- p -

• pack_extra_bodies() : protocols::chemically_conjugated_docking
• pack_missing_sidechains() : core::pack
• pack_polar_hydrogens() : protocols::stepwise::modeler::polar_hydrogens
• pack_rotamers() : core::pack
• pack_rotamers_cleanup() : core::pack
• pack_rotamers_loop() : core::pack
• pack_rotamers_run() : core::pack
• pack_rotamers_setup() : core::pack
• pack_scorefxn_pose_handshake() : core::pack
• PACKER_PALETTE_TAG() : core::pack::task
• packing_helper() : protocols::loop_modeling::refiners
• pad_dash() : core::kinematics
• pad_dash_left() : core::kinematics
• pad_dash_right() : core::kinematics
• pad_sequences() : protocols::pdbinfo_manipulations
• pair_constel_set() : protocols::constel
• pair_constel_set_idx2() : protocols::constel
• pair_first_sort_helper() : protocols::toolbox::rotamer_set_operations
• pair_map_to_comma_strings() : core::conformation::symmetry
• pair_sort_criterion() : protocols::stepwise::legacy::modeler::rna
• parallel_base_test() : protocols::motifs
• paratope_charge() : protocols::antibody
• paratope_sasa() : protocols::antibody
• parse_adduct_string() : core::chemical
• parse_atom_type_data() : core::chemical::sdf
• parse_bond_type_data() : core::chemical::sdf
• parse_constraint_generators() : protocols::constraint_generator
• parse_custom_torsion() : protocols::constraint_generator
• parse_database_session() : protocols::rosetta_scripts
• parse_enum_set() : core::chemical::gasteiger
• parse_filter() : protocols::rosetta_scripts
• parse_filter_or_null() : protocols::rosetta_scripts
• parse_func() : protocols::constraint_generator
• parse_grid_set_from_tag() : protocols::qsar::scoring_grid
• parse_jump_selector() : core::select::jump_selector
• parse_length_str() : protocols::denovo_design::architects
• parse_length_string() : protocols::denovo_design
• parse_lengths() : protocols::denovo_design::components
• parse_loops_from_tag() : protocols::loop_modeling::utilities
• parse_matrix() : protocols::denovo_design::filters
• parse_motif_string() : protocols::denovo_design
• parse_movemap_factory() : core::select::movemap
• parse_movemap_factory_legacy() : protocols::rosetta_scripts
• parse_movemap_tag() : protocols::rosetta_scripts
• parse_mover() : protocols::rosetta_scripts
• parse_mover_or_null() : protocols::rosetta_scripts
• parse_mover_subtag() : protocols::rosetta_scripts
• parse_named_movemap_factory_legacy() : protocols::rosetta_scripts
• parse_NMR_name() : core::scoring::constraints
• parse_NMR_name_old() : core::scoring::constraints
• parse_optional_grid_set_from_tag() : protocols::qsar::scoring_grid
• parse_orientations() : protocols::denovo_design::components
• parse_out_non_standard_residues() : core::sequence
• parse_pdb_code() : protocols::splice
• parse_PDBnum_icode() : core::pose
• parse_plain_text_with_columns() : protocols::antibody::grafting
• parse_res() : protocols::hybridization
• parse_res_agnostic_commands() : core::pack::task
• parse_resfile() : core::pack::task
• parse_resfile_string() : core::pack::task
• parse_resfile_string_with_no_lockdown() : protocols::forge::methods
• parse_residue_level_task_operations() : core::pack::task::operation
• parse_residue_selector() : core::select::residue_selector
• parse_residue_selector_logic_string() : core::select::residue_selector
• parse_residue_selector_xsd_documentation() : core::select::residue_selector
• parse_residue_selectors() : protocols::denovo_design::movers
• parse_resnames() : protocols::helical_bundle
• parse_resnum() : core::pose
• parse_rotamer_sampling_data() : core::pack::task::operation
• parse_score_function() : core::scoring
• parse_seeds() : protocols::seeded_abinitio
• parse_segment_names() : protocols::denovo_design::connection
• parse_selection_block() : core::pose
• parse_sequence() : core::pose
• parse_single_residue_selector() : protocols::jd3
• parse_spans() : protocols::seeded_abinitio
• parse_strand_pair() : protocols::denovo_design
• parse_stub_sets() : protocols::protein_interface_design::movers
• parse_task_operations() : core::pack::task
• parse_torsion_type() : protocols::constraint_generator
• parse_xyz_vector() : protocols::rosetta_scripts
• part_complex() : protocols::protein_interface_design::movers
• partial_align() : protocols::hybridization
• partition_by_symm_jumps() : core::pose::symmetry
• partition_pose_by_jump() : core::pose
• pass_metropolis() : core::pack
• passes_filters() : protocols::ligand_docking
• patch_operation_from_patch_file_line() : core::chemical
• path_basename() : protocols::stepwise::legacy::modeler::rna
• pcs_erf() : core::scoring::nmr::pcs
• pcs_func() : core::scoring::nmr
• pcs_lmmin() : protocols::nmr::pcs
• pct_features_in_common() : protocols::simple_filters
• pdb_filename() : protocols::denovo_design::movers
• pdb_to_pose() : core::pose
• pdbslice() : core::pose , protocols::magnesium
• per_res_rms_at_corresponding_atoms_no_super() : core::scoring
• per_res_sc_sasa() : core::scoring::sasa
• perform_variable_substitution() : protocols::jd3::standard
• PERTURB() : protocols::loops::loop_mover
• perturb_backbone_for_test() : protocols::grafting
• pH_mode_exceptions() : core::chemical
• phi_torsion() : core::id
• phi_torsion_beta_aa() : core::id
• phi_torsion_meta_aramid() : core::id
• phi_torsion_oligourea() : core::id
• phi_torsion_ortho_aramid() : core::id
• phi_torsion_para_aramid() : core::id
• phi_torsion_post_methylene_meta_aramid() : core::id
• phi_torsion_post_methylene_ortho_aramid() : core::id
• phi_torsion_post_methylene_para_aramid() : core::id
• phi_torsion_pre_methylene_meta_aramid() : core::id
• phi_torsion_pre_methylene_ortho_aramid() : core::id
• phi_torsion_pre_methylene_para_aramid() : core::id
• phi_torsion_pre_methylene_post_methylene_meta_aramid() : core::id
• phi_torsion_pre_methylene_post_methylene_ortho_aramid() : core::id
• phi_torsion_pre_methylene_post_methylene_para_aramid() : core::id
• phosphate_base_phosphate_rmsd() : protocols::stepwise::modeler::rna
• phosphate_base_phosphate_square_deviation() : protocols::stepwise::modeler::rna
• phosphate_square_deviation() : protocols::stepwise::modeler::rna
• pick_fragments() : core::fragment::picking_old::vall
• pick_fragments_by_ss() : core::fragment::picking_old::vall
• pick_fragments_by_ss_plus_aa() : core::fragment::picking_old::vall
• pick_loops_chainbreak() : protocols::comparative_modeling
• pick_loops_unaligned() : protocols::comparative_modeling
• pick_loopy_cutpoint() : core::kinematics
• pick_pivots() : protocols::hybridization
• place_atom_positions() : protocols::helical_bundle
• place_de_novo_wat_at_anchor() : protocols::hydrate
• PlaceSimultaneously_DesignMovers_subelement_mangler() : protocols::protein_interface_design::movers
• PlaceSimultaneously_NotifyMovers_subelement_mangler() : protocols::protein_interface_design::movers
• PlaceSimultaneously_StubMinimize_subelement_mangler() : protocols::protein_interface_design::movers
• PlaceSimultaneously_StubSets_subelement_mangler() : protocols::protein_interface_design::movers
• PlaceSimultaneously_subelement_mangler() : protocols::protein_interface_design::movers
• PlaceStub_DesignMovers_subelement_mangler() : protocols::protein_interface_design::movers
• PlaceStub_NotifyMovers_subelement_mangler() : protocols::protein_interface_design::movers
• PlaceStub_StubMinimize_subelement_mangler() : protocols::protein_interface_design::movers
• PlaceStub_subelement_mangler() : protocols::protein_interface_design::movers
• point_graph_dme() : protocols::simple_moves
• point_line_distance() : core::scoring::methods
• point_mutation() : protocols::protein_interface_design
• pointer_equals() : protocols::jd3
• pointer_sorter() : protocols::fldsgn::topology
• points_in_triangle() : core::membrane
• polycubic_interpolation() : core::pack::dunbrack
• polymeric_termini_incomplete() : core::scoring
• pos_mod() : core::scoring::electron_density , core::scoring::electron_density_atomwise , core::scoring::fiber_diffraction , protocols::cryst
• pose1_has_most_CBs() : protocols::sic_dock
• pose_charge() : protocols::antibody
• pose_data_cache_from_sfr() : core::io
• pose_energies_from_sfr() : core::io
• pose_energies_to_json() : protocols::rpc
• pose_from_atom_tree_diff() : core::import_pose::atom_tree_diffs
• pose_from_binary_silent_file() : protocols::checkpoint
• pose_from_file() : core::import_pose
• pose_from_pdb_stream() : core::import_pose
• pose_from_pdbstring() : core::import_pose
• pose_from_pose() : core::io
• pose_from_saccharide_sequence() : core::pose
• pose_from_store() : protocols::indexed_structure_store
• pose_has_nonzero_Bs() : core::scoring::electron_density
• pose_inputter_xsd_type_definition_w_attributes() : protocols::jd3::pose_inputters
• pose_matches_description() : protocols::denovo_design::components
• pose_matches_user_tag() : protocols::jobdist
• pose_max_nbr_radius() : core::pose
• pose_outputter_xsd_type_definition_w_attributes() : protocols::jd3::pose_outputters
• pose_residue_is_terminal() : core::pose
• pose_setup_from_file() : protocols::recces
• pose_setup_turner() : protocols::recces
• pose_tilt_angle_and_center_distance() : protocols::membrane
• pose_tm_com() : protocols::membrane
• pose_to_binary_silent_file() : protocols::checkpoint
• pose_to_pack_data() : core::scoring::packstat
• pose_to_pdb() : core::pose
• pose_to_string() : protocols::network
• pose_with_most_CBs() : protocols::sic_dock
• poseOPs_from_files() : core::import_pose
• poses_from_cmd_line() : protocols::comparative_modeling
• poses_from_files() : core::import_pose
• position_cutpoint_phosphate_torsions() : core::pose::rna
• position_five_prime_phosphate() : protocols::stepwise::modeler::rna::phosphate
• position_five_prime_phosphate_SLOW() : protocols::stepwise::modeler::rna::phosphate
• position_of_atom_on_ring() : core::conformation
• positions_in_secstruct() : protocols::simple_filters
• positions_incompatible_with_task() : protocols::backrub
• positive_pow() : core::pack::dunbrack
• possible_root() : protocols::rna::denovo
• possible_rts() : protocols::stepwise::modeler::rna
• possibly_canonical() : core::chemical::rna
• possibly_canonical_strict() : core::chemical::rna
• post_decoy() : protocols::network
• post_file() : protocols::network
• power_distance() : core::scoring::power_diagram
• pre_and_post_fold_mover_subelements() : protocols::denovo_design::movers
• pre_bump_check() : core::pack::rotamer_set
• pre_erf_opt_tau() : core::scoring::nmr::pre
• pre_erf_opt_tau_xyz() : core::scoring::nmr::pre
• pre_spin_type_from_atom_name() : core::scoring::nmr
• PRE_TALARIS_2013_STANDARD_WTS() : core::scoring
• precision() : core::io::raw_data
• PRECISION() : protocols::dna
• preload_motif_data() : core::scoring::motif
• preload_motif_data_pthread_wrapper() : core::scoring::motif
• prepare_and_write_number_of_electrostatic_interactions_of_residues_to_files() : protocols::features::strand_assembly
• prepare_scratch_residue() : core::pose::rna
• prepare_silent_struct() : protocols::stepwise::monte_carlo
• prepare_WriteToDB_sandwich() : protocols::features::strand_assembly
• prepend_new_residues() : protocols::denovo_design::components
• prestore_sc_oversat() : core::pack::guidance_scoreterms::approximate_buried_unsat_penalty
• pretty_print_atomicoor() : core::chemical
• primary_fixed_domain() : protocols::stepwise::modeler
• print_atom() : core::conformation
• print_atom_info() : protocols::stepwise::modeler::rna
• print_atom_pair_constraints() : core::scoring::constraints
• print_backbone_torsions() : protocols::stepwise::legacy::modeler::rna
• print_base_centroid_atoms_for_rb_entropy() : protocols::recces
• print_base_state() : protocols::stepwise::modeler::rna
• print_buried_unsat_Hbonds() : protocols::ligand_docking
• print_chains() : protocols::constel
• print_chemical_shift_data() : core::scoring::rna::chemical_shift
• print_chis() : core::chemical
• print_ddgs() : protocols
• print_generators() : core::scoring::power_diagram
• print_hbonds() : protocols::rna::denovo
• print_headers() : protocols::hbnet
• print_heavy_atoms() : protocols::stepwise::modeler::rna
• print_individual_atom_info() : protocols::stepwise::modeler::rna
• print_information() : protocols::rosetta_scripts
• print_internal_coords() : protocols::rna::denovo
• print_interres_bond() : protocols::viewer
• print_job_template() : protocols::jd3
• print_list_to_string() : protocols::hbnet
• print_matrix() : protocols::cluster::calibur
• print_network() : protocols::hbnet
• print_network_w_pdb_numbering() : protocols::hbnet
• print_nmer_svm_energy_data() : protocols::simple_filters
• print_node() : core::conformation , protocols::match::output , protocols::viewer
• print_partners() : core::scoring::power_diagram
• print_points() : core::scoring::power_diagram
• print_residues_near_water() : protocols::hydrate
• print_sequence_pdb_nums() : protocols::dna
• print_sequences_pdb_nums() : protocols::dna
• print_string_vector() : protocols::flxbb
• print_sugar_pucker_state() : protocols::stepwise::modeler::rna
• print_template_script() : protocols::rosetta_scripts
• print_torsion_info() : core::pose::rna , protocols::stepwise::modeler::rna
• print_vertices() : core::scoring::power_diagram
• print_WorkingParameters_info() : protocols::stepwise::legacy::modeler::rna
• printbpy() : protocols::sic_dock::scores
• printChi() : protocols::splice
• printxyz() : protocols::loop_grower
• probe_radius_for_atom_type() : protocols::match
• process_decoy() : protocols::features::strand_assembly
• process_input_file() : core::import_pose
• process_last_resonances() : protocols::noesy_assign
• process_line() : protocols::ligand_docking
• process_residue_request() : core::conformation::symmetry
• product() : core::pack::dunbrack
• projperp() : protocols::sic_dock
• promote_sameresidue_child_of_jump_atom() : core::conformation
• PROPERTY_MAP() : core::chemical
• protein_atom_name_to_num() : core::scoring::rna
• prune_1pass() : core::scoring::packstat
• prune_cavity_balls() : core::scoring::packstat
• prune_hidden_cavity_balls() : core::scoring::packstat
• prune_unpaired_residues() : protocols::denovo_design::components
• psc_compare() : core::pack::dunbrack
• psi_torsion() : core::id
• psi_torsion_beta_aa() : core::id
• psi_torsion_meta_aramid() : core::id
• psi_torsion_oligourea() : core::id
• psi_torsion_ortho_aramid() : core::id
• psi_torsion_para_aramid() : core::id
• psi_torsion_post_methylene_meta_aramid() : core::id
• psi_torsion_post_methylene_ortho_aramid() : core::id
• psi_torsion_post_methylene_para_aramid() : core::id
• psi_torsion_pre_methylene_meta_aramid() : core::id
• psi_torsion_pre_methylene_ortho_aramid() : core::id
• psi_torsion_pre_methylene_para_aramid() : core::id
• psi_torsion_pre_methylene_post_methylene_meta_aramid() : core::id
• psi_torsion_pre_methylene_post_methylene_ortho_aramid() : core::id
• psi_torsion_pre_methylene_post_methylene_para_aramid() : core::id
• pss_tr() : core::io::silent
• put_angle_in_0to360() : core::scoring::dna
• put_in_cutpoint() : core::import_pose
• put_line3() : core::scoring::electron_density::SplineInterp
• put_line4() : core::scoring::electron_density::SplineInterp
• PyReturnValuePolicyTest_DummyClassCOP() : protocols::toolbox
• PyReturnValuePolicyTest_DummyClassOP() : protocols::toolbox
• PyReturnValuePolicyTest_PoseCOP() : protocols::toolbox
• PyReturnValuePolicyTest_PoseOP() : protocols::toolbox
• PyReturnValuePolicyTest_ScoreFunctionCOP() : protocols::toolbox
• PyReturnValuePolicyTest_ScoreFunctionCOP2() : protocols::toolbox
• PyReturnValuePolicyTest_ScoreFunctionOP() : protocols::toolbox
• PyReturnValuePolicyTest_SF_ReplicaCOP() : protocols::toolbox
• PyReturnValuePolicyTest_SF_ReplicaOP() : protocols::toolbox