- p -

• p : basic::options::OptionKeys::score::fiber_diffraction , 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
• p_aa_pp : basic::options::OptionKeys::corrections::score
• p_aa_pp_nogridshift : basic::options::OptionKeys::corrections::score
• p_homol_csts : basic::options::OptionKeys::pepspec
• p_value_selection : basic::options::OptionKeys::frags
• pack : loops , loops_kic , test::T500_Packing , test::T650_LoopsKIC
• pack_glycans : basic::options::OptionKeys::carbohydrates::glycan_relax
• pack_max_threshold : basic::options::OptionKeys::motifs
• pack_min_threshold : basic::options::OptionKeys::motifs
• pack_missing_sidechains : basic::options::OptionKeys::packing
• pack_mover : test::Workshop6test
• pack_patch : basic::options::OptionKeys::docking
• pack_phosphate_penalty : basic::options::OptionKeys::score
• PACK_RADIUS : app::delta_score_per_mutation
• pack_rotamers_mover : app::delta_score_per_mutation
• pack_score_cutoff : basic::options::OptionKeys::motifs
• pack_sfxn : basic::options::OptionKeys::cp
• pack_until_converge : basic::options::OptionKeys::ddg
• pack_water_hydrogens : basic::options::OptionKeys::magnesium
• pack_weights : basic::options::OptionKeys::score
• packing : basic::options::OptionKeys::packing
• packing_weight : basic::options::OptionKeys::fingerprint
• packonly_after_graft : basic::options::OptionKeys::antibody
• packstat : basic::options::OptionKeys::packstat
• packstat_pdb : basic::options::OptionKeys::packstat
• padding_score_filter : basic::options::OptionKeys::evolution
• padding_stage2_filter : basic::options::OptionKeys::evolution
• pair_off : basic::options::OptionKeys::FloppyTail
• pairdata_input_pdb_list : basic::options::OptionKeys::robert
• pairing_file : basic::options::OptionKeys::jumps
• pairings : basic::options::OptionKeys::templates
• pales : basic::options::OptionKeys::evaluation
• paper_ab_db : basic::options::OptionKeys::antibody::design
• paper_ab_db_path : basic::options::OptionKeys::antibody::design
• parameters : basic::options::OptionKeys::relax::centroid
• params : basic::options::OptionKeys::dna::specificity , basic::options::OptionKeys::holes
• params_file : basic::options::OptionKeys::flexPepDocking , basic::options::OptionKeys::rna::farna
• params_list : test::T880_Other
• paratope : basic::options::OptionKeys::antibody::design
• parent_selection_kT : basic::options::OptionKeys::lh
• parentlist : basic::options::OptionKeys::evolution
• parin_favorite_output : basic::options::OptionKeys::stepwise::rna
• parse_charge : basic::options::OptionKeys::corrections::chemical
• parse_tagfile : basic::options::OptionKeys::optE
• parse_taskops_file : sequence_recovery
• parser : app::delta_score_per_mutation , app::pyrosetta_toolkit::modules::DesignBreakdown , app::surface_docking::surface_docking , basic::options::OptionKeys::parser , 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 , setup_pyrosetta , toolbox::adjust_library_path
• parser_read_cloud_pdb : basic::options::OptionKeys::enzdes
• parserule : contacts
• partner1 : local
• partner2 : local
• partner2_residue : local
• partner_pdb : basic::options::OptionKeys::sewing
• partners : basic::options::OptionKeys::docking , demo::D090_Ala_scan , demo::D100_Docking , demo::D110_DNA_interface , demo::D120_Ligand_interface
• password : basic::options::OptionKeys::inout::dbms
• patch : basic::options::OptionKeys::rigid , basic::options::OptionKeys::score
• patch_filter_scorefxn : basic::options::OptionKeys::fast_loops
• patch_selectors : basic::options::OptionKeys::chemical
• patchdock : basic::options::OptionKeys::parser
• patchdock_random_entry : basic::options::OptionKeys::parser
• path : app::surface_docking::surface_docking , basic::options::OptionKeys::in::path , basic::options::OptionKeys::inout::dbms , basic::options::OptionKeys::mh::path , basic::options::OptionKeys::out::path
• path_prefix : make_static_database
• patterson : basic::options::OptionKeys::patterson
• pb_potential : basic::options::OptionKeys::pb_potential
• PBP_clustering_at_chain_closure : basic::options::OptionKeys::stepwise::rna
• pca : basic::options::OptionKeys::in::file
• PCS : basic::options::OptionKeys::PCS
• pcs_cluster_coverage : basic::options::OptionKeys::robert
• pcs_cluster_lowscoring : basic::options::OptionKeys::robert
• pcs_dump_cluster : basic::options::OptionKeys::robert
• PCS_frag_cst : basic::options::OptionKeys::in::file
• pcs_maxsub_filter : basic::options::OptionKeys::robert
• pcs_maxsub_rmsd : basic::options::OptionKeys::robert
• PCSTS1 : basic::options::OptionKeys::PCSTS1
• PCSTS2 : basic::options::OptionKeys::PCSTS2
• PCSTS3 : basic::options::OptionKeys::PCSTS3
• PCSTS4 : basic::options::OptionKeys::PCSTS4
• PDB : app::surface_docking::surface_docking
• pdb : basic::options::OptionKeys::in::path , basic::options::OptionKeys::mh::filter , basic::options::OptionKeys::mh::path , basic::options::OptionKeys::out::path , basic::options::OptionKeys::out , contacts , PhiPsi
• pdb1 : basic::options::OptionKeys::assembly
• pdb2 : basic::options::OptionKeys::assembly , basic::options::OptionKeys::chunk
• pdb_comments : basic::options::OptionKeys::out::file
• PDB_components_file : basic::options::OptionKeys::in::file
• 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_gz : basic::options::OptionKeys::out
• pdb_list : basic::options::OptionKeys::pepspec
• PDB_out : demo::D030_Fold_tree , demo::D040_Movemap , demo::D050_Packer_task
• pdb_parents : basic::options::OptionKeys::out::file
• pdb_path : test::G203_Module_SQLPDB
• pdb_pos : basic::options::OptionKeys::dna::specificity
• pdbcode : clean_pdb_keep_ligand
• pdbfile : clean_pdb_keep_ligand
• pdbID : app::pyrosetta_toolkit::modules::SQLPDB , basic::options::OptionKeys::matdes
• pdblist : basic::options::OptionKeys::lh::symfragrm
• pdbname : clean_pdb_keep_ligand , pyrosetta::toolbox::make_rna_rosetta_ready , toolbox::make_rna_rosetta_ready
• pdbnames : pyrosetta::toolbox::make_rna_rosetta_ready , toolbox::make_rna_rosetta_ready
• pdz : basic::options::OptionKeys::chemically_conjugated_docking
• penalize_mixture_func : basic::options::OptionKeys::constraints
• pep_anchor : basic::options::OptionKeys::pepspec
• pep_chain : basic::options::OptionKeys::pepspec
• pep_fold_only : basic::options::OptionKeys::flexPepDocking
• pep_lengths : basic::options::OptionKeys::peptide_deriver
• pep_refine : basic::options::OptionKeys::flexPepDocking
• pepspec : basic::options::OptionKeys::pepspec
• peptide_anchor : basic::options::OptionKeys::flexPepDocking
• peptide_chain : basic::options::OptionKeys::flexPepDocking
• peptide_deriver : basic::options::OptionKeys::peptide_deriver
• peptide_loop_model : basic::options::OptionKeys::flexPepDocking
• peptoid : mrlo
• peptoid_design_positions : peptoid_design
• per_chain_renumbering : basic::options::OptionKeys::out::file
• pert_dock_rot_mag : dddm
• pert_dock_trans_mag : dddm
• pert_init_loop : basic::options::OptionKeys::lh
• 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
• perturb : basic::options::OptionKeys::abinitio
• perturb_CCD_off : basic::options::OptionKeys::AnchoredDesign
• perturb_cycles : basic::options::OptionKeys::AnchoredDesign , basic::options::OptionKeys::FloppyTail
• perturb_KIC_off : basic::options::OptionKeys::AnchoredDesign
• perturb_outer_cycles : basic::options::OptionKeys::loops
• perturb_rigid_body_dofs : basic::options::OptionKeys::symmetry
• perturb_show : basic::options::OptionKeys::AnchoredDesign , basic::options::OptionKeys::FloppyTail
• perturb_temp : basic::options::OptionKeys::AnchoredDesign , basic::options::OptionKeys::FloppyTail
• pH : basic::options::OptionKeys::pH
• pH_mode : basic::options::OptionKeys::pH
• pH_neighbor_pack : basic::options::OptionKeys::pH::calc_pka
• pH_prepack : basic::options::OptionKeys::pH::calc_pka
• pH_relax : basic::options::OptionKeys::pH::calc_pka
• pH_unbound : basic::options::OptionKeys::pH
• phe_tyr_hack : mrlo
• PHI : test::Workshop4test
• phi_psi_range_A : basic::options::OptionKeys::frags::ABEGO
• phil : basic::options::OptionKeys::phil
• 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
• pick_multiple_sizes : basic::options::OptionKeys::templates
• picking : basic::options::OptionKeys::frags::picking
• picking_old_max_score : basic::options::OptionKeys::frags
• pivot_atoms : basic::options::OptionKeys::backrub
• pivot_residues : basic::options::OptionKeys::backrub
• pka_all : basic::options::OptionKeys::pH::calc_pka
• pka_for_chainno : basic::options::OptionKeys::pH::calc_pka
• pka_for_resnos : basic::options::OptionKeys::pH::calc_pka
• pka_rad : basic::options::OptionKeys::pH::calc_pka
• place_adduct_waters : basic::options::OptionKeys::motifs
• place_peptide_on_binding_site : basic::options::OptionKeys::flexPepDocking
• PLAIN_COLUMNS : app::pyrosetta_toolkit::modules::prettytable::prettytable
• plane_radius : basic::options::OptionKeys::mp::visualize
• PlatformBits : build , BuildBindings
• pm : test::C001_Carbohydrates_Demo01
• pmm : test::Workshop4test , test::Workshop5test , test::Workshop8test
• po : PyMOL_demo
• pocket_buried_dist : basic::options::OptionKeys::pocket_grid
• pocket_buried_score : basic::options::OptionKeys::pocket_grid
• pocket_constraint_weight : basic::options::OptionKeys::constraints
• pocket_debug_output : basic::options::OptionKeys::pocket_grid
• pocket_dump_exemplars : basic::options::OptionKeys::pocket_grid
• pocket_dump_pdbs : basic::options::OptionKeys::pocket_grid
• pocket_dump_rama : basic::options::OptionKeys::pocket_grid
• pocket_exemplar_vdw_pen : basic::options::OptionKeys::pocket_grid
• pocket_filter_by_exemplar : basic::options::OptionKeys::pocket_grid
• pocket_grid : basic::options::OptionKeys::pocket_grid
• pocket_grid_size : basic::options::OptionKeys::pocket_grid
• pocket_grid_size_x : basic::options::OptionKeys::pocket_grid
• pocket_grid_size_y : basic::options::OptionKeys::pocket_grid
• pocket_grid_size_z : basic::options::OptionKeys::pocket_grid
• pocket_grid_spacing : basic::options::OptionKeys::pocket_grid
• pocket_ignore_buried : basic::options::OptionKeys::pocket_grid
• pocket_max_size : basic::options::OptionKeys::pocket_grid
• pocket_max_spacing : basic::options::OptionKeys::pocket_grid
• pocket_min_size : basic::options::OptionKeys::pocket_grid
• pocket_ntrials : basic::options::OptionKeys::pocket_grid
• pocket_num_angles : basic::options::OptionKeys::pocket_grid
• pocket_only_buried : basic::options::OptionKeys::pocket_grid
• pocket_probe_radius : basic::options::OptionKeys::pocket_grid
• pocket_psp : basic::options::OptionKeys::pocket_grid
• pocket_restrict_size : basic::options::OptionKeys::pocket_grid
• pocket_search13 : basic::options::OptionKeys::pocket_grid
• pocket_side : basic::options::OptionKeys::pocket_grid
• pocket_sps : basic::options::OptionKeys::pocket_grid
• pocket_static_grid : basic::options::OptionKeys::pocket_grid
• pocket_surface_dist : basic::options::OptionKeys::pocket_grid
• pocket_surface_score : basic::options::OptionKeys::pocket_grid
• pocket_zero_derivatives : basic::options::OptionKeys::constraints
• poi : basic::options::OptionKeys::willmatch
• poidis : basic::options::OptionKeys::willmatch
• polar_charge_cutoff : basic::options::OptionKeys::sasa
• poll_frequency : basic::options::OptionKeys::rbe
• pool : basic::options::OptionKeys::evaluation
• pop_from_ss : basic::options::OptionKeys::ms
• pop_size : basic::options::OptionKeys::ms
• population_weight : basic::options::OptionKeys::cluster
• port : basic::options::OptionKeys::inout::dbms
• pos : make_symmdef_file_denovo , pyrosetta::toolbox::make_rna_rosetta_ready , 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 , test::T201_Scoring_pre_talaris
• 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_input_stream : basic::options::OptionKeys::jd2
• pose_ligand_res : basic::options::OptionKeys::magnesium
• pose_low : test::Workshop7test
• pose_metrics : basic::options::OptionKeys::pose_metrics
• pose_normal_angle_max : basic::options::OptionKeys::mp
• pose_s : PyMOL_demo
• pose_segment_ends : basic::options::OptionKeys::sewing
• pose_segment_starts : basic::options::OptionKeys::sewing
• position_from_topo : basic::options::OptionKeys::mp::setup
• post_minimize : basic::options::OptionKeys::dna::specificity
• post_pre_packing_score : app::delta_score_per_mutation
• post_repack : revert_app
• postfix : tools::CppParser
• pot : test::T850_SubClassing
• potential_cap : basic::options::OptionKeys::pb_potential
• pq_schema : basic::options::OptionKeys::inout::dbms
• pr : test::T500_Packing
• pre_minimize : basic::options::OptionKeys::dna::specificity
• pre_pack : basic::options::OptionKeys::dna::specificity
• pre_packminpack : local
• pre_pre_packing_score : app::delta_score_per_mutation
• pre_process : basic::options::OptionKeys::pH
• pre_talaris2013_geometries : basic::options::OptionKeys::mistakes::chemical
• predicted_burial_fn : basic::options::OptionKeys::evaluation
• prefix : basic::options::OptionKeys::antibody , basic::options::OptionKeys::contactMap , basic::options::OptionKeys::matdes , basic::options::OptionKeys::ms::checkpoint , basic::options::OptionKeys::out , basic::options::OptionKeys::ProQ , basic::options::OptionKeys::templates
• preminimize : basic::options::OptionKeys::stepwise
• preminimize_motif_pdbs : basic::options::OptionKeys::motifs
• preminimize_motif_pdbs_sconly : basic::options::OptionKeys::motifs
• prep_align_prot_to : basic::options::OptionKeys::pepspec
• prep_rot_std_dev : basic::options::OptionKeys::pepspec
• prep_trans_std_dev : basic::options::OptionKeys::pepspec
• prep_use_ref_rotamers : basic::options::OptionKeys::pepspec
• preprocessing_script_version : basic::options::OptionKeys::antibody
• preserve_c_beta : basic::options::OptionKeys::packing
• preserve_crystinfo : basic::options::OptionKeys::in
• preserve_header : basic::options::OptionKeys::run
• pretend_no_ddG_repulsion : basic::options::OptionKeys::optE
• prevent_auto_setup_metal_bb_variants : basic::options::OptionKeys::in
• prevent_repacking : basic::options::OptionKeys::packing
• primary_subsubunit : basic::options::OptionKeys::smhybrid
• print_eggshell : basic::options::OptionKeys::fingerprint
• print_i_calc : basic::options::OptionKeys::score::saxs
• print_intermediate_pdbs : basic::options::OptionKeys::cp
• print_motifs : basic::options::OptionKeys::mh
• print_per_res_diff : basic::options::OptionKeys::ddg
• print_pymol_selection : basic::options::OptionKeys::packing
• print_rdc_values : basic::options::OptionKeys::rdc
• print_reports : basic::options::OptionKeys::cp
• print_scores : basic::options::OptionKeys::mh
• print_template_script : basic::options::OptionKeys::parser
• pro_close_planar_constraint : basic::options::OptionKeys::score
• prob_terminus_ramapert : basic::options::OptionKeys::lh
• probabilities : basic::options::OptionKeys::canonical_sampling::probabilities
• probe_radius : basic::options::OptionKeys::sasa
• probe_specificity : basic::options::OptionKeys::dna::design
• proc_id : basic::options::OptionKeys::run
• process_ligrot_separately : basic::options::OptionKeys::enzdes
• process_store : basic::options::OptionKeys::abinitio
• prof_bug : basic::options::OptionKeys::ProQ
• profile : basic::options::OptionKeys::run
• profile_score : basic::options::OptionKeys::frags::scoring
• prohibit_D_at_negative_phi : basic::options::OptionKeys::cyclic_peptide
• prohibit_L_at_positive_phi : basic::options::OptionKeys::cyclic_peptide
• ProQ : basic::options::OptionKeys::ProQ
• prot_coor : PDBInfo
• protein : basic::options::OptionKeys::stepwise::protein , PDBInfo
• protein_dielectric : basic::options::OptionKeys::score
• protein_letters : pyrosetta::toolbox::mutants , toolbox::mutants
• protein_prepack : basic::options::OptionKeys::stepwise::protein
• protein_scan : basic::options::OptionKeys::dna::design
• protocol : basic::options::OptionKeys::docking::ligand , basic::options::OptionKeys::parser , basic::options::OptionKeys::run
• protonated_H1_adenosine_list : basic::options::OptionKeys::stepwise::rna
• ProtTypes : app::pyrosetta_toolkit::window_modules::protocol_builder::ProtocolBuilder
• ProtTypesDic : app::pyrosetta_toolkit::window_modules::protocol_builder::ProtocolBuilder
• pSer2Asp_centroid : basic::options::OptionKeys::flexPepDocking
• pSer2Glu_centroid : basic::options::OptionKeys::flexPepDocking
• pseudosym : basic::options::OptionKeys::smhybrid
• PSI : test::Workshop4test
• psipred_ss2 : basic::options::OptionKeys::in::file
• pssm : basic::options::OptionKeys::in::file
• publication : basic::options::OptionKeys::chemically_conjugated_docking , basic::options::OptionKeys::FloppyTail
• pure_movebb_substitutions_scale : basic::options::OptionKeys::flexpack::annealer
• put_intra_into_total : basic::options::OptionKeys::score
• 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
• pyrosetta : setup_pyrosetta
• PyRosettaVersion : src
• python_pdb : test::G202_Module_PythonPDB