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• pack_polar_hydrogens() : protocols::stepwise::modeler::polar_hydrogens
• packing_helper() : protocols::loop_modeling::refiners
• pair_first_sort_helper() : protocols::toolbox::rotamer_set_operations
• pair_sort_criterion() : protocols::stepwise::legacy::modeler::rna
• parallel_base_test() : protocols::motifs
• paratope_charge() : protocols::antibody
• paratope_sasa() : protocols::antibody
• parse_bogus_res_tag() : protocols::rosetta_scripts
• parse_filter() : protocols::rosetta_scripts
• parse_movemap() : protocols::rosetta_scripts
• parse_movemapdef() : protocols::elscripts
• parse_mover() : protocols::rosetta_scripts
• parse_mover_subtag() : protocols::rosetta_scripts
• parse_out_non_standard_residues() : protocols::stepwise::setup
• parse_res() : protocols::hybridization
• parse_resfile_string_with_no_lockdown() : protocols::forge::methods
• parse_score_function() : protocols::rosetta_scripts
• parse_scoredef() : protocols::elscripts
• parse_seeds() : protocols::seeded_abinitio
• parse_spans() : protocols::seeded_abinitio
• parse_stub_sets() : protocols::protein_interface_design::movers
• parse_task_operations() : protocols::rosetta_scripts
• parse_taskdef() : protocols::elscripts
• parse_xyz_vector() : protocols::rosetta_scripts
• part_complex() : protocols::protein_interface_design::movers
• partial_align() : protocols::hybridization
• passes_filters() : protocols::ligand_docking
• path_basename() : protocols::stepwise::legacy::modeler::rna
• pct_features_in_common() : protocols::simple_filters
• PERTURB() : protocols::loops::loop_mover
• perturb_backbone_for_test() : protocols::grafting
• phe_tyr_corrections() : protocols::make_rot_lib
• 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_loops_chainbreak() : protocols::comparative_modeling
• pick_loops_unaligned() : protocols::comparative_modeling
• pick_pivots() : protocols::hybridization
• place_atom_positions() : protocols::helical_bundle
• point_graph_dme() : protocols::simple_moves
• pointer_sorter() : protocols::fldsgn::topology
• pose1_has_most_CBs() : protocols::sic_dock
• pose_charge() : protocols::antibody
• pose_energies_to_json() : protocols::rpc
• pose_from_binary_silent_file() : protocols::checkpoint
• pose_matches_user_tag() : protocols::jobdist
• pose_to_binary_silent_file() : protocols::checkpoint
• pose_with_most_CBs() : protocols::sic_dock
• poses_from_cmd_line() : protocols::comparative_modeling
• positions_in_secstruct() : protocols::simple_filters
• possible_root() : protocols::farna
• prepare_and_write_number_of_electrostatic_interactions_of_residues_to_files() : protocols::features::strand_assembly
• prepare_silent_struct() : protocols::stepwise::monte_carlo
• prepare_WriteToDB_sandwich() : protocols::features::strand_assembly
• pretty_print_rd() : protocols::make_rot_lib
• primary_fixed_domain() : protocols::stepwise::modeler
• print_atom_info() : protocols::stepwise::modeler::rna
• print_backbone_torsions() : protocols::stepwise::legacy::modeler::rna
• print_base_state() : protocols::stepwise::modeler::rna
• print_buried_unsat_Hbonds() : protocols::ligand_docking
• print_ddgs() : protocols
• print_hbonds() : protocols::farna
• print_heavy_atoms() : protocols::stepwise::modeler::rna
• print_individual_atom_info() : protocols::stepwise::modeler::rna
• print_internal_coords() : protocols::farna
• print_interres_bond() : protocols::viewer
• print_nmer_svm_energy_data() : protocols::simple_filters
• print_node() : protocols::match::output , protocols::viewer
• print_sequence_pdb_nums() : protocols::dna
• print_sequences_pdb_nums() : protocols::dna
• print_sugar_pucker_state() : protocols::stepwise::modeler::rna
• print_torsion_info() : protocols::stepwise::modeler::rna
• print_WorkingParameters_info() : protocols::stepwise::legacy::modeler::rna
• printbpy() : protocols::sic_dock::scores
• probe_radius_for_atom_type() : protocols::match
• process_input_file() : protocols::farna
• process_last_resonances() : protocols::noesy_assign
• projperp() : protocols::sic_dock
• put_in_cutpoint() : protocols::stepwise::setup
• 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