- p -

• pack_missing_sidechains() : core::pack
• pack_rotamers() : core::pack
• pack_rotamers_loop() : core::pack
• pack_rotamers_run() : core::pack
• pack_rotamers_setup() : core::pack
• pack_scorefxn_pose_handshake() : core::pack
• pad_dash() : core::kinematics
• pad_dash_left() : core::kinematics
• pad_dash_right() : core::kinematics
• pair_sort_citeria() : protocols::swa::rna
• parallel_base_test() : protocols::motifs
• parse_adduct_string() : core::chemical
• parse_atom_type_data() : core::chemical::sdf
• parse_bond_type_data() : core::chemical::sdf
• parse_filter() : protocols::rosetta_scripts
• parse_movemap() : protocols::rosetta_scripts
• parse_movemapdef() : protocols::elscripts
• parse_mover() : protocols::rosetta_scripts
• parse_NMR_name() : core::scoring::constraints
• parse_NMR_name_old() : core::scoring::constraints
• parse_resfile() : core::pack::task
• parse_resfile_string() : core::pack::task
• parse_resfile_string_with_no_lockdown() : protocols::forge::methods
• parse_residues() : protocols::seeded_abinitio
• parse_resnum() : core::pose
• parse_score_function() : protocols::rosetta_scripts
• parse_scoredef() : protocols::elscripts
• parse_seeds() : protocols::seeded_abinitio
• parse_selection_block() : core::pose
• 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
• partition_by_symm_jumps() : core::pose::symmetry
• partition_pose_by_jump() : core::pose
• pass_metropolis() : core::pack
• passes_filters() : protocols::ligand_docking
• patch_linker() : core::chemical
• patch_operation_from_patch_file_line() : core::chemical
• path_basename() : protocols::swa::rna
• pct_features_in_common() : protocols::simple_filters
• pdbslice() : protocols::swa
• peptoid_cis_hack() : protocols::MakeRotLib
• peptoid_trans_hack() : protocols::MakeRotLib
• phe_tyr_corrections() : protocols::MakeRotLib
• phi() : protocols::swa::protein , protocols::swa
• phi_torsion() : core::id
• phosphate_base_phosphate_rmsd() : protocols::swa::rna
• phosphate_base_phosphate_square_deviation() : protocols::swa::rna
• phosphate_square_deviation() : protocols::swa::rna
• PHOSPHORYLATION() : core::chemical
• 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
• point_graph_dme() : protocols::simple_moves
• pointer_sorter() : protocols::fldsgn::topology
• pos_mod() : core::scoring::electron_density , core::scoring::electron_density_atomwise
• pose1_has_most_CBs() : protocols::sic_dock
• pose_from_atom_tree_diff() : core::import_pose::atom_tree_diffs
• pose_from_binary_silent_file() : protocols::checkpoint
• pose_from_pdb() : core::import_pose
• pose_from_pdb_stream() : core::import_pose
• pose_from_pdbstring() : core::import_pose
• pose_from_pose() : core::io::pdb
• pose_from_saccharide_sequence() : core::pose
• pose_matches_user_tag() : protocols::jobdist
• pose_max_nbr_radius() : core::pose
• pose_to_binary_silent_file() : protocols::checkpoint
• pose_to_pack_data() : core::scoring::packstat
• pose_with_most_CBs() : protocols::sic_dock
• poseOPs_from_pdbs() : core::import_pose
• poses_from_cmd_line() : protocols::comparative_modeling
• poses_from_pdbs() : core::import_pose
• possible_root() : protocols::swa::rna , protocols::rna
• possibly_canonical() : core::scoring::rna
• possibly_canonical_strict() : core::scoring::rna
• PRECISION() : protocols::dna
• precision() : core::io::raw_data
• PRECISION() : protocols::motifs
• prepare_scratch_residue() : core::scoring::rna
• pretty_print_rd() : protocols::MakeRotLib
• print_atom() : core::conformation
• print_atom_info() : protocols::swa::rna
• print_backbone_torsions() : protocols::swa::rna
• print_base_state() : protocols::swa::rna
• print_buried_unsat_Hbonds() : protocols::ligand_docking
• print_chemical_shift_data() : core::scoring::rna::chemical_shift
• print_d() : core::io::pdb
• print_ddgs() : protocols
• Print_heavy_atoms() : protocols::swa::rna
• print_i() : core::io::pdb
• print_individual_atom_info() : protocols::swa::rna
• print_internal_coords() : protocols::rna
• print_interres_bond() : protocols::viewer
• print_JobParameters_info() : protocols::swa::rna
• print_node() : core::conformation , protocols::match::output , protocols::viewer , protocols::match::output , core::conformation
• print_ribose_pucker_state() : protocols::swa::rna
• print_sequence_pdb_nums() : protocols::dna
• print_sequences_pdb_nums() : protocols::dna
• Print_torsion_info() : protocols::swa::rna
• probe_radius_for_atom_type() : protocols::match
• process_last_resonances() : protocols::noesy_assign
• process_residue_request() : core::conformation::symmetry
• promote_sameresidue_child_of_jump_atom() : core::conformation
• PROTONATED() : core::chemical
• prune_1pass() : core::scoring::packstat
• prune_cavity_balls() : core::scoring::packstat
• prune_hidden_cavity_balls() : core::scoring::packstat
• psc_compare() : core::pack::dunbrack
• psi() : protocols::swa , protocols::swa::protein
• psi_torsion() : core::id
• pss_tr() : core::io::silent
• put_line() : core::scoring::electron_density::SplineInterp
• PyReturnValuePolicyTest_DummyClassAP() : protocols::toolbox
• PyReturnValuePolicyTest_DummyClassCAP() : protocols::toolbox
• PyReturnValuePolicyTest_DummyClassCOP() : protocols::toolbox
• PyReturnValuePolicyTest_DummyClassOP() : protocols::toolbox
• PyReturnValuePolicyTest_PoseAP() : protocols::toolbox
• PyReturnValuePolicyTest_PoseCAP() : protocols::toolbox
• PyReturnValuePolicyTest_PoseCOP() : protocols::toolbox
• PyReturnValuePolicyTest_PoseOP() : protocols::toolbox
• PyReturnValuePolicyTest_ScoreFunctionCOP() : protocols::toolbox
• PyReturnValuePolicyTest_ScoreFunctionCOP2() : protocols::toolbox
• PyReturnValuePolicyTest_ScoreFunctionOP() : protocols::toolbox
• PyReturnValuePolicyTest_SF_ReplicaAP() : protocols::toolbox
• PyReturnValuePolicyTest_SF_ReplicaCAP() : protocols::toolbox
• PyReturnValuePolicyTest_SF_ReplicaCOP() : protocols::toolbox
• PyReturnValuePolicyTest_SF_ReplicaOP() : protocols::toolbox