- m -

• m_inv_gen() : core::scoring
• magnetic_anisotropy_effect() : core::scoring::rna::chemical_shift
• main_atom_tree_diff_mover() : protocols::jobdist
• main_plain_mover() : protocols::jobdist
• main_plain_pdb_mover() : protocols::jobdist
• main_watchdog() : protocols::boinc::watchdog
• mainchain_path() : core::chemical
• make_aa_bitmap_from_allowed_aas() : protocols::denovo_design::task_operations
• make_aa_bitmap_from_forbidden_aas() : protocols::denovo_design::task_operations
• make_acceptor_atom_graph() : core::chemical
• make_AIM_to_atom_num() : core::io::mmtf
• make_all_atom_information() : core::io::mmtf
• make_apolar_hydrogen_graph() : core::chemical
• make_aromatic_atom_graph() : core::chemical
• make_asymmetric_pose() : core::pose::symmetry
• make_atom_information() : core::io::mmtf
• make_atom_map() : core::pose
• make_atom_num_to_sd_map() : core::io::mmtf
• make_atr_rep_grid() : protocols::ligand_docking
• make_atr_rep_grid_without_ligand() : protocols::ligand_docking
• make_atr_rep_grid_without_ligands() : protocols::ligand_docking
• make_base_pair_aware_fold_tree() : protocols::dna
• make_base_pair_mutation() : protocols::motifs
• make_centroid() : core::chemical
• make_chain() : core::io::mmtf
• make_coarse_pose() : core::import_pose
• make_conditional_index() : core::pack::dunbrack
• make_continuous_true_regions_in_bool_vector() : protocols::enzdes::enzutil
• make_current_group() : core::io::mmtf
• make_cut_at_moving_suite() : protocols::stepwise::modeler
• make_Cx() : protocols::sic_dock
• make_dna_mutations() : protocols::motifs
• make_dna_rigid() : protocols::relax
• make_extended_coarse_pose() : core::import_pose
• make_hbBasetoAcc_unitvector() : core::scoring::hbonds
• make_heavy_atom_graph() : core::chemical
• make_heavy_atom_with_hydrogens_graph() : core::chemical
• make_heavy_atom_with_polar_hydrogens_graph() : core::chemical
• make_hotspot_foldtree() : protocols::protein_interface_design
• make_hydrogen_atom_graph() : core::chemical
• make_index() : core::pack::dunbrack
• make_lengths_str() : protocols::denovo_design::components
• make_linmem_ig() : core::pack::interaction_graph
• make_new_symmetric_PackerTask_by_intersection() : core::pack
• make_new_symmetric_PackerTask_by_requested_method() : core::pack
• make_new_symmetric_PackerTask_by_truncation() : core::pack
• make_new_symmetric_PackerTask_by_union() : core::pack
• make_old_to_new_mapping() : core::io::mmtf
• make_phosphate_nomenclature_matches_mini() : core::pose::rna
• make_polar_hydrogen_graph() : core::chemical
• make_pose_from_frags() : core::fragment
• make_pose_from_saccharide_sequence() : core::pose
• make_pose_from_sequence() : core::pose
• make_pose_from_sequence_() : core::fragment
• make_real_residue_graph() : core::chemical
• make_residue_mask_symmetric() : core::pose::symmetry
• make_rid_posenum() : core::pose , protocols::loops
• make_selection() : protocols::nonlocal
• make_sequence_combinations() : protocols::dna
• make_simple_fold_tree_from_jump_frame() : core::fragment
• make_single_mutants() : protocols::dna
• make_star_foldtree() : protocols::forge::methods
• make_strand_info_str() : protocols::denovo_design::components
• make_stub_scorefxn() : protocols::protein_interface_design::movers
• make_subdirs() : protocols::dna
• make_sure_full_model_info_is_setup() : core::pose::full_model_info
• make_sure_vdw_cached_rep_screen_info_is_setup() : protocols::scoring
• make_symmetric_fibril() : protocols::fibril
• make_symmetric_movemap() : core::pose::symmetry
• make_symmetric_PackerTask_by_truncation() : core::pack
• make_symmetric_pdb_info() : core::pose::symmetry
• make_symmetric_pose() : core::pose::symmetry
• make_symmetric_task() : core::pack
• make_variants_match() : protocols::stepwise::modeler
• makeMap() : protocols::flxbb
• mangled_name_for_VLB() : protocols::protein_interface_design::movers
• map_by_residue_subsets() : protocols::fold_from_loops::utils
• map_char_to_torsion_bin() : core::conformation
• map_constraints_from_original_pose() : core::scoring::constraints
• map_decode_from_model() : core::io::mmtf
• map_mgs() : protocols::denovo_design::components
• map_nodes() : protocols::denovo_design::components
• map_of_weighted_scores() : core::import_pose::atom_tree_diffs
• map_seq1_seq2() : core::sequence
• map_string_to_torsion_bin_string() : core::conformation
• map_to_comma_strings() : core::conformation::symmetry
• map_to_local_numbering() : protocols::stepwise::modeler
• map_torsion_bin_to_char() : core::conformation
• mapping_to_alignment() : core::sequence
• masks() : core::scoring , core::scoring::packstat::old , core::scoring::sasa
• mass() : core::pose
• mass_tracer() : protocols::ligand_docking
• match_template_and_target_sequence() : protocols::tcr
• match_up_to_rna_dna() : protocols::stepwise::modeler::align
• matcher_constraint_combination_name_mangler() : protocols::toolbox::match_enzdes_util
• matcher_constraint_name_mangler() : protocols::toolbox::match_enzdes_util
• matches_ptr() : core::scoring::power_diagram
• max() : protocols::mean_field
• max_allowed_rot_mag() : protocols::rigid
• MAX_BULGE_LENGTH() : core::import_pose
• max_interchain_sites() : protocols::scoring
• max_nstruct_index() : protocols::jd2
• max_rad() : core::scoring::packstat
• max_values_versus_cluster() : protocols::pockets
• MaxAccel() : protocols::md
• maximize_sub1_contact() : protocols::matdes
• MaxVel() : protocols::md
• MDForceFactor() : protocols::md
• mean_and_stdev() : protocols::mpi_refinement
• Medal_main() : protocols::medal
• MedalExchange_main() : protocols::medal
• mem_all_atom_rmsd_no_super() : protocols::membrane
• mem_all_atom_rmsd_with_super() : protocols::membrane
• mem_bb_rmsd_no_super() : protocols::membrane
• mem_bb_rmsd_with_super() : protocols::membrane
• MEMB_HIGHRES_WTS() : core::scoring
• membrane_axis() : protocols::membrane
• Membrane_FAEmbed_from_pose() : core::scoring
• membrane_normal_to_length_15() : protocols::membrane
• MembraneEmbed_from_pose() : core::scoring
• MembraneTopology_from_pose() : core::scoring
• merge() : protocols::forge::methods
• merge_constraints_from_cmdline() : core::scoring::constraints
• merge_constraints_from_cmdline_to_pose() : core::scoring::constraints
• merge_constraints_from_cmdline_to_scorefxn() : core::scoring::constraints
• merge_csts_to_scorefunction() : core::scoring::constraints
• merge_disjoint_vectors() : protocols::stepwise::modeler
• merge_fa_constraints_from_cmdline() : core::scoring::constraints
• merge_fa_constraints_from_cmdline_to_pose() : core::scoring::constraints
• merge_fa_constraints_from_cmdline_to_scorefxn() : core::scoring::constraints
• merge_frags() : core::fragment
• merge_in_other_pose() : protocols::stepwise::modeler
• merge_in_other_pose_by_bond() : protocols::stepwise::modeler
• merge_in_other_pose_by_jump() : protocols::stepwise::modeler
• merge_two_poses() : protocols::stepwise::modeler
• merge_two_poses_using_full_model_info() : protocols::stepwise::modeler
• merge_vectors() : protocols::stepwise::modeler
• mergesort_jobsummaries_list() : protocols::cyclic_peptide_predict
• MG_HOH_DISTANCE() : protocols::magnesium
• MG_LIGAND_DISTANCE_CUTOFF() : protocols::magnesium
• MG_V_DISTANCE() : protocols::magnesium
• min() : protocols::mean_field
• min_checkpoint_namer() : protocols::rna::movers
• min_index() : protocols::ddg
• min_log_namer() : protocols::rna::movers
• min_mod() : core::scoring::electron_density , protocols::cryst
• min_pack() : core::pack
• min_pack_optimize() : core::pack
• min_pack_place_opt_rotamers_on_pose() : core::pack
• min_pack_setup() : core::pack
• min_seg() : protocols::splice
• min_values_versus_cluster() : protocols::pockets
• minimize_all_sampled_floating_bases() : protocols::stepwise::modeler::rna::sugar
• minimize_alt_rotamer() : core::pack
• minimize_magnesium_and_hydration_shell() : protocols::magnesium
• minimize_with_constraints() : protocols::stepwise::modeler::rna
• MinimizeInterface() : protocols::protein_interface_design
• MinimizeLigand_tracer() : protocols::ligand_docking
• missing_O2prime() : core::io::pose_from_sfr
• missing_stubs_build() : core::conformation
• mk_neigh_list() : protocols::constel
• MKDIR() : protocols::sparta
• mm_bond_angle_residue_type_param_set() : core::scoring::mm
• mm_compatible_with_kic() : protocols::recces::scratch
• MM_STD_WTS() : core::scoring
• mode_to_name_map_() : core::simple_metrics::metrics
• modeler_starting_pose_data_list() : protocols::stepwise::modeler::rna::sugar
• modeler_sugar_at_five_prime() : protocols::stepwise::sampler::rna
• modeler_sugar_at_three_prime() : protocols::stepwise::sampler::rna
• modify_atom_properties_from_command_line() : core::chemical
• modify_dbase_with_compatible_backbones() : protocols::splice
• modify_ft_for_residue_insertion() : protocols::denovo_design::components
• modify_ResId_based_object() : protocols::moves
• move_apart() : protocols::docking
• move_ligand_neighbor_to_desired_position() : protocols::ligand_docking
• move_ligand_to_desired_centroid() : protocols::ligand_docking
• move_map_from_loop() : protocols::loops
• move_map_from_loops() : protocols::loops
• move_map_tag_namer() : protocols::rosetta_scripts
• move_together() : protocols::docking
• move_type_from_string() : protocols::stepwise::monte_carlo::mover
• moveable_jump() : core::pose::rna
• movemap_factory_category() : core::select::movemap
• MoveMapBuilder_tracer() : protocols::ligand_docking
• MPI_CLOSE_FILE() : protocols::jd2
• MPI_JOB_DIST_TAG() : protocols::jd2
• mpi_npes() : protocols::wum
• mpi_rank() : protocols::wum
• mpm_mangler() : protocols::rosetta_scripts
• mrb_from_name() : core::chemical
• mrb_map_from_correspondence() : core::chemical
• ms_tr() : protocols::motifs
• mstype_from_name() : protocols::moves
• mt() : protocols::motifs
• mu_torsion_oligourea() : core::id
• mu_tr() : protocols::motifs
• multiply() : protocols::mean_field
• multstubs() : protocols::sic_dock
• mutate() : protocols::ligand_docking::ga_ligand_dock
• mutate_loops_for_search() : protocols::motifs
• mutate_position() : core::pose::rna
• mutate_position_vector_for_search() : protocols::motifs
• mutate_res_if_allowed() : protocols::stepwise::modeler::rna
• mv_tr() : protocols::enzdes
• mvmul() : core::scoring
• mycomp() : protocols::simple_filters