- p -

• p1_theta_deriv() : numeric::deriv
• p_aa_pp() : basic::options::OptionKeys::corrections::score , corrections::score
• p_aa_pp_nogridshift() : basic::options::OptionKeys::corrections::score , corrections::score
• p_homol_csts() : pepspec
• p_value_selection() : basic::options::OptionKeys::frags , frags
• pack_max_threshold() : basic::options::OptionKeys::motifs , motifs
• pack_min_threshold() : basic::options::OptionKeys::motifs , motifs
• pack_missing_sidechains() : packing
• pack_patch() : basic::options::OptionKeys::docking , docking
• pack_phosphate_penalty() : score
• pack_post_graft() : antibody::design , basic::options::OptionKeys::antibody::design
• pack_score_cutoff() : basic::options::OptionKeys::motifs , motifs
• pack_sfxn() : basic::options::OptionKeys::cp , cp
• pack_until_converge() : basic::options::OptionKeys::ddg , ddg
• pack_weights() : score
• packing() : packing
• packing_weight() : basic::options::OptionKeys::fingerprint , fingerprint
• packonly_after_graft() : antibody , basic::options::OptionKeys::antibody
• packstat() : packstat
• packstat_pdb() : packstat
• padding_score_filter() : basic::options::OptionKeys::evolution , evolution
• padding_stage2_filter() : basic::options::OptionKeys::evolution , evolution
• pair_off() : basic::options::OptionKeys::FloppyTail , FloppyTail
• pairdata_input_pdb_list() : robert
• pairing_file() : basic::options::OptionKeys::jumps , jumps
• pairings() : templates
• pales() : basic::options::OptionKeys::evaluation , evaluation
• parameters() : relax::centroid
• params() : basic::options::OptionKeys::dna::specificity , basic::options::OptionKeys::holes , dna::specificity , holes
• params_file() : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• parentlist() : basic::options::OptionKeys::evolution , evolution
• parin_favorite_output() : stepwise::rna
• parse_charge() : basic::options::OptionKeys::corrections::chemical , corrections::chemical
• parse_database_connection() : basic::database
• parse_string_to_boolean_expression() : numeric::expression_parser
• parse_string_to_expression() : numeric::expression_parser
• parse_tagfile() : basic::options::OptionKeys::optE , optE
• parser() : parser
• parser_read_cloud_pdb() : basic::options::OptionKeys::enzdes , enzdes
• partners() : basic::options::OptionKeys::docking , docking
• password() : basic::options::OptionKeys::inout::dbms , inout::dbms
• patch() : rigid , score
• patch_filter_scorefxn() : basic::options::OptionKeys::fast_loops , fast_loops
• patch_selectors() : residues
• patchdock() : parser
• patchdock_random_entry() : parser
• path() : basic::options::OptionKeys::in::path , in::path , out::path
• PATH_SEPARATOR() : platform::file
• pathname() : utility
• patterson() : patterson
• pb_potential() : pb_potential
• PBP_clustering_at_chain_closure() : stepwise::rna
• pca() : basic::options::OptionKeys::in::file , in::file
• PCS() : PCS
• pcs_cluster_coverage() : robert
• pcs_cluster_lowscoring() : robert
• pcs_dump_cluster() : robert
• PCS_frag_cst() : basic::options::OptionKeys::in::file , in::file
• pcs_maxsub_filter() : robert
• pcs_maxsub_rmsd() : robert
• PCSTS1() : PCSTS1
• PCSTS2() : PCSTS2
• PCSTS3() : PCSTS3
• PCSTS4() : PCSTS4
• pdb() : basic::options::OptionKeys::in::path , in::path , out::path , out
• pdb1() : assembly , basic::options::OptionKeys::assembly
• pdb2() : assembly , basic::options::OptionKeys::assembly , basic::options::OptionKeys::chunk , chunk
• pdb_comments() : out::file
• pdb_each_iteration() : basic::options::OptionKeys::dna::design , dna::design
• pdb_gz() : out
• pdb_list() : pepspec
• pdb_parents() : out::file
• pdb_pos() : basic::options::OptionKeys::dna::specificity , dna::specificity
• pdbID() : basic::options::OptionKeys::matdes , matdes
• pdblist() : basic::options::OptionKeys::lh::symfragrm , lh::symfragrm
• pdz() : basic::options::OptionKeys::chemically_conjugated_docking , chemically_conjugated_docking
• penalize_mixture_func() : basic::options::OptionKeys::constraints , constraints
• pep_anchor() : pepspec
• pep_chain() : pepspec
• pep_fold_only() : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• pep_refine() : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• pepspec() : pepspec
• peptide_anchor() : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• peptide_chain() : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• peptide_loop_model() : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• per_chain_renumbering() : out::file
• periodic_range() : basic
• perturb() : abinitio , basic::options::OptionKeys::abinitio
• perturb_CCD_off() : AnchoredDesign , basic::options::OptionKeys::AnchoredDesign
• perturb_cycles() : AnchoredDesign , basic::options::OptionKeys::AnchoredDesign , basic::options::OptionKeys::FloppyTail , FloppyTail
• perturb_KIC_off() : AnchoredDesign , basic::options::OptionKeys::AnchoredDesign
• perturb_rigid_body_dofs() : symmetry
• perturb_show() : AnchoredDesign , basic::options::OptionKeys::AnchoredDesign , basic::options::OptionKeys::FloppyTail , FloppyTail
• perturb_temp() : AnchoredDesign , basic::options::OptionKeys::AnchoredDesign , basic::options::OptionKeys::FloppyTail , FloppyTail
• pH() : pH
• pH_mode() : pH
• pH_neighbor_pack() : pH::calc_pka
• pH_prepack() : pH::calc_pka
• pH_relax() : pH::calc_pka
• pH_unbound() : pH
• phi_psi_range_A() : basic::options::OptionKeys::frags::ABEGO , frags::ABEGO
• phil() : phil
• phipsi_analysis() : pepspec
• pick_multiple_sizes() : templates
• picking() : basic::options::OptionKeys::frags::picking , frags::picking
• picking_old_max_score() : basic::options::OptionKeys::frags , frags
• pind() : basic::sampling::orientations
• pivot_atoms() : backrub , basic::options::OptionKeys::backrub
• pivot_residues() : backrub , basic::options::OptionKeys::backrub
• pka_all() : pH::calc_pka
• pka_for_chainno() : pH::calc_pka
• pka_for_resnos() : pH::calc_pka
• pka_rad() : pH::calc_pka
• place_adduct_waters() : basic::options::OptionKeys::motifs , motifs
• pocket_buried_dist() : pocket_grid
• pocket_buried_score() : pocket_grid
• pocket_constraint_weight() : basic::options::OptionKeys::constraints , constraints
• pocket_debug_output() : pocket_grid
• pocket_dump_exemplars() : pocket_grid
• pocket_dump_pdbs() : pocket_grid
• pocket_dump_rama() : pocket_grid
• pocket_exemplar_vdw_pen() : pocket_grid
• pocket_filter_by_exemplar() : pocket_grid
• pocket_grid() : pocket_grid
• pocket_grid_size() : pocket_grid
• pocket_grid_size_x() : pocket_grid
• pocket_grid_size_y() : pocket_grid
• pocket_grid_size_z() : pocket_grid
• pocket_grid_spacing() : pocket_grid
• pocket_ignore_buried() : pocket_grid
• pocket_max_size() : pocket_grid
• pocket_max_spacing() : pocket_grid
• pocket_min_size() : pocket_grid
• pocket_ntrials() : pocket_grid
• pocket_num_angles() : pocket_grid
• pocket_only_buried() : pocket_grid
• pocket_probe_radius() : pocket_grid
• pocket_psp() : pocket_grid
• pocket_restrict_size() : pocket_grid
• pocket_search13() : pocket_grid
• pocket_side() : pocket_grid
• pocket_sps() : pocket_grid
• pocket_static_grid() : pocket_grid
• pocket_surface_dist() : pocket_grid
• pocket_surface_score() : pocket_grid
• pocket_zero_derivatives() : basic::options::OptionKeys::constraints , constraints
• poi() : willmatch
• poidis() : willmatch
• 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
• polar_charge_cutoff() : sasa
• poll_frequency() : rbe
• 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() : basic::options::OptionKeys::els , basic::options::OptionKeys::evaluation , els , evaluation
• pop_from_ss() : basic::options::OptionKeys::ms , ms
• pop_size() : basic::options::OptionKeys::ms , ms
• population_weight() : basic::options::OptionKeys::cluster , cluster
• pore_radius() : basic::options::OptionKeys::flxbb::layer , flxbb::layer
• port() : basic::options::OptionKeys::inout::dbms , inout::dbms
• pose_input_stream() : basic::options::OptionKeys::jd2 , jd2
• pose_metrics() : pose_metrics , rescore
• post_minimize() : basic::options::OptionKeys::dna::specificity , dna::specificity
• potential_cap() : pb_potential
• pq_schema() : basic::options::OptionKeys::inout::dbms , inout::dbms
• pre_minimize() : basic::options::OptionKeys::dna::specificity , dna::specificity
• pre_pack() : basic::options::OptionKeys::dna::specificity , dna::specificity
• pre_process() : pH
• pre_talaris2013_geometries() : basic::options::OptionKeys::mistakes::chemical , mistakes::chemical
• predicted_burial_fn() : basic::options::OptionKeys::evaluation , evaluation
• predicted_secondary() : basic::options::OptionKeys::frags::scoring , frags::scoring
• prefix() : basic::options::OptionKeys::contactMap , basic::options::OptionKeys::matdes , basic::options::OptionKeys::ms::checkpoint , contactMap , matdes , ms::checkpoint , out , ProQ , templates
• premin() : rot_anl
• preminimize() : stepwise
• preminimize_interface() : basic::options::OptionKeys::dna::design , dna::design
• preminimize_motif_pdbs() : basic::options::OptionKeys::motifs , motifs
• preminimize_motif_pdbs_sconly() : basic::options::OptionKeys::motifs , motifs
• prep_align_prot_to() : pepspec
• prep_rot_std_dev() : pepspec
• prep_trans_std_dev() : pepspec
• prep_use_ref_rotamers() : pepspec
• prepack_interface() : basic::options::OptionKeys::dna::design , dna::design
• preprocessing_script_version() : antibody , basic::options::OptionKeys::antibody
• preserve_c_beta() : packing
• preserve_crystinfo() : basic::options::OptionKeys::in , in
• preserve_header() : run
• preserve_sidechains_pdb1() : assembly , basic::options::OptionKeys::assembly
• preserve_sidechains_pdb2() : assembly , basic::options::OptionKeys::assembly
• pretend_no_ddG_repulsion() : basic::options::OptionKeys::optE , optE
• prevent_repacking() : packing
• primary_subsubunit() : smhybrid
• principal_angle() : numeric
• principal_angle_degrees() : numeric
• principal_angle_radians() : numeric
• principal_component_eigenvalues() : numeric
• principal_components() : numeric
• principal_components_and_eigenvalues() : numeric
• print_eggshell() : basic::options::OptionKeys::fingerprint , fingerprint
• print_grid() : pocket_grid
• print_i_calc() : score::saxs
• print_intermediate_pdbs() : basic::options::OptionKeys::cp , cp
• print_motifs() : basic::options::OptionKeys::mh , mh
• print_per_res_diff() : basic::options::OptionKeys::ddg , ddg
• print_point() : numeric::kdtree
• print_points() : numeric::kdtree
• print_probabilities() : numeric
• print_pymol_selection() : packing
• print_rdc_values() : rdc
• print_reports() : basic::options::OptionKeys::cp , cp
• print_scores() : basic::options::OptionKeys::mh , mh
• print_tree() : numeric::kdtree
• printMatrix() : numeric::kinematic_closure
• printTranspose() : numeric::kinematic_closure
• printVector() : numeric::kinematic_closure
• printVectorTranspose() : numeric::kinematic_closure
• printWikiTable() : options_class
• pro_close_planar_constraint() : score
• prob_perturb_weights() : abinitio , basic::options::OptionKeys::abinitio
• probabilities() : basic::options::OptionKeys::canonical_sampling::probabilities , canonical_sampling::probabilities
• probe_radius() : sasa
• probe_specificity() : basic::options::OptionKeys::dna::design , dna::design
• proc_id() : run
• process() : basic::options
• process_ligrot_separately() : basic::options::OptionKeys::enzdes , enzdes
• process_store() : abinitio , basic::options::OptionKeys::abinitio
• product() : numeric
• prof_bug() : ProQ
• prof_reset() : basic
• prof_show() : basic
• prof_start_function_body() : basic
• prof_stop_function_body() : basic
• profile() : run
• profile_score() : basic::options::OptionKeys::frags::scoring , frags::scoring
• proj_angl() : numeric
• projection_matrix() : numeric
• ProQ() : ProQ
• protein() : run , stepwise::protein
• protein_atr_rep_screen() : stepwise::protein
• protein_prepack() : stepwise::protein
• protein_scan() : basic::options::OptionKeys::dna::design , dna::design
• protocol() : basic::options::OptionKeys::docking::ligand , docking::ligand , parser , run
• protonated_H1_adenosine_list() : stepwise::rna
• pSer2Asp_centroid() : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• pSer2Glu_centroid() : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• pseudosym() : smhybrid
• psipred_ss2() : basic::options::OptionKeys::in::file , in::file
• pssm() : basic::options::OptionKeys::in::file , in::file
• publication() : basic::options::OptionKeys::chemically_conjugated_docking , basic::options::OptionKeys::FloppyTail , chemically_conjugated_docking , FloppyTail
• pure_movebb_substitutions_scale() : basic::options::OptionKeys::flexpack::annealer , flexpack::annealer
• PyAP() : utility
• pymol_chains() : basic