Here is a list of all namespace members with links to the namespace documentation for each member:

- m -

• M : test::T007_TracerIO
• MAGENTA : fmt
• magnesium : basic::options::OptionKeys::magnesium , magnesium
• main() : app::pyrosetta_toolkit::modules::prettytable::prettytable , app::pyrosetta_toolkit::window_modules::ligand_ncaa_ptm_manager::ligand_ncaa_ptm_manager , app::pyrosetta_toolkit::window_modules::options_system::OptionSystemManager , arls_impl , best_ifaceE , build , BuildBindings , BuildPackagedBindings , compare_times , get_scores , make_amb_constr , make_templates , mp_ddG , ObjexxFCL , options , pdb_to_molfile
• MAIN() : PhiPsi , PlotSurfaceContactMap
• main() : predict_ddG , prune_atdiff_top5pct , PyMOLPyRosettaServer , self-test , sidechain_cst_3 , TestBindings , tools::CppParser
• main_exit_callback : utility
• main_module_header : binder
• main_window_class : app::pyrosetta_toolkit::pyrosetta_toolkit , test::G000_Main_GUI
• mainchain_h_rebuild_threshold : basic::options::OptionKeys::packing , packing
• MAJOR : setup
• make_ads_disulf() : app::surface_docking::constraints
• make_axis() : PyMOLPyRosettaServer
• MAKE_BASE_PAIR_MOVE : basic
• MAKE_BASE_STEP_MOVE : basic
• make_compound_statement() : basic::database
• make_consensus_mutations : basic::options::OptionKeys::enzdes , enzdes
• make_data() : PyMOLPyRosettaServer
• make_ensemble_cst : basic::options::OptionKeys::cluster , cluster
• make_implicitly_convertible() : exclude
• make_map() : utility::tools
• make_message() : utility::tag
• make_movie : basic::options::OptionKeys::stepwise::monte_carlo , stepwise::monte_carlo
• make_nonvirtual() : exclude
• make_pdb : basic::options::OptionKeys::holes , holes
• make_PDBLIST() : app::pyrosetta_toolkit::modules::tools::output
• make_PDBLIST_recursively() : app::pyrosetta_toolkit::modules::tools::output
• make_plane_from_three_points() : numeric::geometry
• make_points() : numeric::kdtree
• make_ptr() : fmt::internal
• make_rot_lib : basic::options::OptionKeys::make_rot_lib , make_rot_lib
• make_segtag_with_dashes() : utility
• MAKE_SURE_IS_COPYABLE : exclude
• make_sure_is_copyable() : exclude
• make_tag() : utility
• make_tag_with_dashes() : utility
• make_type() : fmt::internal
• make_vector() : utility::tools
• make_vector1() : utility::tools
• make_voids : basic::options::OptionKeys::holes , holes
• makeContactMap() : calccontacts
• makeContactPDB() : calccontacts
• makeContactProfile() : calccontacts
• makeFile() : make_templates
• makeShellProfile() : calccontacts
• makeVector() : coordlib
• MakeVector() : numeric
• manager : app::pyrosetta_toolkit::window_modules::ligand_ncaa_ptm_manager::ligand_ncaa_ptm_manager
• mangle_type_name() : binder
• mannose : test::C001_Carbohydrates_Demo01
• map_to_obj() : utility::json_spirit
• mapfile : basic::options::OptionKeys::edensity , edensity
• Mapped_obj : utility::json_spirit
• mapreso : basic::options::OptionKeys::edensity , edensity
• mArray : utility::json_spirit
• MASTER_PROCESS_NEW_STRUCTURES : basic
• match : basic::options::OptionKeys::match , basic::options::OptionKeys::mh::match , match , mh::match
• match_grouper : basic::options::OptionKeys::match , match
• match_overlap_ang : basic::options::OptionKeys::willmatch , willmatch
• match_overlap_dis : basic::options::OptionKeys::willmatch , willmatch
• match_pdb : local
• match_rt_limit : basic::options::OptionKeys::remodel , remodel
• match_segments : basic::options::OptionKeys::sewing , sewing
• matdes : basic::options::OptionKeys::matdes , matdes
• Matrix16 : numeric::kinematic_closure
• Matrix8 : numeric::kinematic_closure
• MatrixMult() : numeric::model_quality
• max() : numeric , ObjexxFCL , utility
• max_align_pos : basic::options::OptionKeys::templates , templates
• max_ang_metal : basic::options::OptionKeys::willmatch , willmatch
• max_atoms() : backrub , basic::options::OptionKeys::backrub
• max_bb_deviation : basic::options::OptionKeys::enzdes , enzdes
• max_bb_deviation_from_startstruct : basic::options::OptionKeys::enzdes , enzdes
• max_bbrms : basic::options::OptionKeys::lh , lh
• max_bessel_order : basic::options::OptionKeys::score::fiber_diffraction , score::fiber_diffraction
• max_ca_ca_dist : basic::options::OptionKeys::rigid , rigid
• max_ca_dis : basic::options::OptionKeys::mh::dump , mh::dump
• max_cb_dis : basic::options::OptionKeys::mh::score , mh::score
• max_clash_score : basic::options::OptionKeys::sewing , sewing
• max_contact_pairs : basic::options::OptionKeys::mh::score , mh::score
• max_contacting_ss : basic::options::OptionKeys::score , score
• max_cpu : basic::options::OptionKeys::boinc , boinc
• max_cst_dist : basic::options::OptionKeys::constraints , constraints
• max_cycles : basic::options::OptionKeys::loops::ccd , loops::ccd
• max_ddg_score : basic::options::OptionKeys::frags::nonlocal , frags::nonlocal
• max_depth : basic::options::OptionKeys::motifs , motifs
• max_dis_all : basic::options::OptionKeys::willmatch , willmatch
• max_dis_any : basic::options::OptionKeys::willmatch , willmatch
• max_dis_hb : basic::options::OptionKeys::willmatch , willmatch
• max_dis_hb_colinear : basic::options::OptionKeys::willmatch , willmatch
• max_dis_metal : basic::options::OptionKeys::willmatch , willmatch
• max_emperor_lib_round : basic::options::OptionKeys::lh , lh
• max_emperor_lib_size : basic::options::OptionKeys::lh , lh
• max_failures : basic::options::OptionKeys::cp , cp
• max_files_per_dir : basic::options::OptionKeys::canonical_sampling::sampling , canonical_sampling::sampling
• max_fps : basic::options::OptionKeys::boinc , boinc
• max_gap_extend : basic::options::OptionKeys::cm , cm
• max_gap_open : basic::options::OptionKeys::cm , cm
• max_grid_cache_size : basic::options::OptionKeys::qsar , qsar
• max_helix_length : basic::options::OptionKeys::sewing , sewing
• max_inner_cycles : basic::options::OptionKeys::loops , loops
• MAX_ITER_SECANT : numeric::kinematic_closure
• max_kic_build_attempts : basic::options::OptionKeys::loops , loops
• MAX_KIC_BUILD_ATTEMPTS : loops_kic , test::T650_LoopsKIC
• max_kic_perturber_samples : basic::options::OptionKeys::loops , loops
• max_lib_size : basic::options::OptionKeys::lh , lh
• max_linear_chainbreak : basic::options::OptionKeys::remodel::RemodelLoopMover , remodel::RemodelLoopMover
• max_loop_length : basic::options::OptionKeys::sewing , sewing
• max_loop_rebuild : basic::options::OptionKeys::cm , cm
• max_loophash_per_structure : basic::options::OptionKeys::lh , lh
• max_min_iter : basic::options::OptionKeys::run , run
• max_model : pyrosetta::toolbox::make_rna_rosetta_ready , toolbox::make_rna_rosetta_ready
• max_models : basic::options::OptionKeys::sewing , sewing
• max_motif_per_res : basic::options::OptionKeys::score , score
• max_nstruct : basic::options::OptionKeys::boinc , boinc
• max_nstruct_in_memory : basic::options::OptionKeys::jd2 , jd2
• max_num_strands_to_deal : basic::options::OptionKeys::strand_assembly , strand_assembly
• max_O_N_dis : basic::options::OptionKeys::strand_assembly , strand_assembly
• max_per_res : basic::options::OptionKeys::mh::dump , mh::dump
• max_poses : basic::options::OptionKeys::docking::ligand , docking::ligand
• max_radius : basic::options::OptionKeys::lh , lh
• max_rama_score_increase : basic::options::OptionKeys::loops::ccd , loops::ccd
• max_ref_lib_size : basic::options::OptionKeys::lh , lh
• max_registry_shift : basic::options::OptionKeys::cm::hybridize , cm::hybridize
• max_repeats : basic::options::OptionKeys::docking , docking
• max_res : basic::options::OptionKeys::mh::harvest , mh::harvest
• max_res_in_strand : basic::options::OptionKeys::strand_assembly , strand_assembly
• max_retry_job : basic::options::OptionKeys::run , run
• max_rms : basic::options::OptionKeys::lh , basic::options::OptionKeys::mh::dump , lh , mh::dump
• max_rms_from_native : basic::options::OptionKeys::optE , optE
• max_rmsd : basic::options::OptionKeys::mh::harvest , mh::harvest
• max_rmsd_after_relax : basic::options::OptionKeys::frags::nonlocal , frags::nonlocal
• max_rmsd_against_known_structures : basic::options::OptionKeys::mc , mc
• max_rotbump_energy : basic::options::OptionKeys::packing , packing
• max_sample_per_structure : basic::options::OptionKeys::lh , lh
• max_seqsep : basic::options::OptionKeys::mh::filter , mh::filter
• max_sheet_angle : basic::options::OptionKeys::strand_assembly , strand_assembly
• max_sheet_dis : basic::options::OptionKeys::strand_assembly , strand_assembly
• max_sheet_torsion : basic::options::OptionKeys::strand_assembly , strand_assembly
• max_shrink : basic::options::OptionKeys::templates , templates
• max_ss_num : basic::options::OptionKeys::sewing , sewing
• max_strand_gap_allowed : basic::options::OptionKeys::jumps , jumps
• max_strand_length : basic::options::OptionKeys::sewing , sewing
• max_struct : basic::options::OptionKeys::lh , lh
• max_struct_per_radius : basic::options::OptionKeys::lh , lh
• max_torsion_delta : basic::options::OptionKeys::loops::ccd , loops::ccd
• max_torsion_delta_per_move : basic::options::OptionKeys::loops::ccd , loops::ccd
• max_total_cluster : basic::options::OptionKeys::cluster , cluster
• max_tries_multiplier_for_ccd : basic::options::OptionKeys::stepwise , stepwise
• maxdist2 : basic::options::OptionKeys::mh::filter , mh::filter
• MaxExpressionCOP : numeric::expression_parser
• MaxExpressionOP : numeric::expression_parser
• MAXIT : numeric::kinematic_closure
• maxruntime : basic::options::OptionKeys::run , run
• maxruntime_bufferfactor : basic::options::OptionKeys::run , run
• maxsub() : numeric::model_quality
• may_add_already_added_model : basic::options::OptionKeys::sewing , sewing
• mb_exclude() : exclude
• mc : basic::options::OptionKeys::mc , demo::D060_Folding , loops , loops_kic , mc , test::T400_Refinement , test::T650_LoopsKIC , test::T860_SubClassing_EnergyMethods , test::Workshop5test
• MC_ACCEPT : basic
• mc_kt() : backrub , basic::options::OptionKeys::backrub , basic::options::OptionKeys::canonical_sampling::sampling , canonical_sampling::sampling
• mc_kt_high : basic::options::OptionKeys::enzdes , enzdes
• mc_kt_low : basic::options::OptionKeys::enzdes , enzdes
• mcm_cycles : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• mConfig : utility::json_spirit
• md_schfile : basic::options::OptionKeys::in::file , in::file
• mean : basic::options::OptionKeys::ddg , ddg , numeric , numeric::statistics
• measure_sequence_recovery : basic::options::OptionKeys::optE::rescore , optE::rescore
• median() : numeric
• mem_tr : basic
• Membed_init : basic::options::OptionKeys::membrane , membrane
• membrane() : abinitio , basic::options::OptionKeys::abinitio , basic::options::OptionKeys::in , basic::options::OptionKeys::membrane , basic::options::OptionKeys::ProQ , in , membrane , ProQ
• membrane_axis : basic::options::OptionKeys::edensity , edensity
• membrane_center : basic::options::OptionKeys::membrane , membrane
• membrane_normal : basic::options::OptionKeys::membrane , membrane
• membrane_pdb : basic::options::OptionKeys::out , out
• membrane_pdb_thickness : basic::options::OptionKeys::out , out
• membrane_rsd : basic::options::OptionKeys::mp::setup , mp::setup
• memory_limit : basic::options::OptionKeys::wum , wum
• memory_test_cycles : basic::options::OptionKeys::run , run
• MemoryWriter : fmt
• Menv_penalties : basic::options::OptionKeys::membrane , membrane
• merge_motifs : basic::options::OptionKeys::mh , mh
• merge_motifs_one_per_bin : basic::options::OptionKeys::mh , mh
• merge_scores : basic::options::OptionKeys::mh , mh
• merge_similar_motifs : basic::options::OptionKeys::mh , mh
• MessageListenerCOP : basic::mpi
• MessageListenerOP : basic::mpi
• metal_dist_cutoff : basic::options::OptionKeys::bunsat_calc2 , bunsat_calc2
• metals_angle_constraint_multiplier : basic::options::OptionKeys::in , in
• metals_detection_LJ_multiplier : basic::options::OptionKeys::in , in
• metals_distance_constraint_multiplier : basic::options::OptionKeys::in , in
• MetaMaxExpressionCOP : numeric::expression_parser
• MetaMaxExpressionOP : numeric::expression_parser
• MetaMinExpressionCOP : numeric::expression_parser
• MetaMinExpressionOP : numeric::expression_parser
• method : basic::options::OptionKeys::sasa , sasa
• methylate : basic::options::OptionKeys::dna::specificity , dna::specificity
• MetricValueBaseCOP : basic
• MetricValueBaseOP : basic
• mFork() : BuildBindings
• mfork() : self-test , TestBindings
• mg_res : basic::options::OptionKeys::magnesium , magnesium
• mh : basic::options::OptionKeys::mh , mh
• Mhbond_depth : basic::options::OptionKeys::membrane , membrane
• middle_offset : loops_kic , test::T650_LoopsKIC
• midpoint() : numeric
• min : basic::options::OptionKeys::ddg , basic::options::OptionKeys::rot_anl , ddg , numeric , ObjexxFCL , rot_anl , utility
• min_align_pos : basic::options::OptionKeys::templates , templates
• min_all_jumps : basic::options::OptionKeys::enzdes , enzdes
• min_atoms() : backrub , basic::options::OptionKeys::backrub
• min_bbrms : basic::options::OptionKeys::lh , lh
• min_bin_val : basic::options::OptionKeys::mh::harvest , mh::harvest
• min_breakout_fast_loops : basic::options::OptionKeys::fast_loops , fast_loops
• min_breakout_good_loops : basic::options::OptionKeys::fast_loops , fast_loops
• min_cacb_deviation : basic::options::OptionKeys::enzdes , enzdes
• min_cav_ball_radius : basic::options::OptionKeys::packstat , packstat
• min_cluster_overlap : basic::options::OptionKeys::packstat , packstat
• min_contact_pairs : basic::options::OptionKeys::mh::score , mh::score
• min_contacts_per_res : basic::options::OptionKeys::frags::nonlocal , frags::nonlocal
• min_cover_fraction : basic::options::OptionKeys::mh::score , mh::score
• min_cst : basic::options::OptionKeys::ddg , ddg
• min_cst_weights : basic::options::OptionKeys::ddg , ddg
• min_cycles : basic::options::OptionKeys::relax::range , relax::range
• min_decoy_rms_to_native : basic::options::OptionKeys::optE , optE
• min_dis_hb : basic::options::OptionKeys::willmatch , willmatch
• min_fast_loops : basic::options::OptionKeys::fast_loops , fast_loops
• min_final_hbonds : basic::options::OptionKeys::cyclic_peptide , cyclic_peptide
• min_frag_size : basic::options::OptionKeys::templates , templates
• min_gap_extend : basic::options::OptionKeys::cm , cm
• min_gap_open : basic::options::OptionKeys::cm , cm
• min_genkic_hbonds : basic::options::OptionKeys::cyclic_peptide , cyclic_peptide
• min_good_loops : basic::options::OptionKeys::fast_loops , fast_loops
• min_hash_score : basic::options::OptionKeys::sewing , sewing
• min_helix_length : basic::options::OptionKeys::sewing , sewing
• min_lh_fragments : basic::options::OptionKeys::sewing , sewing
• min_loop_length : basic::options::OptionKeys::sewing , sewing
• min_loop_size : basic::options::OptionKeys::cm , cm
• min_max_start_seq_sep : basic::options::OptionKeys::resample , resample
• min_motif_score : basic::options::OptionKeys::sewing , sewing
• min_mover : app::delta_score_per_mutation , test::Workshop5test , test::Workshop7test
• min_nr_large_frags : basic::options::OptionKeys::templates , templates
• min_nr_small_frags : basic::options::OptionKeys::templates , templates
• min_num_ring : basic::options::OptionKeys::gen_pharmacophore , gen_pharmacophore
• min_num_strands_to_deal : basic::options::OptionKeys::strand_assembly , strand_assembly
• min_O_N_dis : basic::options::OptionKeys::strand_assembly , strand_assembly
• min_pack : basic::options::OptionKeys
• min_padding : basic::options::OptionKeys::templates , templates
• min_rb : basic::options::OptionKeys::matdes::mutalyze , matdes::mutalyze
• min_receptor_bb : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• min_res_in_strand : basic::options::OptionKeys::strand_assembly , strand_assembly
• min_rms : basic::options::OptionKeys::docking::ligand , basic::options::OptionKeys::lh , docking::ligand , lh
• min_score : basic::options::OptionKeys::score::saxs , score::saxs
• min_score_score : basic::options::OptionKeys::score , score
• min_seq_sep : basic::options::OptionKeys::frags::contacts , frags::contacts
• min_seqsep : basic::options::OptionKeys::james , james
• min_sequence_separation : basic::options::OptionKeys::pose_metrics , pose_metrics
• min_sheet_angle : basic::options::OptionKeys::strand_assembly , strand_assembly
• min_sheet_dis : basic::options::OptionKeys::strand_assembly , strand_assembly
• min_sheet_torsion : basic::options::OptionKeys::strand_assembly , strand_assembly
• min_shortest_dis_sidechain_inter_sheet : basic::options::OptionKeys::strand_assembly , strand_assembly
• min_strand_length : basic::options::OptionKeys::sewing , sewing
• min_surface_accessibility : basic::options::OptionKeys::packstat , packstat
• min_tolerance : basic::options::OptionKeys::relax , basic::options::OptionKeys::run , basic::options::OptionKeys::stepwise , relax , run , stepwise
• min_type : basic::options::OptionKeys::dna::specificity , basic::options::OptionKeys::relax , basic::options::OptionKeys::run , basic::options::OptionKeys::stepwise , dna::specificity , loops_kic , relax , run , stepwise , test::T650_LoopsKIC
• min_unaligned_len() : abinitio::star , basic::options::OptionKeys::abinitio::star
• min_with_cst : basic::options::OptionKeys::ddg , ddg
• minbb : basic::options::OptionKeys::smhybrid , smhybrid
• mindist2 : basic::options::OptionKeys::mh::filter , mh::filter
• MinExpressionCOP : numeric::expression_parser
• MinExpressionOP : numeric::expression_parser
• mini : basic::options::OptionKeys::relax , relax
• minimization_patch : basic::options::OptionKeys::ddg , ddg
• minimization_scorefunction : basic::options::OptionKeys::ddg , ddg
• minimization_threshold : basic::options::OptionKeys::docking , docking
• minimize : basic::options::OptionKeys::dna::design , basic::options::OptionKeys::holes , basic::options::OptionKeys::magnesium , basic::options::OptionKeys::motifs , basic::options::OptionKeys::rna::farna::minimize , dna::design , holes , magnesium , motifs , rna::farna::minimize
• minimize_after_nmsearch : basic::options::OptionKeys::lh , lh
• minimize_all_ligand_torsions : basic::options::OptionKeys::enzdes , enzdes
• minimize_and_score_native_pose : basic::options::OptionKeys::stepwise::rna , stepwise::rna
• minimize_and_score_sugar : basic::options::OptionKeys::stepwise::rna , stepwise::rna
• minimize_backbone : basic::options::OptionKeys::docking::ligand , docking::ligand
• minimize_bond_angles : basic::options::OptionKeys::relax , relax
• minimize_bond_lengths : basic::options::OptionKeys::relax , relax
• minimize_bondangle_subset : basic::options::OptionKeys::relax , relax
• minimize_bondlength_subset : basic::options::OptionKeys::relax , relax
• minimize_bps : basic::options::OptionKeys::rna::farna::minimize , rna::farna::minimize
• minimize_dna : basic::options::OptionKeys::motifs , motifs
• minimize_during_scoring : basic::options::OptionKeys::magnesium , magnesium
• minimize_ligand : basic::options::OptionKeys::docking::ligand , docking::ligand
• minimize_ligand_torsions : basic::options::OptionKeys::enzdes , enzdes
• minimize_max_iter : basic::options::OptionKeys::loops , loops
• minimize_mg_coord_constraint_distance : basic::options::OptionKeys::magnesium , magnesium
• minimize_movemap() : backrub , basic::options::OptionKeys::backrub
• minimize_res : basic::options::OptionKeys::in::file , basic::options::OptionKeys::stepwise::rna , in::file , stepwise::rna
• minimize_rna : basic::options::OptionKeys::rna::farna , rna::farna
• minimize_rounds : basic::options::OptionKeys::rna::farna::minimize , rna::farna::minimize
• minimize_sidechains : basic::options::OptionKeys , core::options::OptionKeys
• minimize_single_res_frequency : basic::options::OptionKeys::stepwise::monte_carlo , stepwise::monte_carlo
• minimize_tolerance : basic::options::OptionKeys::dna::specificity , dna::specificity
• minimize_waters : basic::options::OptionKeys::stepwise , stepwise
• minimizer_rename_tag : basic::options::OptionKeys::stepwise::rna , stepwise::rna
• minimizer_score_fxn : basic::options::OptionKeys::cp , cp
• minimizer_use_coordinate_constraints : basic::options::OptionKeys::rna::farna::minimize , rna::farna::minimize
• minirelax_repeats : basic::options::OptionKeys::relax , relax
• minirelax_sdev : basic::options::OptionKeys::relax , relax
• minmover : test::T400_Refinement , test::T850_SubClassing
• MINMOVER_APPLY : basic
• MINOR : setup
• minpack_disable_bumpcheck : basic::options::OptionKeys::packing , packing
• minpack_inner_iteration_scale : basic::options::OptionKeys::packing , packing
• minpack_temp_schedule : basic::options::OptionKeys::packing , packing
• MINUS_FLAG : fmt
• missing_density_to_jump : basic::options::OptionKeys::in , in
• missing_res : basic::options::OptionKeys::stepwise::rna , stepwise::rna
• missing_res2 : basic::options::OptionKeys::stepwise::rna , stepwise::rna
• mistakes : basic::options::OptionKeys::mistakes , mistakes
• mm : app::delta_score_per_mutation , loops_kic , test::G200_Module_Region , test::T150_PyMOL_Integration , test::T650_LoopsKIC
• mm4060 : test::Workshop5test
• mm_bend_weight() : backrub , basic::options::OptionKeys::backrub
• mm_loop_file : basic::options::OptionKeys::loops , loops
• mObject : utility::json_spirit
• mod() : numeric , ObjexxFCL
• mode : basic::options::OptionKeys::dna::specificity , basic::options::OptionKeys::inout::dbms , basic::options::OptionKeys::sewing , contacts , dna::specificity , inout::dbms , sewing
• model_B : basic::options::OptionKeys::patterson , patterson
• model_file_name : basic::options::OptionKeys::sewing , sewing
• model_h3() : antibody , basic::options::OptionKeys::antibody
• model_should_have_at_least_1_E : basic::options::OptionKeys::sewing , sewing
• model_should_have_at_least_1_E_at_terminal_segment : basic::options::OptionKeys::sewing , sewing
• model_should_have_at_least_1_H : basic::options::OptionKeys::sewing , sewing
• model_should_have_this_num_of_ss : basic::options::OptionKeys::sewing , sewing
• modelID : app::pyrosetta_toolkit::modules::SQLPDB
• models_to_dump : basic::options::OptionKeys::sewing , sewing
• modifiedres : clean_pdb_keep_ligand
• modp() : numeric::kinematic_closure
• modres : amino_acids
• modrf() : numeric::kinematic_closure
• module_function_suffix : binder
• module_header : binder
• modulo() : numeric , ObjexxFCL
• mol : assign_charges
• molfile2params_quick() : pyrosetta::toolbox::load_ligand , toolbox::load_ligand
• monolith_rosetta_library_name : BuildBindings
• monte_carlo : basic::options::OptionKeys::magnesium , basic::options::OptionKeys::stepwise::monte_carlo , magnesium , stepwise::monte_carlo
• montecarlo : basic::options::OptionKeys::magnesium::montecarlo
• MonteCarlo : basic::options::OptionKeys::MonteCarlo
• montecarlo() : magnesium::montecarlo
• MonteCarlo() : MonteCarlo
• motif_begin : basic::options::OptionKeys::dna::specificity , dna::specificity
• motif_build_defs : basic::options::OptionKeys::motifs , motifs
• motif_build_positions : basic::options::OptionKeys::motifs , motifs
• motif_filename : basic::options::OptionKeys::motifs , motifs
• motif_flexible_loop_file : basic::options::OptionKeys::motifs , motifs
• motif_ignore_symmmetry : basic::options::OptionKeys::score , score
• motif_match_radius : basic::options::OptionKeys::mh , mh
• motif_mode : basic::options::OptionKeys::full_model , full_model
• motif_out_file : basic::options::OptionKeys::mh , mh
• motif_output_directory : basic::options::OptionKeys::motifs , motifs
• motif_residues : basic::options::OptionKeys::score , score
• motif_size : basic::options::OptionKeys::dna::specificity , dna::specificity
• motif_type : basic::options::OptionKeys::mh::filter , mh::filter
• motifs : basic::options::OptionKeys::mh::path , basic::options::OptionKeys::motifs , mh::path , motifs
• motifs_BB_BB : basic::options::OptionKeys::mh::path , mh::path
• motifs_BB_PH : basic::options::OptionKeys::mh::path , mh::path
• motifs_BB_PO : basic::options::OptionKeys::mh::path , mh::path
• motifs_PH_PO : basic::options::OptionKeys::mh::path , mh::path
• motifs_SC_BB : basic::options::OptionKeys::mh::path , mh::path
• motifs_SC_SC : basic::options::OptionKeys::mh::path , mh::path
• move : basic::options::OptionKeys::stepwise , stepwise
• move_anchor_frequency : basic::options::OptionKeys::fold_and_dock , fold_and_dock
• move_anchor_points : basic::options::OptionKeys::fold_and_dock , fold_and_dock
• move_first_rigid_body : basic::options::OptionKeys::rna::farna , rna::farna
• move_jumps_between_chains : basic::options::OptionKeys::stepwise::protein , stepwise::protein
• move_ligand : basic::options::OptionKeys::remodel , remodel
• movemap : basic::options::OptionKeys::in::file , demo::D040_Movemap , in::file , loops , loops_kic , test::T400_Refinement , test::T650_LoopsKIC , test::Workshop4test , test::Workshop5test , test::Workshop7test , test::Workshop8test
• movemap_from_blueprint : basic::options::OptionKeys::flxbb , flxbb
• mover_3mer : loops , test::T400_Refinement , test::Workshop4test
• moving_jump : basic::options::OptionKeys::dna::specificity , dna::specificity
• mp : basic::options::OptionKeys::mp , mp
• mpi_batch_relax_absolute_max : basic::options::OptionKeys::lh , lh
• mpi_batch_relax_chunks : basic::options::OptionKeys::lh , lh
• MPI_batchsize_by_level : basic::options::OptionKeys::cyclic_peptide , cyclic_peptide
• MPI_bcast : basic::options::OptionKeys::canonical_sampling::probabilities , canonical_sampling::probabilities
• MPI_choose_highest : basic::options::OptionKeys::cyclic_peptide , cyclic_peptide
• MPI_FAIL : utility::io::mpi_stream
• mpi_fast_nonblocking_output : basic::options::OptionKeys::jd2 , jd2
• mpi_feedback : basic::options::OptionKeys::lh , lh
• MPI_FILE_BUF : basic
• mpi_file_buf_job_distributor : basic::options::OptionKeys::jd2 , jd2
• MPI_FILE_STATUS : utility::io::mpi_stream
• mpi_filebuf_jobdistributor : basic::options::OptionKeys::jd2 , jd2
• MPI_GATHER_BARRIER : basic
• mpi_init() : src
• MPI_JD2_WAITS_FOR_ARCHIVE : basic
• mpi_loophash_scan_type : basic::options::OptionKeys::lh , lh
• mpi_loophash_split_size : basic::options::OptionKeys::lh , lh
• MPI_MASTER_BCAST_COORDS : basic
• MPI_MASTER_BCAST_NEW_COMM_SIZE : basic
• MPI_MASTER_BCAST_NEW_POOL_RANKS : basic
• MPI_MASTER_BCAST_NUM_STRUCTURES_TO_ADD : basic
• MPI_MASTER_BCAST_WINNING_RANKS : basic
• MPI_MASTER_BCAST_WINNING_STRUCTURES : basic
• mpi_master_cpu_weight : basic::options::OptionKeys::lh , lh
• mpi_master_save_score_only : basic::options::OptionKeys::lh , lh
• mpi_master_schfile : basic::options::OptionKeys::lh , lh
• mpi_metropolis_temp : basic::options::OptionKeys::lh , lh
• MPI_NOTIFY_ARCHIVE : basic
• mpi_nowait_for_remaining_jobs : basic::options::OptionKeys::jd2 , jd2
• mpi_nprocs() : utility
• mpi_ostream : utility::io::mpi_stream
• mpi_outbound_wu_buffer_size : basic::options::OptionKeys::lh , lh
• MPI_output_fraction : basic::options::OptionKeys::cyclic_peptide , cyclic_peptide
• mpi_packmin_init : basic::options::OptionKeys::lh , lh
• MPI_POOL_MASTER_THINKS : basic
• MPI_POOL_SLAVE_THINKS : basic
• MPI_processes_by_level : basic::options::OptionKeys::cyclic_peptide , cyclic_peptide
• mpi_rank() : utility
• mpi_rank_dir : basic::options::OptionKeys::out::path , out::path
• mpi_read_structure_for_emperor : basic::options::OptionKeys::lh , lh
• mpi_resume : basic::options::OptionKeys::lh , lh
• mpi_safe_std_err() : utility::options
• mpi_save_state_interval : basic::options::OptionKeys::lh , lh
• MPI_SEND_ACCEPTED : basic
• MPI_SEND_UPDATE : basic
• MPI_SLAVE_REPORT_NEW_COORDS : basic
• MPI_SLAVE_REPORT_SIZES : basic
• MPI_sort_by : basic::options::OptionKeys::cyclic_peptide , cyclic_peptide
• MPI_stop_after_time : basic::options::OptionKeys::cyclic_peptide , cyclic_peptide
• MPI_STREAM_CLOSE : utility::io::mpi_stream
• MPI_STREAM_FILE_EXIST : utility::io::mpi_stream
• MPI_STREAM_FLUSH : utility::io::mpi_stream
• MPI_STREAM_MSG : utility::io::mpi_stream
• MPI_STREAM_OPEN : utility::io::mpi_stream
• MPI_STREAM_OPEN_APPEND : utility::io::mpi_stream
• MPI_STREAM_SEND : utility::io::mpi_stream
• MPI_STREAM_TAG : utility::io::mpi_stream
• MPI_SUCCESS_APPEND : utility::io::mpi_stream
• MPI_SUCCESS_NEW : utility::io::mpi_stream
• MPI_SYNC_POOL_DIFF : basic
• MPI_sync_pools : basic::options::OptionKeys::canonical_sampling::probabilities , canonical_sampling::probabilities
• mpi_tags : basic::mpi
• mpi_timeout_factor : basic::options::OptionKeys::jd2 , jd2
• mpi_tracer_to_file : basic::options::OptionKeys::out , out
• mpi_weight_minimization : basic::options::OptionKeys::optE , optE
• mpi_work_partition_job_distributor : basic::options::OptionKeys::jd2 , jd2
• mpi_wostream : utility::io::mpi_stream
• MPIBARRIER : basic
• MPIBARRIER_BEGIN : basic
• MPIBARRIER_END : basic
• MPICANONICALSAMPLING : basic
• MPICOMMCREATION : basic
• MPIH_ADD_FIRST_STRUCTURE : basic
• MPIH_EVAL_AGAINST_NBR : basic
• MPIH_EVAL_CHECK_PROGRESS : basic
• MPIH_EVAL_COMMUNICATE_NEW : basic
• MPIH_PREPARE_WRITE_STRUCTURES : basic
• MPIH_UPDATE_EVAL : basic
• MPIH_WRITE_STRUCT : basic
• MPIJobDistributor() : src
• MPIPOOLCOMMUNICATION : basic
• ms : basic::options::OptionKeys::ms , ms
• msd_job_dist : basic::options::OptionKeys::run , run
• msd_randomize : basic::options::OptionKeys::run , run
• msg_name() : utility
• MSWORD_FRIENDLY : app::pyrosetta_toolkit::modules::prettytable::prettytable
• mtzfile : basic::options::OptionKeys::cryst , cryst
• multi_cool_annealer : basic::options::OptionKeys::packing , packing
• multi_objective_functions : basic::options::OptionKeys::lh , lh
• multibody : basic::options::OptionKeys::docking , docking
• multifastrelax() : abinitio , basic::options::OptionKeys::abinitio
• multiple_origin : basic::options::OptionKeys::fingerprint , fingerprint
• multiple_processes_writing_to_one_directory : basic::options::OptionKeys::run , run
• multiplier : basic::options::OptionKeys::mh::harvest , mh::harvest
• multiply() : numeric
• multiply_matrix() : PyMOLPyRosettaServer
• MULTIPLY_SYMBOL : numeric::expression_parser
• MultiplyExpressionCOP : numeric::expression_parser
• MultiplyExpressionOP : numeric::expression_parser
• MULTIPOLE_ENERGIES : basic
• MULTIPOLE_SETUP : basic
• multMatrix() : numeric::kinematic_closure
• multTransMatrix() : numeric::kinematic_closure
• murphp : basic::options::OptionKeys::murphp , murphp
• mut_file : basic::options::OptionKeys::ddg , ddg
• mut_only : basic::options::OptionKeys::ddg , ddg
• mutalyze : basic::options::OptionKeys::matdes::mutalyze , matdes::mutalyze
• mutant_aa : demo::D090_Ala_scan
• mutant_file : basic::options::OptionKeys::mp::mutate_relax , mp::mutate_relax
• mutant_pose : app::delta_score_per_mutation
• mutants_list : protocols::pmut_scan
• mutate_framework_for_cluster() : antibody::design , basic::options::OptionKeys::antibody::design
• mutate_rate : basic::options::OptionKeys::ms , ms
• mutate_relax : basic::options::OptionKeys::mp::mutate_relax , mp::mutate_relax
• mutate_residue() : demo::D090_Ala_scan , mp_ddG , predict_ddG , pyrosetta::toolbox , toolbox
• mutate_same_name3 : basic::options::OptionKeys::docking::ligand , docking::ligand
• mutation : basic::options::OptionKeys::mp::mutate_relax , mp::mutate_relax
• mute : basic::options::OptionKeys::out , out
• mutRM() : app::pyrosetta_toolkit::modules::help
• mutSA() : app::pyrosetta_toolkit::modules::help
• mutSP() : app::pyrosetta_toolkit::modules::help
• mValue : utility::json_spirit
• mWait() : BuildBindings
• my_loop : loops , loops_kic , test::T650_LoopsKIC
• my_loops : loops , loops_kic , test::T650_LoopsKIC