- m -

• M : test::T007_TracerIO
• magnesium : basic::options::OptionKeys::magnesium
• main : app::pyrosetta_toolkit::window_modules::ligand_ncaa_ptm_manager::ligand_ncaa_ptm_manager , app::pyrosetta_toolkit::window_modules::options_system::OptionSystemManager
• 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
• MAJOR : setup
• make_consensus_mutations : basic::options::OptionKeys::enzdes
• make_ensemble_cst : basic::options::OptionKeys::cluster
• make_movie : basic::options::OptionKeys::stepwise::monte_carlo
• make_pdb : basic::options::OptionKeys::holes
• make_rot_lib : basic::options::OptionKeys::make_rot_lib
• MAKE_SURE_IS_COPYABLE : exclude
• make_voids : basic::options::OptionKeys::holes
• manager : app::pyrosetta_toolkit::window_modules::ligand_ncaa_ptm_manager::ligand_ncaa_ptm_manager
• mannose : test::C001_Carbohydrates_Demo01
• mapfile : basic::options::OptionKeys::edensity
• mapreso : basic::options::OptionKeys::edensity
• match : basic::options::OptionKeys::match , basic::options::OptionKeys::mh::match
• match_grouper : basic::options::OptionKeys::match
• match_overlap_ang : basic::options::OptionKeys::willmatch
• match_overlap_dis : basic::options::OptionKeys::willmatch
• match_pdb : local
• match_rt_limit : basic::options::OptionKeys::remodel
• match_segments : basic::options::OptionKeys::sewing
• matdes : basic::options::OptionKeys::matdes
• max_align_pos : basic::options::OptionKeys::templates
• max_ang_metal : basic::options::OptionKeys::willmatch
• max_atoms : basic::options::OptionKeys::backrub
• max_bb_deviation : basic::options::OptionKeys::enzdes
• max_bb_deviation_from_startstruct : basic::options::OptionKeys::enzdes
• max_bbrms : basic::options::OptionKeys::lh
• max_bessel_order : basic::options::OptionKeys::score::fiber_diffraction
• max_ca_ca_dist : basic::options::OptionKeys::rigid
• max_ca_dis : basic::options::OptionKeys::mh::dump
• max_cb_dis : basic::options::OptionKeys::mh::score
• max_clash_score : basic::options::OptionKeys::sewing
• max_contact_pairs : basic::options::OptionKeys::mh::score
• max_contacting_ss : basic::options::OptionKeys::score
• max_cpu : basic::options::OptionKeys::boinc
• max_cst_dist : basic::options::OptionKeys::constraints
• max_cycles : basic::options::OptionKeys::loops::ccd
• max_ddg_score : basic::options::OptionKeys::frags::nonlocal
• max_depth : basic::options::OptionKeys::motifs
• max_dis_all : basic::options::OptionKeys::willmatch
• max_dis_any : basic::options::OptionKeys::willmatch
• max_dis_hb : basic::options::OptionKeys::willmatch
• max_dis_hb_colinear : basic::options::OptionKeys::willmatch
• max_dis_metal : basic::options::OptionKeys::willmatch
• max_emperor_lib_round : basic::options::OptionKeys::lh
• max_emperor_lib_size : basic::options::OptionKeys::lh
• max_failures : basic::options::OptionKeys::cp
• max_files_per_dir : basic::options::OptionKeys::canonical_sampling::sampling
• max_fps : basic::options::OptionKeys::boinc
• max_gap_extend : basic::options::OptionKeys::cm
• max_gap_open : basic::options::OptionKeys::cm
• max_grid_cache_size : basic::options::OptionKeys::qsar
• max_helix_length : basic::options::OptionKeys::sewing
• max_inner_cycles : basic::options::OptionKeys::loops
• MAX_ITER_SECANT : numeric::kinematic_closure
• max_kic_build_attempts : basic::options::OptionKeys::loops
• MAX_KIC_BUILD_ATTEMPTS : loops_kic , test::T650_LoopsKIC
• max_kic_perturber_samples : basic::options::OptionKeys::loops
• max_lib_size : basic::options::OptionKeys::lh
• max_linear_chainbreak : basic::options::OptionKeys::remodel::RemodelLoopMover
• max_loop_length : basic::options::OptionKeys::sewing
• max_loop_rebuild : basic::options::OptionKeys::cm
• max_loophash_per_structure : basic::options::OptionKeys::lh
• max_min_iter : basic::options::OptionKeys::run
• max_model : pyrosetta::toolbox::make_rna_rosetta_ready , toolbox::make_rna_rosetta_ready
• max_models : basic::options::OptionKeys::sewing
• max_motif_per_res : basic::options::OptionKeys::score
• max_nstruct : basic::options::OptionKeys::boinc
• max_nstruct_in_memory : basic::options::OptionKeys::jd2
• max_num_strands_to_deal : basic::options::OptionKeys::strand_assembly
• max_O_N_dis : basic::options::OptionKeys::strand_assembly
• max_per_res : basic::options::OptionKeys::mh::dump
• max_poses : basic::options::OptionKeys::docking::ligand
• max_radius : basic::options::OptionKeys::lh
• max_rama_score_increase : basic::options::OptionKeys::loops::ccd
• max_ref_lib_size : basic::options::OptionKeys::lh
• max_registry_shift : basic::options::OptionKeys::cm::hybridize
• max_repeats : basic::options::OptionKeys::docking
• max_res : basic::options::OptionKeys::mh::harvest
• max_res_in_strand : basic::options::OptionKeys::strand_assembly
• max_retry_job : basic::options::OptionKeys::run
• max_rms : basic::options::OptionKeys::lh , basic::options::OptionKeys::mh::dump
• max_rms_from_native : basic::options::OptionKeys::optE
• max_rmsd : basic::options::OptionKeys::mh::harvest
• max_rmsd_after_relax : basic::options::OptionKeys::frags::nonlocal
• max_rmsd_against_known_structures : basic::options::OptionKeys::mc
• max_rotbump_energy : basic::options::OptionKeys::packing
• max_sample_per_structure : basic::options::OptionKeys::lh
• max_seqsep : basic::options::OptionKeys::mh::filter
• max_sheet_angle : basic::options::OptionKeys::strand_assembly
• max_sheet_dis : basic::options::OptionKeys::strand_assembly
• max_sheet_torsion : basic::options::OptionKeys::strand_assembly
• max_shrink : basic::options::OptionKeys::templates
• max_ss_num : basic::options::OptionKeys::sewing
• max_strand_gap_allowed : basic::options::OptionKeys::jumps
• max_strand_length : basic::options::OptionKeys::sewing
• max_struct : basic::options::OptionKeys::lh
• max_struct_per_radius : basic::options::OptionKeys::lh
• max_torsion_delta : basic::options::OptionKeys::loops::ccd
• max_torsion_delta_per_move : basic::options::OptionKeys::loops::ccd
• max_total_cluster : basic::options::OptionKeys::cluster
• max_tries_multiplier_for_ccd : basic::options::OptionKeys::stepwise
• maxdist2 : basic::options::OptionKeys::mh::filter
• MAXIT : numeric::kinematic_closure
• maxruntime : basic::options::OptionKeys::run
• maxruntime_bufferfactor : basic::options::OptionKeys::run
• may_add_already_added_model : basic::options::OptionKeys::sewing
• mc : basic::options::OptionKeys::mc , demo::D060_Folding , loops , loops_kic , test::T400_Refinement , test::T650_LoopsKIC , test::T860_SubClassing_EnergyMethods , test::Workshop5test
• mc_kt : basic::options::OptionKeys::backrub , basic::options::OptionKeys::canonical_sampling::sampling
• mc_kt_high : basic::options::OptionKeys::enzdes
• mc_kt_low : basic::options::OptionKeys::enzdes
• mcm_cycles : basic::options::OptionKeys::flexPepDocking
• md_schfile : basic::options::OptionKeys::in::file
• mean : basic::options::OptionKeys::ddg
• measure_sequence_recovery : basic::options::OptionKeys::optE::rescore
• mem_tr : basic
• Membed_init : basic::options::OptionKeys::membrane
• membrane : basic::options::OptionKeys::abinitio , basic::options::OptionKeys::in , basic::options::OptionKeys::membrane , basic::options::OptionKeys::ProQ
• membrane_axis : basic::options::OptionKeys::edensity
• membrane_center : basic::options::OptionKeys::membrane
• membrane_normal : basic::options::OptionKeys::membrane
• membrane_pdb : basic::options::OptionKeys::out
• membrane_pdb_thickness : basic::options::OptionKeys::out
• membrane_rsd : basic::options::OptionKeys::mp::setup
• memory_limit : basic::options::OptionKeys::wum
• memory_test_cycles : basic::options::OptionKeys::run
• Menv_penalties : basic::options::OptionKeys::membrane
• merge_motifs : basic::options::OptionKeys::mh
• merge_motifs_one_per_bin : basic::options::OptionKeys::mh
• merge_scores : basic::options::OptionKeys::mh
• merge_similar_motifs : basic::options::OptionKeys::mh
• metal_dist_cutoff : basic::options::OptionKeys::bunsat_calc2
• metals_angle_constraint_multiplier : basic::options::OptionKeys::in
• metals_detection_LJ_multiplier : basic::options::OptionKeys::in
• metals_distance_constraint_multiplier : basic::options::OptionKeys::in
• method : basic::options::OptionKeys::sasa
• methylate : basic::options::OptionKeys::dna::specificity
• mg_res : basic::options::OptionKeys::magnesium
• mh : basic::options::OptionKeys::mh
• Mhbond_depth : basic::options::OptionKeys::membrane
• middle_offset : loops_kic , test::T650_LoopsKIC
• min : basic::options::OptionKeys::ddg , basic::options::OptionKeys::rot_anl
• min_align_pos : basic::options::OptionKeys::templates
• min_all_jumps : basic::options::OptionKeys::enzdes
• min_atoms : basic::options::OptionKeys::backrub
• min_bbrms : basic::options::OptionKeys::lh
• min_bin_val : basic::options::OptionKeys::mh::harvest
• min_breakout_fast_loops : basic::options::OptionKeys::fast_loops
• min_breakout_good_loops : basic::options::OptionKeys::fast_loops
• min_cacb_deviation : basic::options::OptionKeys::enzdes
• min_cav_ball_radius : basic::options::OptionKeys::packstat
• min_cluster_overlap : basic::options::OptionKeys::packstat
• min_contact_pairs : basic::options::OptionKeys::mh::score
• min_contacts_per_res : basic::options::OptionKeys::frags::nonlocal
• min_cover_fraction : basic::options::OptionKeys::mh::score
• min_cst : basic::options::OptionKeys::ddg
• min_cst_weights : basic::options::OptionKeys::ddg
• min_cycles : basic::options::OptionKeys::relax::range
• min_decoy_rms_to_native : basic::options::OptionKeys::optE
• min_dis_hb : basic::options::OptionKeys::willmatch
• min_fast_loops : basic::options::OptionKeys::fast_loops
• min_final_hbonds : basic::options::OptionKeys::cyclic_peptide
• min_frag_size : basic::options::OptionKeys::templates
• min_gap_extend : basic::options::OptionKeys::cm
• min_gap_open : basic::options::OptionKeys::cm
• min_genkic_hbonds : basic::options::OptionKeys::cyclic_peptide
• min_good_loops : basic::options::OptionKeys::fast_loops
• min_hash_score : basic::options::OptionKeys::sewing
• min_helix_length : basic::options::OptionKeys::sewing
• min_lh_fragments : basic::options::OptionKeys::sewing
• min_loop_length : basic::options::OptionKeys::sewing
• min_loop_size : basic::options::OptionKeys::cm
• min_max_start_seq_sep : basic::options::OptionKeys::resample
• min_motif_score : basic::options::OptionKeys::sewing
• min_mover : app::delta_score_per_mutation , test::Workshop5test , test::Workshop7test
• min_nr_large_frags : basic::options::OptionKeys::templates
• min_nr_small_frags : basic::options::OptionKeys::templates
• min_num_ring : basic::options::OptionKeys::gen_pharmacophore
• min_num_strands_to_deal : basic::options::OptionKeys::strand_assembly
• min_O_N_dis : basic::options::OptionKeys::strand_assembly
• min_pack : basic::options::OptionKeys
• min_padding : basic::options::OptionKeys::templates
• min_rb : basic::options::OptionKeys::matdes::mutalyze
• min_receptor_bb : basic::options::OptionKeys::flexPepDocking
• min_res_in_strand : basic::options::OptionKeys::strand_assembly
• min_rms : basic::options::OptionKeys::docking::ligand , basic::options::OptionKeys::lh
• min_score : basic::options::OptionKeys::score::saxs
• min_score_score : basic::options::OptionKeys::score
• min_seq_sep : basic::options::OptionKeys::frags::contacts
• min_seqsep : basic::options::OptionKeys::james
• min_sequence_separation : basic::options::OptionKeys::pose_metrics
• min_sheet_angle : basic::options::OptionKeys::strand_assembly
• min_sheet_dis : basic::options::OptionKeys::strand_assembly
• min_sheet_torsion : basic::options::OptionKeys::strand_assembly
• min_shortest_dis_sidechain_inter_sheet : basic::options::OptionKeys::strand_assembly
• min_strand_length : basic::options::OptionKeys::sewing
• min_surface_accessibility : basic::options::OptionKeys::packstat
• min_tolerance : basic::options::OptionKeys::relax , basic::options::OptionKeys::run , basic::options::OptionKeys::stepwise
• min_type : basic::options::OptionKeys::dna::specificity , basic::options::OptionKeys::relax , basic::options::OptionKeys::run , basic::options::OptionKeys::stepwise , loops_kic , test::T650_LoopsKIC
• min_unaligned_len : basic::options::OptionKeys::abinitio::star
• min_with_cst : basic::options::OptionKeys::ddg
• minbb : basic::options::OptionKeys::smhybrid
• mindist2 : basic::options::OptionKeys::mh::filter
• mini : basic::options::OptionKeys::relax
• minimization_patch : basic::options::OptionKeys::ddg
• minimization_scorefunction : basic::options::OptionKeys::ddg
• minimization_threshold : basic::options::OptionKeys::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
• minimize_after_nmsearch : basic::options::OptionKeys::lh
• minimize_all_ligand_torsions : basic::options::OptionKeys::enzdes
• minimize_and_score_native_pose : basic::options::OptionKeys::stepwise::rna
• minimize_and_score_sugar : basic::options::OptionKeys::stepwise::rna
• minimize_backbone : basic::options::OptionKeys::docking::ligand
• minimize_bond_angles : basic::options::OptionKeys::relax
• minimize_bond_lengths : basic::options::OptionKeys::relax
• minimize_bondangle_subset : basic::options::OptionKeys::relax
• minimize_bondlength_subset : basic::options::OptionKeys::relax
• minimize_bps : basic::options::OptionKeys::rna::farna::minimize
• minimize_dna : basic::options::OptionKeys::motifs
• minimize_during_scoring : basic::options::OptionKeys::magnesium
• minimize_ligand : basic::options::OptionKeys::docking::ligand
• minimize_ligand_torsions : basic::options::OptionKeys::enzdes
• minimize_max_iter : basic::options::OptionKeys::loops
• minimize_mg_coord_constraint_distance : basic::options::OptionKeys::magnesium
• minimize_movemap : basic::options::OptionKeys::backrub
• minimize_res : basic::options::OptionKeys::in::file , basic::options::OptionKeys::stepwise::rna
• minimize_rna : basic::options::OptionKeys::rna::farna
• minimize_rounds : basic::options::OptionKeys::rna::farna::minimize
• minimize_sidechains : basic::options::OptionKeys , core::options::OptionKeys
• minimize_single_res_frequency : basic::options::OptionKeys::stepwise::monte_carlo
• minimize_tolerance : basic::options::OptionKeys::dna::specificity
• minimize_waters : basic::options::OptionKeys::stepwise
• minimizer_rename_tag : basic::options::OptionKeys::stepwise::rna
• minimizer_score_fxn : basic::options::OptionKeys::cp
• minimizer_use_coordinate_constraints : basic::options::OptionKeys::rna::farna::minimize
• minirelax_repeats : basic::options::OptionKeys::relax
• minirelax_sdev : basic::options::OptionKeys::relax
• minmover : test::T400_Refinement , test::T850_SubClassing
• MINOR : setup
• minpack_disable_bumpcheck : basic::options::OptionKeys::packing
• minpack_inner_iteration_scale : basic::options::OptionKeys::packing
• minpack_temp_schedule : basic::options::OptionKeys::packing
• missing_density_to_jump : basic::options::OptionKeys::in
• missing_res : basic::options::OptionKeys::stepwise::rna
• missing_res2 : basic::options::OptionKeys::stepwise::rna
• mistakes : basic::options::OptionKeys::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 : basic::options::OptionKeys::backrub
• mm_loop_file : basic::options::OptionKeys::loops
• mode : basic::options::OptionKeys::dna::specificity , basic::options::OptionKeys::inout::dbms , basic::options::OptionKeys::sewing , contacts
• model_B : basic::options::OptionKeys::patterson
• model_file_name : basic::options::OptionKeys::sewing
• model_h3 : basic::options::OptionKeys::antibody
• model_should_have_at_least_1_E : basic::options::OptionKeys::sewing
• model_should_have_at_least_1_E_at_terminal_segment : basic::options::OptionKeys::sewing
• model_should_have_at_least_1_H : basic::options::OptionKeys::sewing
• model_should_have_this_num_of_ss : basic::options::OptionKeys::sewing
• modelID : app::pyrosetta_toolkit::modules::SQLPDB
• models_to_dump : basic::options::OptionKeys::sewing
• modifiedres : clean_pdb_keep_ligand
• modres : amino_acids
• module_function_suffix : binder
• module_header : binder
• mol : assign_charges
• monolith_rosetta_library_name : BuildBindings
• monte_carlo : basic::options::OptionKeys::magnesium , basic::options::OptionKeys::stepwise::monte_carlo
• montecarlo : basic::options::OptionKeys::magnesium::montecarlo
• MonteCarlo : basic::options::OptionKeys::MonteCarlo
• motif_begin : basic::options::OptionKeys::dna::specificity
• motif_build_defs : basic::options::OptionKeys::motifs
• motif_build_positions : basic::options::OptionKeys::motifs
• motif_filename : basic::options::OptionKeys::motifs
• motif_flexible_loop_file : basic::options::OptionKeys::motifs
• motif_ignore_symmmetry : basic::options::OptionKeys::score
• motif_match_radius : basic::options::OptionKeys::mh
• motif_mode : basic::options::OptionKeys::full_model
• motif_out_file : basic::options::OptionKeys::mh
• motif_output_directory : basic::options::OptionKeys::motifs
• motif_residues : basic::options::OptionKeys::score
• motif_size : basic::options::OptionKeys::dna::specificity
• motif_type : basic::options::OptionKeys::mh::filter
• motifs : basic::options::OptionKeys::mh::path , basic::options::OptionKeys::motifs
• motifs_BB_BB : basic::options::OptionKeys::mh::path
• motifs_BB_PH : basic::options::OptionKeys::mh::path
• motifs_BB_PO : basic::options::OptionKeys::mh::path
• motifs_PH_PO : basic::options::OptionKeys::mh::path
• motifs_SC_BB : basic::options::OptionKeys::mh::path
• motifs_SC_SC : basic::options::OptionKeys::mh::path
• move : basic::options::OptionKeys::stepwise
• move_anchor_frequency : basic::options::OptionKeys::fold_and_dock
• move_anchor_points : basic::options::OptionKeys::fold_and_dock
• move_first_rigid_body : basic::options::OptionKeys::rna::farna
• move_jumps_between_chains : basic::options::OptionKeys::stepwise::protein
• move_ligand : basic::options::OptionKeys::remodel
• movemap : basic::options::OptionKeys::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
• mover_3mer : loops , test::T400_Refinement , test::Workshop4test
• moving_jump : basic::options::OptionKeys::dna::specificity
• mp : basic::options::OptionKeys::mp
• mpi_batch_relax_absolute_max : basic::options::OptionKeys::lh
• mpi_batch_relax_chunks : basic::options::OptionKeys::lh
• MPI_batchsize_by_level : basic::options::OptionKeys::cyclic_peptide
• MPI_bcast : basic::options::OptionKeys::canonical_sampling::probabilities
• MPI_choose_highest : basic::options::OptionKeys::cyclic_peptide
• mpi_fast_nonblocking_output : basic::options::OptionKeys::jd2
• mpi_feedback : basic::options::OptionKeys::lh
• mpi_file_buf_job_distributor : basic::options::OptionKeys::jd2
• mpi_filebuf_jobdistributor : basic::options::OptionKeys::jd2
• mpi_loophash_scan_type : basic::options::OptionKeys::lh
• mpi_loophash_split_size : basic::options::OptionKeys::lh
• mpi_master_cpu_weight : basic::options::OptionKeys::lh
• mpi_master_save_score_only : basic::options::OptionKeys::lh
• mpi_master_schfile : basic::options::OptionKeys::lh
• mpi_metropolis_temp : basic::options::OptionKeys::lh
• mpi_nowait_for_remaining_jobs : basic::options::OptionKeys::jd2
• mpi_outbound_wu_buffer_size : basic::options::OptionKeys::lh
• MPI_output_fraction : basic::options::OptionKeys::cyclic_peptide
• mpi_packmin_init : basic::options::OptionKeys::lh
• MPI_processes_by_level : basic::options::OptionKeys::cyclic_peptide
• mpi_rank_dir : basic::options::OptionKeys::out::path
• mpi_read_structure_for_emperor : basic::options::OptionKeys::lh
• mpi_resume : basic::options::OptionKeys::lh
• mpi_save_state_interval : basic::options::OptionKeys::lh
• MPI_sort_by : basic::options::OptionKeys::cyclic_peptide
• MPI_stop_after_time : basic::options::OptionKeys::cyclic_peptide
• MPI_STREAM_TAG : utility::io::mpi_stream
• MPI_sync_pools : basic::options::OptionKeys::canonical_sampling::probabilities
• mpi_timeout_factor : basic::options::OptionKeys::jd2
• mpi_tracer_to_file : basic::options::OptionKeys::out
• mpi_weight_minimization : basic::options::OptionKeys::optE
• mpi_work_partition_job_distributor : basic::options::OptionKeys::jd2
• ms : basic::options::OptionKeys::ms
• msd_job_dist : basic::options::OptionKeys::run
• msd_randomize : basic::options::OptionKeys::run
• MSWORD_FRIENDLY : app::pyrosetta_toolkit::modules::prettytable::prettytable
• mtzfile : basic::options::OptionKeys::cryst
• multi_cool_annealer : basic::options::OptionKeys::packing
• multi_objective_functions : basic::options::OptionKeys::lh
• multibody : basic::options::OptionKeys::docking
• multifastrelax : basic::options::OptionKeys::abinitio
• multiple_origin : basic::options::OptionKeys::fingerprint
• multiple_processes_writing_to_one_directory : basic::options::OptionKeys::run
• multiplier : basic::options::OptionKeys::mh::harvest
• murphp : basic::options::OptionKeys::murphp
• mut_file : basic::options::OptionKeys::ddg
• mut_only : basic::options::OptionKeys::ddg
• mutalyze : basic::options::OptionKeys::matdes::mutalyze
• mutant_aa : demo::D090_Ala_scan
• mutant_file : basic::options::OptionKeys::mp::mutate_relax
• mutant_pose : app::delta_score_per_mutation
• mutants_list : protocols::pmut_scan
• mutate_framework_for_cluster : basic::options::OptionKeys::antibody::design
• mutate_rate : basic::options::OptionKeys::ms
• mutate_relax : basic::options::OptionKeys::mp::mutate_relax
• mutate_same_name3 : basic::options::OptionKeys::docking::ligand
• mutation : basic::options::OptionKeys::mp::mutate_relax
• mute : basic::options::OptionKeys::out
• my_loop : loops , loops_kic , test::T650_LoopsKIC
• my_loops : loops , loops_kic , test::T650_LoopsKIC