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

- 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 : basic::options::OptionKeys::pepspec , 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 : basic::options::OptionKeys::packing , packing
• pack_patch : basic::options::OptionKeys::docking , docking
• pack_phosphate_penalty : basic::options::OptionKeys::score , score
• pack_post_graft() : antibody::design , basic::options::OptionKeys::antibody::design
• PACK_ROTAMERS : basic
• 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 : basic::options::OptionKeys::score , score
• packing : basic::options::OptionKeys::packing , packing
• packing_weight : basic::options::OptionKeys::fingerprint , fingerprint
• packonly_after_graft() : antibody , basic::options::OptionKeys::antibody
• packstat : basic::options::OptionKeys::packstat , packstat
• packstat_pdb : basic::options::OptionKeys::packstat , packstat
• padding_score_filter : basic::options::OptionKeys::evolution , evolution
• padding_stage2_filter : basic::options::OptionKeys::evolution , evolution
• Pair : utility::json_spirit
• pair_off : basic::options::OptionKeys::FloppyTail , FloppyTail
• pairdata_input_pdb_list : basic::options::OptionKeys::robert , robert
• pairing_file : basic::options::OptionKeys::jumps , jumps
• pairings : basic::options::OptionKeys::templates , templates
• pales : basic::options::OptionKeys::evaluation , evaluation
• ParameterList : numeric::kinematic_closure
• ParameterMatrix : numeric::kinematic_closure
• parameters : basic::options::OptionKeys::relax::centroid , 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 : basic::options::OptionKeys::stepwise::rna , 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 : basic::options::OptionKeys::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 : basic::options::OptionKeys::rigid , basic::options::OptionKeys::score , rigid , score
• patch_filter_scorefxn : basic::options::OptionKeys::fast_loops , fast_loops
• patch_selectors : basic::options::OptionKeys::residues , residues
• patchdock : basic::options::OptionKeys::parser , parser
• patchdock_random_entry : basic::options::OptionKeys::parser , parser
• path() : basic::options::OptionKeys::in::path , basic::options::OptionKeys::out::path , in::path , out::path
• PATH_SEPARATOR() : platform::file
• pathname() : utility
• PathOption : basic::options
• PathOptionKey : basic::options
• PathVectorOption : basic::options
• PathVectorOptionKey : basic::options
• patterson : basic::options::OptionKeys::patterson , patterson
• pb_potential : basic::options::OptionKeys::pb_potential , pb_potential
• PBP_clustering_at_chain_closure : basic::options::OptionKeys::stepwise::rna , stepwise::rna
• pca : basic::options::OptionKeys::in::file , in::file
• PCS : basic::options::OptionKeys::PCS , PCS
• pcs_cluster_coverage : basic::options::OptionKeys::robert , robert
• pcs_cluster_lowscoring : basic::options::OptionKeys::robert , robert
• pcs_dump_cluster : basic::options::OptionKeys::robert , robert
• PCS_frag_cst : basic::options::OptionKeys::in::file , in::file
• pcs_maxsub_filter : basic::options::OptionKeys::robert , robert
• pcs_maxsub_rmsd : basic::options::OptionKeys::robert , robert
• PCSTS1 : basic::options::OptionKeys::PCSTS1 , PCSTS1
• PCSTS2 : basic::options::OptionKeys::PCSTS2 , PCSTS2
• PCSTS3 : basic::options::OptionKeys::PCSTS3 , PCSTS3
• PCSTS4 : basic::options::OptionKeys::PCSTS4 , PCSTS4
• pdb : basic::options::OptionKeys::in::path , basic::options::OptionKeys::out::path , basic::options::OptionKeys::out , in::path , out::path , out
• pdb1() : assembly , basic::options::OptionKeys::assembly
• pdb2() : assembly , basic::options::OptionKeys::assembly , basic::options::OptionKeys::chunk , chunk
• pdb_comments : basic::options::OptionKeys::out::file , out::file
• pdb_each_iteration : basic::options::OptionKeys::dna::design , dna::design
• pdb_gz : basic::options::OptionKeys::out , out
• pdb_list : basic::options::OptionKeys::pepspec , pepspec
• pdb_parents : basic::options::OptionKeys::out::file , 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 : basic::options::OptionKeys::pepspec , pepspec
• pep_chain : basic::options::OptionKeys::pepspec , pepspec
• pep_fold_only : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• pep_refine : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• pepspec : basic::options::OptionKeys::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 : basic::options::OptionKeys::out::file , 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 : basic::options::OptionKeys::symmetry , 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 : basic::options::OptionKeys::pH , pH
• pH_mode : basic::options::OptionKeys::pH , pH
• pH_neighbor_pack : basic::options::OptionKeys::pH::calc_pka , pH::calc_pka
• pH_prepack : basic::options::OptionKeys::pH::calc_pka , pH::calc_pka
• pH_relax : basic::options::OptionKeys::pH::calc_pka , pH::calc_pka
• pH_unbound : basic::options::OptionKeys::pH , pH
• phi_psi_range_A : basic::options::OptionKeys::frags::ABEGO , frags::ABEGO
• phil : basic::options::OptionKeys::phil , phil
• phipsi_analysis : basic::options::OptionKeys::pepspec , pepspec
• 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 , 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 : basic::options::OptionKeys::pH::calc_pka , pH::calc_pka
• pka_for_chainno : basic::options::OptionKeys::pH::calc_pka , pH::calc_pka
• pka_for_resnos : basic::options::OptionKeys::pH::calc_pka , pH::calc_pka
• pka_rad : basic::options::OptionKeys::pH::calc_pka , pH::calc_pka
• place_adduct_waters : basic::options::OptionKeys::motifs , motifs
• PLUS_SYMBOL : numeric::expression_parser
• pocket_buried_dist : basic::options::OptionKeys::pocket_grid , pocket_grid
• pocket_buried_score : basic::options::OptionKeys::pocket_grid , pocket_grid
• pocket_constraint_weight : basic::options::OptionKeys::constraints , constraints
• pocket_debug_output : basic::options::OptionKeys::pocket_grid , pocket_grid
• pocket_dump_exemplars : basic::options::OptionKeys::pocket_grid , pocket_grid
• pocket_dump_pdbs : basic::options::OptionKeys::pocket_grid , pocket_grid
• pocket_dump_rama : basic::options::OptionKeys::pocket_grid , pocket_grid
• pocket_exemplar_vdw_pen : basic::options::OptionKeys::pocket_grid , pocket_grid
• pocket_filter_by_exemplar : basic::options::OptionKeys::pocket_grid , pocket_grid
• pocket_grid : basic::options::OptionKeys::pocket_grid , pocket_grid
• pocket_grid_size : basic::options::OptionKeys::pocket_grid , pocket_grid
• pocket_grid_size_x : basic::options::OptionKeys::pocket_grid , pocket_grid
• pocket_grid_size_y : basic::options::OptionKeys::pocket_grid , pocket_grid
• pocket_grid_size_z : basic::options::OptionKeys::pocket_grid , pocket_grid
• pocket_grid_spacing : basic::options::OptionKeys::pocket_grid , pocket_grid
• pocket_ignore_buried : basic::options::OptionKeys::pocket_grid , pocket_grid
• pocket_max_size : basic::options::OptionKeys::pocket_grid , pocket_grid
• pocket_max_spacing : basic::options::OptionKeys::pocket_grid , pocket_grid
• pocket_min_size : basic::options::OptionKeys::pocket_grid , pocket_grid
• pocket_ntrials : basic::options::OptionKeys::pocket_grid , pocket_grid
• pocket_num_angles : basic::options::OptionKeys::pocket_grid , pocket_grid
• pocket_only_buried : basic::options::OptionKeys::pocket_grid , pocket_grid
• pocket_probe_radius : basic::options::OptionKeys::pocket_grid , pocket_grid
• pocket_psp : basic::options::OptionKeys::pocket_grid , pocket_grid
• pocket_restrict_size : basic::options::OptionKeys::pocket_grid , pocket_grid
• pocket_search13 : basic::options::OptionKeys::pocket_grid , pocket_grid
• pocket_side : basic::options::OptionKeys::pocket_grid , pocket_grid
• pocket_sps : basic::options::OptionKeys::pocket_grid , pocket_grid
• pocket_static_grid : basic::options::OptionKeys::pocket_grid , pocket_grid
• pocket_surface_dist : basic::options::OptionKeys::pocket_grid , pocket_grid
• pocket_surface_score : basic::options::OptionKeys::pocket_grid , pocket_grid
• pocket_zero_derivatives : basic::options::OptionKeys::constraints , constraints
• poi : basic::options::OptionKeys::willmatch , willmatch
• poidis : basic::options::OptionKeys::willmatch , 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 : basic::options::OptionKeys::sasa , sasa
• poll_frequency : basic::options::OptionKeys::rbe , rbe
• 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 : basic::options::OptionKeys::els , basic::options::OptionKeys::evaluation , els , evaluation
• POOL_RMSD_ADD_STRUCTURE : basic
• POOL_RMSD_EVALUATE : basic
• POOL_RMSD_MASTER_EVALUATE : basic
• 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_COPY : basic
• pose_input_stream : basic::options::OptionKeys::jd2 , jd2
• pose_metrics : basic::options::OptionKeys::pose_metrics , basic::options::OptionKeys::rescore , pose_metrics , rescore
• post_minimize : basic::options::OptionKeys::dna::specificity , dna::specificity
• potential_cap : basic::options::OptionKeys::pb_potential , 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 : basic::options::OptionKeys::pH , 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 , basic::options::OptionKeys::out , basic::options::OptionKeys::ProQ , basic::options::OptionKeys::templates , contactMap , matdes , ms::checkpoint , out , ProQ , templates
• premin : basic::options::OptionKeys::rot_anl , rot_anl
• preminimize : basic::options::OptionKeys::stepwise , 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 : basic::options::OptionKeys::pepspec , pepspec
• prep_rot_std_dev : basic::options::OptionKeys::pepspec , pepspec
• prep_trans_std_dev : basic::options::OptionKeys::pepspec , pepspec
• prep_use_ref_rotamers : basic::options::OptionKeys::pepspec , pepspec
• prepack_interface : basic::options::OptionKeys::dna::design , dna::design
• preprocessing_script_version() : antibody , basic::options::OptionKeys::antibody
• preserve_c_beta : basic::options::OptionKeys::packing , packing
• preserve_crystinfo() : basic::options::OptionKeys::in , in
• preserve_header : basic::options::OptionKeys::run , 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
• pretty_print : utility::json_spirit
• prevent_repacking : basic::options::OptionKeys::packing , packing
• primary_subsubunit : basic::options::OptionKeys::smhybrid , 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 : basic::options::OptionKeys::pocket_grid , pocket_grid
• print_i_calc : basic::options::OptionKeys::score::saxs , 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 : basic::options::OptionKeys::packing , packing
• print_rdc_values : basic::options::OptionKeys::rdc , 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 : basic::options::OptionKeys::score , score
• prob_perturb_weights() : abinitio , basic::options::OptionKeys::abinitio
• probabilities : basic::options::OptionKeys::canonical_sampling::probabilities , canonical_sampling::probabilities
• probe_radius : basic::options::OptionKeys::sasa , sasa
• probe_specificity : basic::options::OptionKeys::dna::design , dna::design
• proc_id : basic::options::OptionKeys::run , run
• process() : basic::options
• process_ligrot_separately() : basic::options::OptionKeys::enzdes , enzdes
• process_store() : abinitio , basic::options::OptionKeys::abinitio
• product() : numeric
• prof_bug : basic::options::OptionKeys::ProQ , ProQ
• prof_reset() : basic
• prof_show() : basic
• prof_start_function_body() : basic
• prof_stop_function_body() : basic
• profile : basic::options::OptionKeys::run , run
• profile_score : basic::options::OptionKeys::frags::scoring , frags::scoring
• ProfTag : basic
• proj_angl() : numeric
• projection_matrix() : numeric
• ProQ : basic::options::OptionKeys::ProQ , ProQ
• protein : basic::options::OptionKeys::run , basic::options::OptionKeys::stepwise::protein , run , stepwise::protein
• protein_atr_rep_screen : basic::options::OptionKeys::stepwise::protein , stepwise::protein
• protein_prepack : basic::options::OptionKeys::stepwise::protein , stepwise::protein
• protein_scan : basic::options::OptionKeys::dna::design , dna::design
• protocol() : basic::options::OptionKeys::docking::ligand , basic::options::OptionKeys::parser , basic::options::OptionKeys::run , docking::ligand , parser , run
• protonated_H1_adenosine_list : basic::options::OptionKeys::stepwise::rna , stepwise::rna
• pSer2Asp_centroid : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• pSer2Glu_centroid : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• PseudoMatrix : numeric::kinematic_closure
• pseudosym : basic::options::OptionKeys::smhybrid , smhybrid
• PseudoVector : numeric::kinematic_closure
• 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
• PyExitCallbackCOP : utility
• PyExitCallbackOP : utility
• pymol_chains() : basic