window_modules.full_control.FullControlWindow.FullControlWindow
• Pair_impl() : utility::json_spirit::Pair_impl< Config >
• parent() : numeric::ClusteringTreeNode , numeric::kdtree::KDNode , utility::file::PathName
• parse() : loadPDB.Protein , loadPDB.ProteinChain , numeric::expression_parser::ArithmeticASTExpression , numeric::expression_parser::ArithmeticASTFactor , numeric::expression_parser::ArithmeticASTFunction , numeric::expression_parser::ArithmeticASTRestExpression , numeric::expression_parser::ArithmeticASTRestTerm , numeric::expression_parser::ArithmeticASTTerm , numeric::expression_parser::ArithmeticASTValue , tools.CppParser.ClangXML , tools.CppParser.GccXML
• parse_arg_index() : fmt::BasicFormatter< Char >
• parse_arg_name() : fmt::BasicFormatter< Char >
• parse_block_mapping_first_key() : yaml.parser.Parser
• parse_block_mapping_key() : yaml.parser.Parser
• parse_block_mapping_value() : yaml.parser.Parser
• parse_block_node() : yaml.parser.Parser
• parse_block_node_or_indentless_sequence() : yaml.parser.Parser
• parse_block_sequence_entry() : yaml.parser.Parser
• parse_block_sequence_first_entry() : yaml.parser.Parser
• parse_document_content() : yaml.parser.Parser
• parse_document_end() : yaml.parser.Parser
• parse_document_start() : yaml.parser.Parser
• parse_flags() : fmt::internal::PrintfFormatter< Char >
• parse_flow_mapping_empty_value() : yaml.parser.Parser
• parse_flow_mapping_first_key() : yaml.parser.Parser
• parse_flow_mapping_key() : yaml.parser.Parser
• parse_flow_mapping_value() : yaml.parser.Parser
• parse_flow_node() : yaml.parser.Parser
• parse_flow_sequence_entry() : yaml.parser.Parser
• parse_flow_sequence_entry_mapping_end() : yaml.parser.Parser
• parse_flow_sequence_entry_mapping_key() : yaml.parser.Parser
• parse_flow_sequence_entry_mapping_value() : yaml.parser.Parser
• parse_flow_sequence_first_entry() : yaml.parser.Parser
• parse_header() : fmt::internal::PrintfFormatter< Char >
• parse_implicit_document_start() : yaml.parser.Parser
• parse_indentless_sequence_entry() : yaml.parser.Parser
• parse_my_tag() : basic::database::DatabaseSessionOptions , basic::resource_manager::locator::DatabaseResourceLocator , basic::resource_manager::locator::FileListResourceLocator , basic::resource_manager::locator::FileSystemResourceLocator , basic::resource_manager::locator::NullResourceLocator , basic::resource_manager::ResourceLocator , basic::resource_manager::ResourceOptions
• parse_node() : yaml.parser.Parser
• parse_strand_ids() : ExposedStrandMover
• parse_stream_start() : yaml.parser.Parser
• parser() : numeric::CalculatorParser
• path() : utility::file::FileName , utility::file::PathName
• PathName() : utility::file::PathName
• PathOption() : utility::options::PathOption
• PathOptionKey() : utility::options::PathOptionKey
• PathVectorOption() : utility::options::PathVectorOption
• PathVectorOptionKey() : utility::options::PathVectorOptionKey
• PausableSignalHub() : utility::signals::PausableSignalHub< ResultType, Signal >
• pause() : utility::signals::PausableSignalHub< ResultType, Signal >
• pausing() : utility::signals::PausableSignalHub< ResultType, Signal >
• pdb_alias() : app.pyrosetta_toolkit.modules.PythonPDB.PythonPDB
• pdb_atom_alias() : app.pyrosetta_toolkit.modules.PythonPDB.PythonPDB
• pdb_chain_alias() : app.pyrosetta_toolkit.modules.PythonPDB.PythonPDB
• PDB_IOBenchmark() : PDB_IOBenchmark
• pdb_residue_alias() : app.pyrosetta_toolkit.modules.PythonPDB.PythonPDB
• peek() : utility::io::icstream , utility::io::irstream , utility::io::izstream , yaml.reader.Reader
• peek_event() : yaml.parser.Parser
• peek_token() : yaml.scanner.Scanner
• PeptoidDesignMover() : PeptoidDesignMover
• PerformanceBenchmark() : PerformanceBenchmark
• period_certification() : numeric::random::mt19937_RG
• periodic() : numeric::interpolation::Histogram< typename, typename >
• Permute() : basic::sampling::orientations::Permute
• phi() : numeric::EulerAngles< typename > , numeric::sphericalVector< typename >
• phi_degrees() : numeric::EulerAngles< typename >
• phi_radians() : numeric::EulerAngles< typename >
• PhProtocol() : PhProtocol
• pi() : numeric::NumericTraits< T > , numeric::NumericTraits< double > , numeric::NumericTraits< float > , numeric::NumericTraits< long double >
• pi_2() : numeric::NumericTraits< T > , numeric::NumericTraits< double > , numeric::NumericTraits< float > , numeric::NumericTraits< long double >
• pi_2_over_3() : numeric::NumericTraits< T > , numeric::NumericTraits< double > , numeric::NumericTraits< float > , numeric::NumericTraits< long double >
• pi_3_over_4() : numeric::NumericTraits< T > , numeric::NumericTraits< double > , numeric::NumericTraits< float > , numeric::NumericTraits< long double >
• pi_over_180() : numeric::NumericTraits< T > , numeric::NumericTraits< double > , numeric::NumericTraits< float > , numeric::NumericTraits< long double >
• pi_over_2() : numeric::NumericTraits< T > , numeric::NumericTraits< double > , numeric::NumericTraits< float > , numeric::NumericTraits< long double >
• pi_over_3() : numeric::NumericTraits< T > , numeric::NumericTraits< double > , numeric::NumericTraits< float > , numeric::NumericTraits< long double >
• pi_over_4() : numeric::NumericTraits< T > , numeric::NumericTraits< double > , numeric::NumericTraits< float > , numeric::NumericTraits< long double >
• pipe() : fmt::File
• pivot() : numeric::MathMatrix< T >
• plot_graph() : src.PyMolLink.PyMOLMover
• plot_score_vs_rmsd() : app.pyrosetta_toolkit.modules.ScoreAnalysis.ScoreAnalysis
• point() : numeric::HomogeneousTransform< T >
• Point() : numeric::interpolation::spline::Point
• point() : numeric::kdtree::KDNode
• Pointers_and_References() : Pointers_and_References
• PolycubicSpline() : numeric::interpolation::spline::PolycubicSpline
• Polynomial_1d() : numeric::Polynomial_1d
• pop() : numeric::expression_parser::TokenSet , ObjexxFCL::internal::ObserverGraph
• pop_back() : ObjexxFCL::Chunk< T > , ObjexxFCL::ChunkVector< typename > , utility::keys::ClassKeyVector< K, T, C > , utility::keys::KeyVector< K, T > , utility::keys::SmallKeyVector< K, T >
• pop_next_message_for_node_of_type() : utility::SimulateMPIData
• pop_next_message_of_type() : utility::SimulateMPIData
• pop_node() : utility::tag::XMLErrorHandler
• populate_energy_term_listbox() : app.pyrosetta_toolkit.window_modules.full_control.FullControlWindow.FullControlWindow
• populate_restype_listbox() : app.pyrosetta_toolkit.window_modules.full_control.FullControlWindow.FullControlWindow
• populate_variant_listbox() : app.pyrosetta_toolkit.window_modules.full_control.FullControlWindow.FullControlWindow
• populateETerms() : app.pyrosetta_toolkit.window_modules.scorefunction.ScoreFxnControl.ScoreFxnControl
• populateScoreList() : app.pyrosetta_toolkit.window_modules.scorefunction.ScoreFxnControl.ScoreFxnControl
• pos_in_history_queue() : utility::recent_history_queue
• pose_num() : sidechain_cst_3.Residue
• PosePyObserver() : PosePyObserver
• PosePyObserver2() : PosePyObserver2
• positive() : ObjexxFCL::DynamicIndexRange , ObjexxFCL::IndexRange
• positive_value() : ObjexxFCL::IndexRange
• precision() : fmt::AlignSpec , fmt::FormatSpec , fmt::TypeSpec< TYPE > , numeric::IOTraits< T > , numeric::IOTraits< double > , numeric::IOTraits< float > , numeric::IOTraits< int > , numeric::IOTraits< long double > , numeric::IOTraits< long int > , numeric::IOTraits< short int > , numeric::IOTraits< unsigned int > , numeric::IOTraits< unsigned long int > , numeric::IOTraits< unsigned short int > , ObjexxFCL::TypeTraits< T > , ObjexxFCL::TypeTraits< double > , ObjexxFCL::TypeTraits< float > , ObjexxFCL::TypeTraits< int > , ObjexxFCL::TypeTraits< long double > , ObjexxFCL::TypeTraits< long int > , ObjexxFCL::TypeTraits< short int > , ObjexxFCL::TypeTraits< unsigned int > , ObjexxFCL::TypeTraits< unsigned long int > , ObjexxFCL::TypeTraits< unsigned short int >
• predicate_cmp_filename() : utility::predicate_cmp_filename
• predict() : utility::libsvm::Svm_rosetta
• predict_probability() : utility::libsvm::Svm_rosetta
• prefix() : utility::options::OptionCollection , yaml.reader.Reader
• prefix_code() : binder::Binder , binder::ClassBinder
• prepack_input_structure() : supercharge
• prepack_pose() : PhProtocol
• prepare_anchor() : yaml.emitter.Emitter
• prepare_for_output() : utility::tag::XMLSchemaAttribute , utility::tag::XMLSchemaComplexType , utility::tag::XMLSchemaElement , utility::tag::XMLSchemaModelGroup , utility::tag::XMLSchemaRestriction , utility::tag::XMLSchemaTopLevelElement
• prepare_for_query() : numeric::coordinate_fitting::CoordinateArray_RMSD_FlatLookup< Real > , numeric::coordinate_fitting::FlatLookup< QueryType, EntryType, Real >
• prepare_int_buffer() : fmt::BasicWriter< Char >
• prepare_rotamer_sets() : InteractionGraphPerformanceBenchmark
• prepare_sequence_of_subelement_sets() : utility::tag::XMLSchemaComplexTypeGeneratorImpl
• prepare_subelement_choice_opt() : utility::tag::XMLSchemaComplexTypeGeneratorImpl
• prepare_subelement_choice_req() : utility::tag::XMLSchemaComplexTypeGeneratorImpl
• prepare_subelement_repeatable() : utility::tag::XMLSchemaComplexTypeGeneratorImpl
• prepare_subelement_single_instance_optional() : utility::tag::XMLSchemaComplexTypeGeneratorImpl
• prepare_subelement_single_instance_required() : utility::tag::XMLSchemaComplexTypeGeneratorImpl
• prepare_subelement_single_instance_required_ordered() : utility::tag::XMLSchemaComplexTypeGeneratorImpl
• prepare_tag() : yaml.emitter.Emitter
• prepare_tag_handle() : yaml.emitter.Emitter
• prepare_tag_prefix() : yaml.emitter.Emitter
• prepare_version() : yaml.emitter.Emitter
• prepend_channel_name() : basic::Tracer
• pretty() : numeric::expression_parser::ASTPrinter
• prev() : utility::list_element< T >
• prevRes() : app.pyrosetta_toolkit.window_modules.design.ResfileDesignWindow.ResfileDesignWindow , app.pyrosetta_toolkit.window_modules.full_control.FullControlWindow.FullControlWindow
• PrimaryKey() : basic::database::schema_generator::PrimaryKey
• print() : basic::database::schema_generator::Column , basic::database::schema_generator::Constraint , basic::database::schema_generator::DbBigInt , basic::database::schema_generator::DbDataType , basic::database::schema_generator::DbDouble , basic::database::schema_generator::DbInteger , basic::database::schema_generator::DbReal , basic::database::schema_generator::DbText , basic::database::schema_generator::DbTextKey , basic::database::schema_generator::DbUUID , basic::database::schema_generator::ForeignKey , basic::database::schema_generator::GreaterThanConstraint , basic::database::schema_generator::Index , basic::database::schema_generator::PrimaryKey , basic::database::schema_generator::Schema , basic::database::schema_generator::UniqueConstraint , basic::MetricValue< T >
• Print() : basic::sampling::orientations::Quaternion
• print() : basic::sampling::orientations::QuaternionGrid
• Print() : basic::sampling::orientations::QuatSet
• print() : fmt::BufferedFile , numeric::expression_parser::TokenSet
• print_all_hbonds() : app.pyrosetta_toolkit.window_main.frames.SimpleAnalysisFrame.SimpleAnalysisFrame
• print_current_options() : app.pyrosetta_toolkit.window_modules.options_system.OptionSystemManager.OptionSystemManager
• print_energy() : app.pyrosetta_toolkit.window_main.frames.SimpleAnalysisFrame.SimpleAnalysisFrame
• print_full_energy() : app.pyrosetta_toolkit.window_main.frames.SimpleAnalysisFrame.SimpleAnalysisFrame
• print_hbonds() : app.pyrosetta_toolkit.window_main.frames.SimpleAnalysisFrame.SimpleAnalysisFrame , PhProtocol
• print_header() : utility::io::mpi_stream::basic_mpi_ostreambase< Elem, Tr, ElemA, ByteT, ByteAT > , utility::io::mpi_stream::basic_mpi_streambuf< Elem, Tr, ElemA, ByteT, ByteAT >
• print_netcharge_and_mutations() : supercharge
• print_numbering() : app.pyrosetta_toolkit.pyrosetta_toolkit.main_window
• print_option_info() : app.pyrosetta_toolkit.window_main.frames.SimpleAnalysisFrame.SimpleAnalysisFrame
• print_pose() : app.pyrosetta_toolkit.window_main.frames.SimpleAnalysisFrame.SimpleAnalysisFrame
• print_roc_curve() : numeric::RocCurve
• print_sheets() : ExposedStrandMover
• print_sheets_extras() : ExposedStrandMover
• print_to_curr_pos() : numeric::expression_parser::TokenSet
• PrintEuler() : basic::sampling::orientations::Quaternion
• PrintfArgFormatter() : fmt::internal::PrintfArgFormatter< Char >
• PrintfFormatter() : fmt::internal::PrintfFormatter< Char >
• priority() : basic::Tracer
• private_index() : utility::keys::AutoKey< O, S, C > , utility::keys::Key , utility::keys::UserKey< O, S, C > , utility::keys::VariantKey< K >
• process_anchor() : yaml.emitter.Emitter
• process_directives() : yaml.parser.Parser
• process_empty_scalar() : yaml.parser.Parser
• process_fragfile() : DockFragmentsMover
• process_packet() : PyMOLPyRosettaServer.PR_PyMOLServer
• process_scalar() : yaml.emitter.Emitter
• process_tag() : yaml.emitter.Emitter
• processBackSpacePress() : app.pyrosetta_toolkit.window_modules.interactive_terminal.interactive_terminal.TkConsoleView
• processDownPress() : app.pyrosetta_toolkit.window_modules.interactive_terminal.interactive_terminal.TkConsoleView
• processed() : utility::SimulateMPIMessage
• processEnterPress() : app.pyrosetta_toolkit.window_modules.interactive_terminal.interactive_terminal.TkConsoleView
• processKeyPress() : app.pyrosetta_toolkit.window_modules.interactive_terminal.interactive_terminal.TkConsoleView
• processTabPress() : app.pyrosetta_toolkit.window_modules.interactive_terminal.interactive_terminal.TkConsoleView
• processUpPress() : app.pyrosetta_toolkit.window_modules.interactive_terminal.interactive_terminal.TkConsoleView
• ProfileThis() : basic::ProfileThis
• project_normal() : numeric::xyzTriple< typename > , numeric::xyzVector< typename >
• project_parallel() : numeric::xyzTriple< typename > , numeric::xyzVector< typename >
• projected_normal() : numeric::xyzTriple< typename > , numeric::xyzVector< typename >
• projected_parallel() : numeric::xyzTriple< typename > , numeric::xyzVector< typename >
• proxy() : ObjexxFCL::CArrayP< typename >
• Proxy() : ObjexxFCL::CArrayP< typename >
• proxy() : ObjexxFCL::FArray< typename >
• ProxySentinel() : ObjexxFCL::internal::ProxySentinel
• psi() : numeric::EulerAngles< typename >
• psi_degrees() : numeric::EulerAngles< typename >
• psi_radians() : numeric::EulerAngles< typename >
• ptr_registry() : utility::factory::Factory< typename >
• ptr_registry_transfer() : utility::factory::Factory< typename >
• pure_test_p() : test.T850_SubClassing.PyOverloadTest , utility::py::OverloadTest
• pure_test_ref() : test.T850_SubClassing.PyOverloadTest , utility::py::OverloadTest
• push() : ObjexxFCL::internal::ObserverGraph
• push_back() : fmt::Buffer< T > , numeric::IntervalSet< typename > , ObjexxFCL::Chunk< T > , ObjexxFCL::ChunkVector< typename > , utility::keys::ClassKeyVector< K, T, C > , utility::keys::KeyVector< K, T > , utility::keys::SmallKeyVector< K, T > , utility::options::VectorOption_T_< K, T >
• push_node() : utility::tag::XMLErrorHandler
• push_to_front_of_history_queue() : utility::recent_history_queue
• put() : utility::io::mpi_stream::basic_mpi_ostream< Elem, Tr, ElemA, ByteT, ByteAT > , utility::io::ocstream , utility::io::orstream , utility::io::ozstream , zlib_stream::basic_zip_ostream< Elem, Tr, ElemA, ByteT, ByteAT >
• put_back_from_zip_stream() : zlib_stream::basic_unzip_streambuf< Elem, Tr, ElemA, ByteT, ByteAT >
• put_long_as_uint32() : utility::io::mpi_stream::basic_mpi_ostream< Elem, Tr, ElemA, ByteT, ByteAT > , zlib_stream::basic_zip_ostream< Elem, Tr, ElemA, ByteT, ByteAT >
• putback() : utility::io::icstream , utility::io::irstream , utility::io::izstream
• px() : numeric::HomogeneousTransform< T > , numeric::xyzTransform< typename >
• py() : numeric::HomogeneousTransform< T > , numeric::xyzTransform< typename >
• pythag() : basic::svd::SVD_Solver
• pz() : numeric::HomogeneousTransform< T > , numeric::xyzTransform< typename >