- p -

• p : basic::options::OptionKeys::score::fiber_diffraction , docking , kmeans_adaptive_kernel_density_bb_dependent_rotlib , kmeans_bb_dependent_rotlib , kmeans_common , loops , loops_kic
• P : pyrosetta.distributed.cluster.exceptions , pyrosetta.distributed.cluster.multiprocessing , pyrosetta.distributed.cluster.tools
• p : 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
• P : 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 , vancomycin
• pack2 : vancomycin
• 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_nloop : basic::options::OptionKeys::hydrate
• pack_patch : basic::options::OptionKeys::docking
• pack_phosphate_penalty : basic::options::OptionKeys::score::rna
• pack_protein_side_chains : basic::options::OptionKeys::stepwise
• 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
• packer_palette : basic::options::OptionKeys::packing::packer_palette
• packet_queue : pyrosetta.network.rosetta_udp_to_tcp_bridge
• 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_all_res : basic::options::OptionKeys::constel
• pair_list : BundleDumper
• pair_off : basic::options::OptionKeys::FloppyTail , basic::options::OptionKeys
• pair_target_mutations : basic::options::OptionKeys::constel
• pair_target_resnum : basic::options::OptionKeys::constel
• pairdata_input_pdb_list : basic::options::OptionKeys::robert
• paired_residues : test.T020_Pose_Bindings
• 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
• paraBBMB_constraints_energy_filter_multiplier : basic::options::OptionKeys::cyclic_peptide
• paraBBMB_positions : basic::options::OptionKeys::cyclic_peptide
• paraBBMB_sidechain_distance_filter_multiplier : basic::options::OptionKeys::cyclic_peptide
• param : PREcst
• parameters : basic::options::OptionKeys::relax::centroid
• params : basic::options::OptionKeys::dna::specificity , basic::options::OptionKeys::holes
• params_custom_file_name : basic::options::OptionKeys::motifs
• params_directory_path : basic::options::OptionKeys::motifs
• params_file : basic::options::OptionKeys::flexPepDocking
• 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_script_once_only : basic::options::OptionKeys::jd2
• parse_tagfile : basic::options::OptionKeys::optE
• parse_taskops_file : bur_nodon_tyr , sequence_recovery
• ParseIterations : kic_runner
• parser : 3d_histogram , app_runner , auto-DRRAFTER_setup , auto-DRRAFTER_setup_next_round , autocorrelation , average_rmsds , basic::options::OptionKeys::parser , cache_trajectory , closure_error , combine_pdbs , correlation_time , delete_job , 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 , DRRAFTER , drrafter_rna , dummy-distribution , enumerate_junctions , execute , explosion_error , finalize_models , find_lowest_scoring_relaxed_struct , gaussian-sampling , general_RNP_setup_script , get_final_ddG_scores , get_lowest_scoring_relaxed_models , histogram , internal_coordinates , job_manager , kic_runner , legacy_score_vs_rmsd , make_comparison , percent_subangstrom , pivot_selection , plot , progress_bar , pyrosetta.tests.distributed.cluster.print_discovered_test_cases , pyrosetta.tests.distributed.test_dask , relax_starting_structure , run_backbone , run_sidechain , score_vs_rmsd , score_vs_time , setup_for_complex_scoring_general , solution_counts , subloop_histogram , submit_jobs , test.T009_Exceptions , torsion_vs_time , wipe_cache
• parser_read_cloud_pdb : basic::options::OptionKeys::enzdes
• partial_hydrate_dew : basic::options::OptionKeys::hydrate
• partial_thread : basic::options::OptionKeys::partial_thread
• partner1 : devel::metal_interface , local
• partner2 : devel::metal_interface , local
• partner2_residue : devel::metal_interface , local
• partner_pdb : basic::options::OptionKeys::legacy_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_name_for_residue : basic::options::OptionKeys::make_rot_lib
• patch_selectors : basic::options::OptionKeys::chemical
• patchdock : basic::options::OptionKeys::parser
• patchdock_random_entry : basic::options::OptionKeys::parser
• path : basic::options::OptionKeys::in::path , basic::options::OptionKeys::inout::dbms , basic::options::OptionKeys::mh::path , basic::options::OptionKeys::out::path , closure_error , explosion_error , solution_counts , subloop_histogram
• path_prefix : make_static_database
• path_size : SewAssembler
• paths : closure_error , explosion_error
• pattern : legacy_score_vs_rmsd
• 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::nmr::pcs
• 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 : basic::options::OptionKeys::in::path , basic::options::OptionKeys::mh::filter , basic::options::OptionKeys::mh::path , basic::options::OptionKeys::out::path , basic::options::OptionKeys::out , kic_runner
• pdb1 : basic::options::OptionKeys::assembly , erraser_analysis
• pdb2 : basic::options::OptionKeys::assembly , basic::options::OptionKeys::chunk , erraser_analysis
• pdb_comments : basic::options::OptionKeys::out::file
• PDB_components_directory : basic::options::OptionKeys::in::file
• PDB_components_overrides : basic::options::OptionKeys::in::file
• pdb_database : test.G203_Module_SQLPDB
• PDB_diagnostic : basic::options::OptionKeys::PDB_diagnostic
• 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_id : erraser_single_res_analysis
• pdb_info : create_a3b_hbs
• pdb_list : basic::options::OptionKeys::pepspec , bur_nodon_tyr , erraser_single_res_analysis
• 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
• pdb_string : execute , run_backbone , run_sidechain
• pdb_to_one_letter : mutant_modeler
• pdbcode : clean_pdb_keep_ligand
• pdbfile : clean_pdb_keep_ligand
• pdbID : basic::options::OptionKeys::matdes
• pdblist : basic::options::OptionKeys::lh::symfragrm
• pdbname : clean_pdb_keep_ligand , predPRE
• pdz : basic::options::OptionKeys::chemically_conjugated_docking
• peak : PREcst
• peakx : hist2d
• peaky : hist2d
• 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 : test.C001_Carbohydrates_Demo01
• peptide_anchor : basic::options::OptionKeys::flexPepDocking
• peptide_chain : basic::options::OptionKeys::DisulfideInsertion , basic::options::OptionKeys::flexPepDocking
• peptide_deriver : basic::options::OptionKeys::peptide_deriver
• peptide_loop_model : basic::options::OptionKeys::flexPepDocking
• peptide_pdb : cov_creator
• peptide_pdb_res : cov_creator
• peptide_res : cov_creator
• peptoid_design_positions : peptoid_design
• per_chain_renumbering : basic::options::OptionKeys::out::file
• perfect_alignment : filterImperfectAln
• perform_ABOXYZ_bin_analysis : basic::options::OptionKeys::cluster::energy_based_clustering
• periodicity : basic::options::OptionKeys::edensity
• pert_dock_rbpm : pna
• pert_dock_rot_mag : a3b_hddm , dddm , oddm , tddm
• pert_dock_trans_mag : a3b_hddm , dddm , oddm , tddm
• pert_init_loop : basic::options::OptionKeys::lh
• pert_mc : orn_macrocycle , pna
• pert_mc_temp : a3b_hddm , dddm , oddm , tddm
• pert_mm : vancomycin
• pert_mm2 : vancomycin
• pert_mover : test.Workshop7test
• pert_num : a3b_hddm , dddm , hbs_design , oddm , oop_design , peptoid_design , tddm
• pert_pep_mm : orn_macrocycle
• pert_pep_num_rep : a3b_hddm , dddm , oddm , tddm
• pert_pep_random : orn_macrocycle
• pert_pep_repeat : orn_macrocycle
• pert_pep_shear : orn_macrocycle
• pert_pep_shear_E : a3b_hddm , dddm , oddm , tddm
• pert_pep_shear_H : a3b_hddm , dddm , oddm , tddm
• pert_pep_shear_L : a3b_hddm , dddm , oddm , tddm
• pert_pep_shear_temp : a3b_hddm , dddm , oddm , tddm
• pert_pep_small : orn_macrocycle
• pert_pep_small_E : a3b_hddm , dddm , oddm , tddm
• pert_pep_small_H : a3b_hddm , dddm , oddm , tddm
• pert_pep_small_L : a3b_hddm , dddm , oddm , tddm
• pert_pep_small_temp : a3b_hddm , dddm , oddm , tddm
• pert_sequence : orn_macrocycle
• 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
• pert_trial : orn_macrocycle
• 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 : evaluate_beta_mutants
• phe2 : evaluate_beta_mutants
• phe2_rt : evaluate_beta_mutants
• phe_min : evaluate_beta_mutants
• phe_mm : evaluate_beta_mutants
• phe_pos : evaluate_beta_mutants
• phi : 3d_histogram , dummy-distribution , kmeans_adaptive_kernel_density_bb_dependent_rotlib , kmeans_bb_dependent_rotlib , kmeans_common , oop_conformations , plot , spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib , test.T150_PyMOL_Integration
• PHI : test.Workshop4test
• phi_bin : kmeans_adaptive_kernel_density_bb_dependent_rotlib , kmeans_bb_dependent_rotlib
• phi_bins : plot
• phi_constraint_prob_cutoff : basic::options::OptionKeys::trRosetta
• phi_constraint_weight : basic::options::OptionKeys::trRosetta
• phi_function : plot
• phi_hist : plot
• phi_nonpivot_style : styles.rama
• phi_pivot_style : styles.rama
• phi_psi_range_A : basic::options::OptionKeys::frags::ABEGO
• phil : basic::options::OptionKeys::phil
• philst : kmeans_adaptive_kernel_density_bb_dependent_rotlib
• PhiNByX_1 : test.Workshop9test
• PhiNByX_2 : test.Workshop9test
• phis : kmeans_adaptive_kernel_density_bb_dependent_rotlib , plot
• 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_line : styles.blue , styles.green , styles.rainbow , styles.red
• pivot_residues : basic::options::OptionKeys::backrub
• pivot_string : run_backbone
• pivots : run_backbone , subloop_histogram
• pivots_to_keys : subloop_histogram
• 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
• plane_radius : basic::options::OptionKeys::mp::visualize
• Platform : build , update_ui_project
• PlatformBits : build , update_ui_project
• plot_dist : plot_hb
• plot_psi : plot_hb
• plot_theta : plot_hb
• plural : helpers
• plus_pos : oop_conformations
• pm : test.C001_Carbohydrates_Demo01
• pmm : test.Workshop4test , test.Workshop5test , test.Workshop8test
• pna : pna
• pnc : pna
• png : pna
• pnt : pna
• pnu : pna
• 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_limit_exemplar_color : basic::options::OptionKeys::pocket_grid
• pocket_limit_small_exemplars : 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
• pointwat_wat_bonus : basic::options::OptionKeys::corrections::water
• pointwat_wat_bonus_width : basic::options::OptionKeys::corrections::water
• pointwater_params : basic::options::OptionKeys::corrections::water
• polar_charge_cutoff : basic::options::OptionKeys::sasa
• polar_hydrogens : basic::options::OptionKeys::stepwise::polar_hydrogens
• poll_frequency : basic::options::OptionKeys::rbe
• polygon : subloop_histogram
• polymeric_context : basic::options::OptionKeys::make_rot_lib
• pool : basic::options::OptionKeys::evaluation , cal_vdw_radius_pool , enumerate_junctions
• pop_from_ss : basic::options::OptionKeys::ms
• pop_size : basic::options::OptionKeys::ms
• population_based_conformer_sampling : basic::options::OptionKeys::carbohydrates::glycan_sampler
• population_weight : basic::options::OptionKeys::cluster
• port : basic::options::OptionKeys::cloud , basic::options::OptionKeys::inout::dbms , basic::options::OptionKeys::run::PyMOLMover
• pos : make_symmdef_file_denovo
• pose : beta_nonlocal , beta_sc_scan , create_a3b_hbs , demo.D010_Pose_structure , demo.D020_Pose_scoring , demo.D040_Movemap , demo.D050_Packer_task , demo.D060_Folding , docking
• Pose : evaluate_beta_mutants
• pose : oop_scan , orn_macrocycle , pna , PyMOL_demo , test.T007_TracerIO , test.T009_Exceptions , test.T020_Pose_Bindings , test.T100_basic , test.T150_core , test.T150_PyMOL_Integration , test.T190_Bindings_Utility , 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 , test_nu_angles , test_terpenes , torsion_scoring , trivial_alascan
• pose1 : test.T008_Serialization , test.T020_Pose_Bindings
• pose1_l : test.T008_Serialization
• pose2 : test.T008_Serialization , test.T020_Pose_Bindings , test.T201_Scoring_pre_talaris , test.T500_Packing
• pose2_l : test.T008_Serialization
• pose3 : test.T020_Pose_Bindings , test.T100_basic
• pose4 : test.T100_basic
• pose_frag : test.T400_Refinement
• pose_from_sequence : pyrosetta.distributed.io
• 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_output_directory : basic::options::OptionKeys::ligand_evolution
• pose_s : PyMOL_demo
• pose_segment_ends : basic::options::OptionKeys::legacy_sewing , basic::options::OptionKeys::sewing
• pose_segment_starts : basic::options::OptionKeys::legacy_sewing , basic::options::OptionKeys::sewing
• poses : basic::options::OptionKeys::mp::assembly
• poses_from_files : pyrosetta.distributed.io
• poses_from_multimodel_pdb : pyrosetta.distributed.io
• poses_from_sequences : pyrosetta.distributed.io
• poses_from_silent : pyrosetta.distributed.io
• position_from_topo : basic::options::OptionKeys::mp::setup
• positive_states : basic::options::OptionKeys::msd
• post_highresdock_fa_atr_rep_score : basic::options::OptionKeys::motifs
• post_minimize : basic::options::OptionKeys::dna::specificity
• post_repack : revert_app
• postfix : create_a3b_hbs
• pot : test.T850_SubClassing
• potential_cap : basic::options::OptionKeys::pb_potential
• potential_file : PB_potential
• pq_schema : basic::options::OptionKeys::inout::dbms
• Pr : kmeans_adaptive_kernel_density_bb_dependent_rotlib
• pr : spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib , test.T500_Packing
• pr2 : test.T500_Packing
• Pr_pp : kmeans_adaptive_kernel_density_bb_dependent_rotlib
• pre : basic::options::OptionKeys::nmr::pre
• PRE : PREcst , predPRE
• pre_bump_check : basic::options::OptionKeys::hydrate
• pre_centroid : basic::options::OptionKeys::remodel::staged_sampling
• pre_minimize : basic::options::OptionKeys::dna::specificity
• pre_pack : basic::options::OptionKeys::dna::specificity
• pre_packminpack : local
• pre_process : basic::options::OptionKeys::pH
• pre_talaris2013_geometries : basic::options::OptionKeys::mistakes::chemical
• precompute_ig : basic::options::OptionKeys::packing
• predicted_burial_fn : basic::options::OptionKeys::evaluation
• prefix : basic::options::OptionKeys::antibody , basic::options::OptionKeys::contactMap , basic::options::OptionKeys::dump_trajectory , basic::options::OptionKeys::matdes , basic::options::OptionKeys::ms::checkpoint , basic::options::OptionKeys::out , basic::options::OptionKeys::ProQ , basic::options::OptionKeys::templates , create_a3b_hbs , erraser_single_res_analysis
• preglycosylate_residues : basic::options::OptionKeys::carbohydrates::glycopeptide_docking
• preglycosylate_sugar_names : basic::options::OptionKeys::carbohydrates::glycopeptide_docking
• 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
• prepack_only : basic::options::OptionKeys::carbohydrates::glycan_dock
• prepend_n_residues : oop_creator
• preprocessing_script_version : basic::options::OptionKeys::antibody
• prerelax : basic::options::OptionKeys::cluster::energy_based_clustering
• 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_anchor_repacking : basic::options::OptionKeys::carbohydrates::glycopeptide_docking
• prevent_auto_setup_metal_bb_variants : basic::options::OptionKeys::in
• prevent_repacking : basic::options::OptionKeys::packing
• prhos : kmeans_adaptive_kernel_density_bb_dependent_rotlib
• primary_cdrs : basic::options::OptionKeys::antibody::design
• primary_hs : inverse_rotlib_dump
• primary_hs_stub_lib : scaffold_matcher
• primary_residue_selector : test.T020_Pose_Bindings
• primary_subsubunit : basic::options::OptionKeys::smhybrid
• print_cutoff : b3a_distro
• print_data : basic::options::OptionKeys::epr_deer
• 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 , XMLprinter
• print_rdc_values : basic::options::OptionKeys::rdc
• print_reports : basic::options::OptionKeys::cp
• print_scores : basic::options::OptionKeys::mh
• pro_close_planar_constraint : basic::options::OptionKeys::score
• prob : spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib
• prob_br_move : local
• prob_terminus_ramapert : basic::options::OptionKeys::lh
• probabilities : basic::options::OptionKeys::canonical_sampling::probabilities
• probe_radius : basic::options::OptionKeys::sasa , bur_nodon_tyr
• 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
• project : conf
• ProQ : basic::options::OptionKeys::ProQ
• protein : basic::options::OptionKeys::stepwise::protein
• protein_dielectric : basic::options::OptionKeys::score
• protein_discovery_locus : basic::options::OptionKeys::motifs
• protein_flexibility : basic::options::OptionKeys::hydrate
• protein_grid : basic::options::OptionKeys::protein_grid
• protein_one_letter : DRRAFTER
• protein_pack_all : basic::options::OptionKeys::rna::denovo::minimize
• protein_packing : basic::options::OptionKeys::rna::denovo::minimize
• protein_packing_distance : basic::options::OptionKeys::rna::denovo::minimize
• protein_pdb : cov_creator
• protein_pdb_res : cov_creator
• protein_prepack : basic::options::OptionKeys::stepwise::protein
• protein_res : cov_creator
• protein_residues : mutant_modeler
• protein_residues_1letter : mutant_modeler
• 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
• prox_ct_max : basic::options::OptionKeys::constel
• prox_nres : basic::options::OptionKeys::constel
• prox_tt_max : basic::options::OptionKeys::constel
• prpp : kmeans_adaptive_kernel_density_bb_dependent_rotlib
• pSer2Asp_centroid : basic::options::OptionKeys::flexPepDocking
• pSer2Glu_centroid : basic::options::OptionKeys::flexPepDocking
• pseudosym : basic::options::OptionKeys::smhybrid
• psi : 3d_histogram , dummy-distribution , kmeans_adaptive_kernel_density_bb_dependent_rotlib , kmeans_bb_dependent_rotlib , kmeans_common , oop_conformations , plot , spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib , test.T150_PyMOL_Integration
• PSI : test.Workshop4test
• psi_bin : kmeans_adaptive_kernel_density_bb_dependent_rotlib , kmeans_bb_dependent_rotlib
• psi_bins : plot
• psi_function : plot
• psi_hist : plot
• psi_nonpivot_style : styles.rama
• psi_pivot_style : styles.rama
• psilst : kmeans_adaptive_kernel_density_bb_dependent_rotlib
• psipred_alpha_helix_prob_cutoff : basic::options::OptionKeys::helical_bundle_predict
• psipred_beta_strand_prob_cutoff : basic::options::OptionKeys::helical_bundle_predict
• psipred_file : basic::options::OptionKeys::helical_bundle_predict
• psipred_ss2 : basic::options::OptionKeys::in::file
• psis : kmeans_adaptive_kernel_density_bb_dependent_rotlib , plot
• pssm : basic::options::OptionKeys::in::file
• pts : add_xyz_to_pose
• publication : basic::options::OptionKeys::chemically_conjugated_docking , basic::options::OptionKeys::FloppyTail , basic::options::OptionKeys
• pucker1 : erraser_analysis
• pucker2 : erraser_analysis
• pure_movebb_substitutions_scale : basic::options::OptionKeys::flexpack::annealer
• put_intra_into_total : basic::options::OptionKeys::score
• pv : test.T850_SubClassing
• py_set : test.T040_Types
• pybind_source : make_bindings_via_cmake
• pygments_style : conf
• pymol : a3b_hddm , docking , loops_kic , oddm , PyMOL_demo , scaffold_matcher , tddm , test.T150_PyMOL_Integration , test.T650_LoopsKIC , test.Workshop3test
• PyMOLMover : basic::options::OptionKeys::run::PyMOLMover
• pyrosetta_rosetta_modules : rosetta
• python_module_name : make_bindings_via_cmake
• python_pdb : test.G202_Module_PythonPDB