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

- p -

• p : docking , loops , loops_kic , test::G100_Functions_Input , test::G101_Functions_Output , test::G102_Functions_General , test::G103_Functions_Analysis , test::G104_Functions_Sequence , test::G200_Module_Region , test::G205_Module_RegionalScoring , test::T650_LoopsKIC , test::Workshop4test
• P : test::Workshop4test
• p1_theta_deriv() : numeric::deriv
• P_omega0() : numeric::crick_equations
• pack : loops , loops_kic , test::T500_Packing , test::T650_LoopsKIC
• pack_extra_bodies() : apps::public1::scenarios::chemically_conjugated_docking
• pack_mover : test::Workshop6test
• PACK_RADIUS : app::delta_score_per_mutation
• PACK_ROTAMERS : basic
• pack_rotamers_mover : app::delta_score_per_mutation
• packer_task() : demo::D050_Packer_task
• pad() : ObjexxFCL
• padded() : ObjexxFCL
• Pair : utility::json_spirit
• pair_close_interface() : calccontacts
• pair_close_internal() : calccontacts
• pair_up() : prune_atdiff_top5pct
• ParameterList : numeric::kinematic_closure
• ParameterMatrix : numeric::kinematic_closure
• params_from_pubchem() : toolbox::load_ligand
• params_list : test::T880_Other
• parse() : extract_scores_and_constraints , yaml
• parse_and_pair() : calccontacts
• parse_database_connection() : basic::database
• parse_full_name() : exclude
• parse_rosettascript() : src::protocols::rosetta_scripts
• parse_string_to_boolean_expression() : numeric::expression_parser
• parse_string_to_expression() : numeric::expression_parser
• parse_taskops_file : sequence_recovery
• parseAndWrapModule() : tools::CppParser
• parseAtomList() : loadPDB
• parseByChain() : loadPDB
• parser : app::delta_score_per_mutation , app::pyrosetta_toolkit::modules::DesignBreakdown , app::surface_docking::surface_docking , demo::D010_Pose_structure , demo::D020_Pose_scoring , demo::D030_Fold_tree , demo::D040_Movemap , demo::D050_Packer_task , demo::D060_Folding , demo::D070_Refinement , demo::D080_Loop_modeling , demo::D090_Ala_scan , demo::D100_Docking , demo::D110_DNA_interface , demo::D120_Ligand_interface
• parserule : contacts
• parseTranslationUnit() : tools::CppParser
• partner() : PDBInfo , PhiPsi
• partner1 : local
• partner2 : local
• partner2_residue : local
• partners : demo::D090_Ala_scan , demo::D100_Docking , demo::D110_DNA_interface , demo::D120_Ligand_interface
• path : app::surface_docking::surface_docking
• path_prefix : make_static_database
• PATH_SEPARATOR() : platform::file
• pathname() : utility
• PathOption : basic::options
• PathOptionKey : basic::options
• PathVectorOption : basic::options
• PathVectorOptionKey : basic::options
• PDB : app::surface_docking::surface_docking
• pdb : contacts , PhiPsi
• pdb_database : test::G203_Module_SQLPDB
• pdb_filename : demo::D010_Pose_structure , demo::D020_Pose_scoring , demo::D040_Movemap , demo::D050_Packer_task , demo::D060_Folding , demo::D070_Refinement , demo::D080_Loop_modeling , demo::D090_Ala_scan , demo::D100_Docking , demo::D110_DNA_interface , demo::D120_Ligand_interface
• PDB_out : demo::D030_Fold_tree , demo::D040_Movemap , demo::D050_Packer_task
• pdb_path : test::G203_Module_SQLPDB
• pdbcode : clean_pdb_keep_ligand
• pdbfile : clean_pdb_keep_ligand
• pdbID : app::pyrosetta_toolkit::modules::SQLPDB
• pdbname : clean_pdb_keep_ligand , toolbox::make_rna_rosetta_ready
• pdbnames : toolbox::make_rna_rosetta_ready
• peptoid : mrlo
• peptoid_design_positions : peptoid_design
• perform_build() : BuildPackagedBindings
• periodic_range() : basic
• pert_dock_rot_mag : dddm
• pert_dock_trans_mag : dddm
• pert_mc_temp : dddm
• pert_mover : test::Workshop7test
• pert_num : dddm , hbs_design , oop_design , peptoid_design
• pert_pep_num_rep : dddm
• pert_pep_shear_E : dddm
• pert_pep_shear_H : dddm
• pert_pep_shear_L : dddm
• pert_pep_shear_temp : dddm
• pert_pep_small_E : dddm
• pert_pep_small_H : dddm
• pert_pep_small_L : dddm
• pert_pep_small_temp : dddm
• pert_ter_num_rep : dddm
• pert_ter_shear_E : dddm
• pert_ter_shear_H : dddm
• pert_ter_shear_L : dddm
• pert_ter_shear_temp : dddm
• pert_ter_small_E : dddm
• pert_ter_small_H : dddm
• pert_ter_small_L : dddm
• pert_ter_small_temp : dddm
• phe_tyr_hack : mrlo
• PHI : test::Workshop4test
• PhiNByX_1 : test::Workshop9test
• PhiNByX_2 : test::Workshop9test
• PhiPsi() : PhiPsi
• pi : numeric::constants::d , numeric::constants::f , numeric::constants::ld , numeric::constants::r
• pi_2 : numeric::constants::d , numeric::constants::f , numeric::constants::ld , numeric::constants::r
• pi_2_over_3 : numeric::constants::d , numeric::constants::f , numeric::constants::ld , numeric::constants::r
• pi_over_180 : numeric::constants::d , numeric::constants::f , numeric::constants::ld , numeric::constants::r
• pi_over_2 : numeric::constants::d , numeric::constants::f , numeric::constants::ld , numeric::constants::r
• pi_over_3 : numeric::constants::d , numeric::constants::f , numeric::constants::ld , numeric::constants::r
• pick_random_index_from_cdf() : numeric::random
• pind() : basic::sampling::orientations
• PLAIN_COLUMNS : app::pyrosetta_toolkit::modules::prettytable::prettytable
• plane3points() : app::surface_docking::surf_param
• PlatformBits : BuildBindings
• plot3d() : PyMOLPyRosettaServer
• PLUS_SYMBOL : numeric::expression_parser
• pmm : test::Workshop4test , test::Workshop5test , test::Workshop8test
• po : PyMOL_demo
• point2lines2() : app::surface_docking::surf_param
• point2lines3() : app::surface_docking::surf_param
• point_intersect_plane() : app::surface_docking::surf_param
• point_value16() : numeric::kinematic_closure
• point_value2() : numeric::kinematic_closure
• point_value4() : numeric::kinematic_closure
• point_value6() : numeric::kinematic_closure
• point_value8() : numeric::kinematic_closure
• poly : numeric::kinematic_closure
• Polynomial_1dCOP : numeric
• Polynomial_1dOP : numeric
• polyProduct12x4() : numeric::kinematic_closure
• polyProduct2x2() : numeric::kinematic_closure
• polyProduct4sq() : numeric::kinematic_closure
• polyProduct4x2() : numeric::kinematic_closure
• polyProduct4x4() : numeric::kinematic_closure
• polyProduct6x6() : numeric::kinematic_closure
• polyProduct8sq() : numeric::kinematic_closure
• polyProduct8x8() : numeric::kinematic_closure
• POOL_RMSD_ADD_STRUCTURE : basic
• POOL_RMSD_EVALUATE : basic
• POOL_RMSD_MASTER_EVALUATE : basic
• popLigands() : loadPDB
• pos : make_symmdef_file_denovo , toolbox::make_rna_rosetta_ready
• pose : app::surface_docking::surface_docking , demo::D010_Pose_structure , demo::D020_Pose_scoring , demo::D040_Movemap , demo::D050_Packer_task , demo::D060_Folding , PyMOL_demo , test::T007_TracerIO , test::T010_LoadPDB , test::T100_Basic , test::T150_PyMOL_Integration , test::T200_Scoring , test::T250_Constraints , test::T400_Refinement , test::T500_Packing , test::T700_FoldTree , test::T850_SubClassing , test::T860_SubClassing_EnergyMethods , test::T870_SubClassing_EnergyMethods2 , test::Workshop2test , test::Workshop3test , test::Workshop4test , test::Workshop6test , test::Workshop7test , test::Workshop8test , test::Workshop9test
• pose2 : test::T010_LoadPDB
• pose3 : test::T010_LoadPDB , test::T100_Basic
• pose4 : test::T100_Basic
• POSE_COPY : basic
• pose_frag : test::T400_Refinement
• pose_from_params() : toolbox::load_ligand
• pose_from_pubchem() : toolbox::load_ligand
• pose_from_rcsb() : toolbox , toolbox::rcsb
• pose_from_sequence() : src , toolbox::mutants
• pose_fs : test::T010_LoadPDB
• pose_high : test::Workshop7test
• pose_low : test::Workshop7test
• pose_s : PyMOL_demo
• pose_scoring() : demo::D020_Pose_scoring
• pose_structure() : demo::D010_Pose_structure
• post_pre_packing_score : app::delta_score_per_mutation
• post_repack : revert_app
• postfix : tools::CppParser
• postproc() : exclude
• pow() : ObjexxFCL
• PP() : numeric::crick_equations
• pr : test::T500_Packing
• pre_packminpack : local
• pre_pre_packing_score : app::delta_score_per_mutation
• prepareBoostLibs() : BuildPackagedBindings
• prepareMiniLibs() : BuildBindings
• preparePythonLibs() : BuildPackagedBindings
• prepareRosettaLibs() : BuildPackagedBindings
• pretty_print : utility::json_spirit
• principal_angle() : numeric
• principal_angle_degrees() : numeric
• principal_angle_radians() : numeric
• principal_component_eigenvalues() : numeric
• principal_components() : numeric
• principal_components_and_eigenvalues() : numeric
• principal_components_and_eigenvalues_ndimensions() : numeric
• print_() : BuildBindings
• print_all_phi_psi() : app::pyrosetta_toolkit::modules::tools::analysis
• print_all_residue_energies() : app::pyrosetta_toolkit::modules::tools::analysis
• print_ddG_breakdown() : mp_ddG , predict_ddG
• print_glossary() : app::pyrosetta_toolkit::modules::help
• print_point() : numeric::kdtree
• print_points() : numeric::kdtree
• print_probabilities() : numeric
• print_score_labels_to_file() : mp_ddG , predict_ddG
• print_surf_move() : app::surface_docking::surf_param
• print_tree() : numeric::kdtree
• printMatrix() : numeric::kinematic_closure
• printResList() : loadPDB
• printTranspose() : numeric::kinematic_closure
• printVector() : numeric::kinematic_closure
• printWikiTable() : options_class
• process() : basic::options
• process_file() : ObjexxFCL
• product() : numeric
• prof_reset() : basic
• prof_show() : basic
• prof_start_function_body() : basic
• prof_stop_function_body() : basic
• ProfTag : basic
• proj_angl() : numeric
• projection_matrix() : numeric
• prot_coor : PDBInfo
• protein : PDBInfo
• protein_letters : toolbox::mutants
• ProtTypes : app::pyrosetta_toolkit::window_modules::protocol_builder::ProtocolBuilder
• ProtTypesDic : app::pyrosetta_toolkit::window_modules::protocol_builder::ProtocolBuilder
• PseudoMatrix : numeric::kinematic_closure
• PseudoVector : numeric::kinematic_closure
• PSI : test::Workshop4test
• pv : test::T850_SubClassing
• pwd : app::pyrosetta_toolkit::modules::tools::general_tools , app::pyrosetta_toolkit::modules::tools::interfaces , app::pyrosetta_toolkit::window_modules::vicinity_options::vicinity_window
• py3k : app::pyrosetta_toolkit::modules::prettytable::prettytable
• py_modules : app::pyrosetta_toolkit::modules::prettytable::setup
• PyExitCallbackCOP : utility::py
• PyExitCallbackOP : utility::py
• pymol : loops_kic , PyMOL_demo , test::T150_PyMOL_Integration , test::T650_LoopsKIC , test::Workshop3test
• pymol_chains() : basic
• PyMOL_Mover : src::PyMolLink
• PyMOL_Observer : src::PyMolLink
• PyRosettaVersion : src
• pythag() : numeric::linear_algebra
• python_pdb : test::G202_Module_PythonPDB