- 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
• pack : loops , loops_kic , test::T500_Packing , test::T650_LoopsKIC
• pack_mover : test::Workshop6test
• PACK_RADIUS : app::delta_score_per_mutation
• pack_rotamers_mover : app::delta_score_per_mutation
• params_list : test::T880_Other
• parse_taskops_file : sequence_recovery
• 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
• 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
• 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
• 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
• 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
• PLAIN_COLUMNS : app::pyrosetta_toolkit::modules::prettytable::prettytable
• PlatformBits : BuildBindings
• pmm : test::Workshop4test , test::Workshop5test , test::Workshop8test
• po : PyMOL_demo
• 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_frag : test::T400_Refinement
• pose_fs : test::T010_LoadPDB
• pose_high : test::Workshop7test
• pose_low : test::Workshop7test
• pose_s : PyMOL_demo
• post_pre_packing_score : app::delta_score_per_mutation
• post_repack : revert_app
• postfix : tools::CppParser
• pr : test::T500_Packing
• pre_packminpack : local
• pre_pre_packing_score : app::delta_score_per_mutation
• 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
• 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
• pymol : loops_kic , PyMOL_demo , test::T150_PyMOL_Integration , test::T650_LoopsKIC , test::Workshop3test
• PyMOL_Mover : src::PyMolLink
• PyMOL_Observer : src::PyMolLink
• PyRosettaVersion : src
• python_pdb : test::G202_Module_PythonPDB