- p -

• P() : draw_gen_env_dep_pair_decompose.m , gen_env_dep_pair.m , gen_env_dep_pair_decompose.m , draw_gen_env_dep_pair.m
• p_a_r_ang1() : draw_gen_env_dep_orient_decompose.m , gen_env_dep_orient.m , gen_env_dep_orient_decompose.m , gen_env_dep_orient_draw.m
• p_a_r_ang2() : draw_gen_env_dep_orient_decompose.m , gen_env_dep_orient_draw.m , gen_env_dep_orient_decompose.m , gen_env_dep_orient.m
• P_env_ref() : cal_env.m
• P_i() : calc_NtoP.m
• p_r_ang() : gen_env_dep_orient_decompose.m , gen_env_dep_orient_draw.m , gen_env_dep_orient.m , draw_gen_env_dep_orient_decompose.m
• pack14() : gpu_pack14.h
• pack_interface() : rna_protein_test.cc
• pack_it() : stepwise_helix_test.cc
• pack_o2prime() : rna_test.cc
• pack_phosphates() : pack_phosphates.cc
• pack_polar_hydrogens() : pack_polar_hydrogens.cc
• pack_rotamers_test() : test1.cc
• pack_sidechains() : OLD_TRIAL_protein_helix_assemble.cc
• packing_score() : pack_ddg.cc
• packmin_unbound_pep() : pepspec.cc , pep_spec_flx.mov.cc , pep_spec_flx.cc , pep_spec.cc , pep_ref.cc , pep_rama.cc , pep_prepspec.cc , pep_paapp.cc , pep_spec.06-23.cc , pep_gly.cc
• packRotamers() : CycDsulf.cc
• pair() : load_pair_env_table.m , load_pair_env_table_ref.m , load_pair_env_table.m , load_pair_env_table_ref.m , load_pair_env_table.m , load_pair_env_table_ref.m , load_pair_env_table.m , load_pair_env_table_ref.m , load_pair_env_table.m , load_pair_env_table_ref.m , load_pair_env_table.m , load_pair_env_table_ref.m , load_pair_env_table.m , load_pair_env_table_ref.m , load_pair_env_table.m , load_pair_env_table_ref.m , load_pair_env_table.m , load_pair_env_table_ref.m , load_pair_env_table.m , draw_gen_env_dep_pair.m , draw_gen_env_dep_pair_decompose.m , draw_matrix.m , load_pair_env_table.m , load_pair_env_table_ref.m , load_pair_env_table.m , load_pair_env_table_ref.m , load_pair_env_table.m , load_pair_env_table_ref.m , load_pair_env_table.m , load_pair_env_table_ref.m , load_pair_env_table.m , load_pair_env_table_ref.m , load_pair_env_table.m , load_pair_env_table_ref.m , load_pair_env_table.m , load_pair_env_table_ref.m , load_pair_env_table.m , load_pair_env_table_ref.m , load_pair_env_table.m , load_pair_env_table_ref.m , load_pair_env_table.m , load_pair_env_table_ref.m , load_pair_env_table.m , load_pair_env_table_ref.m , load_pair_env_table.m , load_pair_env_table_ref.m , gen_env_dep_pair.m , gen_env_dep_pair_decompose.m , load_pair_env_table.m , load_pair_env_table_ref.m
• pair_counts() : load_tables.m
• pair_old() : load_tables.m
• pairE_test() : test_multithreaded_ramapp_load.cc
• parse_chains() : minimization_test.cc , msd.cc
• parse_extra_atom_list() : bettercluster.cc , design_cycpeptide_MPI.cc
• parse_into_stub() : transform_loodo.cc
• parse_nonstandard_angles() : fit_helixparams.cc
• parse_nonstandard_bondlengths() : fit_helixparams.cc
• parse_numbers() : boost_hacks.cc
• parse_pathway_test() : stepwise_template_test.cc
• parse_pdb_pos() : dna_spec_test.cc , motif_scan.cc , simple_dna_regression_test.cc
• parse_position() : find_position_matches_using_inverse_rotamers.cc
• parse_resfile() : msd.cc , minimization_test.cc , find_consensus_mutations.cc
• parse_resfiles() : minimization_test.cc , msd.cc
• parse_sequence() : adding_peptoids.cc
• parse_ss_regions() : holes2_training_data.cc
• parsefilelist() : design_cycpeptide_MPI.cc
• pass_VDW_replusion_screen_fast() : parin_test.cc
• pass_VDW_replusion_screen_slow() : parin_test.cc
• passes_quality_check() : detect_tight_clusters.cc
• PATH() : test_CarbohydrateInfo.cc , test_carbohydrate_scoring.cc , test_carbohydrate_docking.cc
• path_distance_OK() : pdbstats_test.cc
• pca_align_BROKEN() : pca_simple.hh , pca_simplie.hh
• pct_features_in_common() : compare_features.cc
• pdb_id() : atom_energy_breakdown.cc , per_residue_energies.cc , residue_energy_breakdown.cc
• pdb_little_motif_test() : coarse_rna_test.cc
• pdb_scoring() : rna_pdb_scoring.cc
• pdb_stats() : coarse_rna_test.cc
• pdb_to_silent_file() : swa_rna_util.cc
• pdb_to_silent_file_simple() : convert_pdb_to_silent_file.cc
• pdbslice() : stepwise_test.cc
• pdbstats_test() : coarse_rna_test.cc
• peek() : hubdenovo.cc
• pep_anchor() : pepspec.cc
• pep_begin() : pepspec.cc
• pep_chain() : pepspec.cc
• pep_end() : pepspec.cc
• pep_energies_analysis() : pep_analysis.cc , pep_gly.cc
• pep_jump() : pepspec.cc
• pep_phipsi_analysis() : pep_spec_flx.mov.cc , pepspec.cc , pep_spec_flx.cc , pep_spec.06-23.cc , pep_rama.cc , pep_prepspec.cc , pep_analysis.cc , pep_spec.cc
• pep_rmsd_analysis() : pepspec.cc , pepspec_anchor_dock.cc , pepspec.cc , pepspec_anchor_dock.cc , pep_spec_flx.mov.cc , pep_spec_flx.cc , pep_spec.cc , pep_spec.06-23.cc , pep_prepspec.cc , pep_prep.cc , pep_analysis.cc
• pep_scan_analysis() : pep_analysis.cc , pep_gly.cc
• peptide_plane_test() : stepwise_test.cc
• peptide_plane_test_OLD() : stepwise_test.cc
• performMinimization() : CycDsulf.cc
• periodic_range() : test_bbmc.org.cc , test_bbmc.cc
• periodic_test_function() : check_cubic_conv.cc
• permutate() : close_homolog_refinement.cc
• perturb() : loodo.cc
• perturb_and_rescore() : triazolamer_creator.cc
• perturb_bb() : test_KIC_betapeptide.cc , make_ideal_betapeptide.cc
• perturb_bb_and_relax() : design_cycpeptide_MPI.cc
• perturb_pep_bb() : pep_gly.cc , pepspec.cc , pep_spec_flx.mov.cc , pep_spec_flx.cc , pep_spec.cc , pep_ref.cc , pep_rama.cc , pep_prepspec.cc , pep_paapp.cc , pep_spec.06-23.cc
• PHI_BINRANGE() : peptoid_rotlib_test2.cc
• phosphate_stats() : dna_spec_test.cc , simple_dna_regression_test.cc
• pick_correct_solution() : broken_kick.cc
• pick_fragments() : make_frag_ssdep.cc
• pick_normal_sampling() : pick_normal_sampling.hh
• pick_pathological_solution() : broken_kick.cc
• pick_random_solution() : kick_n_terminus.cc
• picking_test() : vllb.cc
• pid() : capri15_scoring.hh
• place_sf4() : coiled_coil.cc
• place_water_acceptor() : hydrate.cc
• place_water_donor() : hydrate.cc
• place_waters_and_minimize() : use_asn_motifs.cc , dna_motifs_collector.cc , ligand_motifs.cc
• place_zns() : coiled_coil_zn.cc
• plot() : draw_gen_env_dep_orient_decompose.m , gen_env_dep_orient_decompose.m
• plot_scoreterm() : plot_scoreterm.cc
• points_in_triangle() : mpframework_test2.cc
• polar_pdbstats_from_pose() : polar_pdbstats.cc
• polar_pdbstats_test() : polar_pdbstats.cc
• populate_database_with_dummy_data() : sweep_respair_energies.cc
• pos_mod() : cryst_gen.cc , pdb_gen_cryst.cc , cryst_gen.cc
• pose2bin() : cycgly_bbg8t3a.cc , cycgly_target.cc , cycsamp.cc , rblinker2.cc , rblinker2_overlay_bound.cc , rblinker2_test.cc
• pose2frags() : design_frags.cc , minimize.cc
• pose_cbcount() : isct_test.cc , genP23.cc , genI213_nocontacts.cc , genI213_gensym.cc , genI213_2comp.cc , symdock_enum_3_1.cc , symdock_enum.cc
• pose_from_posedata() : bettercluster.cc
• pose_from_scratch() : rama_energy.cc
• pose_list_compare() : lariat_modeling.cc , turner_test_double_helix.cc
• pose_nbratom_center_of_mass() : find_buns.cc
• pose_pos_from_pdb_pos() : capri15.cc
• pose_resid_from_PDB() : phil.hh
• pose_to_string() : test_serialize.cc
• poses_from_cmd_line() : score_aln2.cc , score_aln.cc , partial_thread.cc , fix_alignment_to_match_pdb.cc , FastGap.cc , hybrid.cc , thread_fast.cc , aln_to_disulf.cc , contact_map_from_homologs.cc , tj_util.hh , minimalCstHomology.cc
• poses_from_cmd_line_noPDBtag() : tj_util.hh
• posewrap_from_command_line() : smhybrid.cc
• positions_incompatible_with_task() : backrub_pilot.cc
• possible_disulfide() : disulfides.hh
• post_rebuild_bulge_assembly() : swa_rna_main.cc
• power_set() : diversify_conotoxin.cc
• powi() : Svm.cc
• pproj() : gpu_mat_vec.hh
• pre_fill_dfire() : draw_gen_env_dep_pair_decompose.m , gen_env_dep_pair_decompose.m
• pre_fill_dfire_2D() : draw_gen_env_dep_orient_decompose.m , gen_env_dep_orient_decompose.m
• predict_AE() : SID_rescore.cc
• predict_chem_map_test() : rna_predict_chem_map.cc
• predict_disorder() : ResidueDisorder.cc
• predict_ss() : abego_predict.cc , hle_predict.cc
• Prepare() : grower_prep.cc
• prepare_beta_sandwiches() : PrepareGraphNodes.cc
• prepare_full_length_start_model() : easy_target_test.cc
• prepare_helix_bundles() : PrepareGraphNodes.cc
• prepare_smotifs() : PrepareGraphNodes.cc
• prepare_start_model() : easy_target_test.cc
• prepare_threaded_model() : rna_thread.cc
• present_in_native() : unalignedEvaluate.cc
• print() : ostream.h , core.h , color.h , draw_gen_env_dep_orient_decompose.m , gen_env_dep_orient_decompose.m
• print_all_torsions_test() : rna_test.cc
• print_atom_info() : tgtres_polar_sho_energies.cc
• print_atom_pdbid() : cnl_env_lost_hbs.cc
• print_backtrace() : backtrace.hh
• print_base_centroid_atoms() : rb_entropy.cc
• print_cst_file() : hbscan.cc
• print_ddgs() : score_ddgs.cc , ddg_monomer.cc
• print_debug_information() : jcluster.cc
• print_dm() : jcluster.cc
• print_energies() : analyze_ddG.cc , surfacescore.cc
• print_graph() : undirected_graph.cc
• print_hb_counts() : lig_polar_sat.cc
• print_hb_partners() : cnl_env_lost_hbs.cc
• print_hbond() : sel_hbonds.cc
• print_hbonds_test() : rna_test.cc
• print_header() : score_ddgs.cc
• print_internal_coord_test() : rna_test.cc
• print_internal_coordinates() : fold_tree.cc , partial_pose.cc
• print_interres_bond() : ligand_evis.cc
• print_matrix_to_file() : cs_align.cc
• print_motifs() : make_motif_tables.cc
• print_movemap() : char_native.cc , smhybrid.cc , matdes_design_2comp.cc , matdes_design.cc , design_symm_no_hack_elec.cc , design_symm_110330_good.cc , design_symm.cc , design_symm.bak.110314.cc
• print_node() : ligand_evis.cc
• print_passed() : filter.cc
• print_pdb_info() : interface_energy.cc
• print_pep_analysis() : pep_spec_flx.cc , pepspec.cc
• print_pep_csts() : pep_prep.cc , pepspec_anchor_dock.cc
• print_res_freqs() : pep_opt.cc , pep_opt_parallel.cc
• print_res_ids() : list_cnl_ngbs.cc
• print_rot_vec() : analyze_casp9.cc , angle_recovery_stats.cc
• print_rot_vector() : angle_recovery_stats.cc
• print_scorefxn() : pep_opt.cc , pep_opt_parallel.cc
• print_scores() : make_motif_tables.cc
• print_secstruct_test() : rna_test.cc
• print_seq_map() : score_aln.cc , score_aln2.cc , thread_fast.cc , hybrid.cc
• print_string_stdout() : Svm.cc
• print_surface_score_by_res() : surfacescore.cc
• print_torsions_check() : rna_test.cc
• print_tree() : atom_tree_check.cc
• print_vals() : metric.cc
• print_vector() : vector_math.cc
• print_verbose_ddgs() : score_ddgs.cc
• printbits() : rblinker2_test.cc , rblinker2_overlay_bound.cc , rblinker2.cc , cycgly_target.cc , cycsamp.cc , cycgly_bbg8t3a.cc
• printbits16() : gpu_bit_utils.hh
• printbits32() : gpu_bit_utils.hh
• printBondAngles() : print_phipsi.cc
• printEnergies() : CycDsulf.cc
• printf() : draw_gen_env_dep_orient_decompose.m , cal_env.m , gen_env_dep_orient.m , gen_env_dep_orient_decompose.m , gen_vdw_radius_soft.m , printf.h
• printScoreTermsPose() : CycDsulf.cc
• Prm() : gen_vdw_radius.m
• process_file_list() : ligand_motifs.cc , dna_motifs_collector.cc , ligand_motifs.cc
• process_for_motifs() : ligand_motifs.cc , dna_motifs_collector.cc , ligand_motifs.cc , extract_motifs.cc
• process_pose() : sc.cc
• process_ss_str() : smhybrid.cc
• process_the_pose() : fa_to_cenrot_score.cc
• processChild() : evolution.cc
• processChildren() : evolution.cc
• processChildrenIntensification() : evolution.cc
• processRegions() : contactMap.cc
• proclose_test() : test1.cc
• proj() : helix_assembly.cc , gpu_mat_vec.hh
• project_line() : cryst_gen.cc
• projectionMAT() : gpu_mat_vec.hh
• projperp() : gentetra.cc , symdock_enum_3_1.cc
• proline_rama_pdbstats_from_pose() : pdbstats_test.cc
• prot_anchor() : pepspec.cc
• prot_begin() : pepspec.cc
• prot_chain() : pepspec.cc
• prot_end() : pepspec.cc
• protein_helix_test() : OLD_TRIAL_protein_helix_assemble.cc
• protein_motif_offset() : zf_relax.cc
• protocols_main() : kick_n_terminus.cc
• prune_away_cnl() : cnl_env_lost_hbs.cc
• prune_cb_pairs() : symdock_enum_3_1.cc , tcdock.cc
• PSI_BINRANGE() : peptoid_rotlib_test2.cc
• psI_petf_sf4_dis() : rblinker.cc
• ptr() : format.h
• put_constraints_on_helix() : OLD_TRIAL_protein_helix_assemble.cc
• put_it_in_list() : rna_test.cc
• Pvdw() : gen_vdw_radius_soft.m
• PYBIND11_MODULE() : T40.stl.ref.cpp , T42.stl.names.set.ref.cpp , T42.stl.names.ref.cpp , T42.stl.names.multiset.ref.cpp , T42.stl.names.multimap.ref.cpp , T42.stl.names.multi.ref.cpp , T42.stl.names.map.ref.cpp , T60.pybind11.ref.cpp , T33.buffer_protocol.ref.cpp , T32.call_guard.ref.cpp , T43.stl.pybind11_include_stl.ref.cpp , T50.add_on_binder.ref.cpp , T50.namespace_binder.ref.cpp , T60.custom_shared.ref.cpp , T70.module_local.ref.cpp , T70.options.ref.cpp , T71.module_local.ref.cpp , T80.custom_trampoline.ref.cpp , T81.custom_trampoline_with_args.ref.cpp , T07.class.ref.cpp , T30.include.ref.cpp , T00.basic.ref.cpp , T01.enum.ref.cpp , T02.function.ref.cpp , T05.default.ref.cpp , T07.class.match_args.ref.cpp , T08.constructor.ref.cpp , T09.overload.ref.cpp , T10.inheritance.ref.cpp , T10.virtual_inheritance.ref.cpp , T11.override.ref.cpp , T12.insertion_operator.ref.cpp , T12.operator.ref.cpp , T15.copy.ref.cpp , T15.inner_class.fwd.ref.cpp , T15.inner_class.ref.cpp , T17.anonymous.ref.cpp , T20.template.ref.cpp , T20.template.variadic.ref.cpp , T31.include_for_class.ref.cpp
• pymol() : mkresfile_i213.cc
• pymol_struct_type_test() : rna_test.cc