- m -

main_exit_callback : utility
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_voids : basic::options::OptionKeys::holes
mapfile : basic::options::OptionKeys::edensity
mapreso : basic::options::OptionKeys::edensity
master_wu_per_send : basic::options::OptionKeys::els
match : basic::options::OptionKeys::match
match_grouper : basic::options::OptionKeys::match
match_overlap_ang : basic::options::OptionKeys::willmatch
match_overlap_dis : basic::options::OptionKeys::willmatch
match_rt_limit : basic::options::OptionKeys::remodel
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_ca_ca_dist : basic::options::OptionKeys::rigid
max_cav_ball_radius : basic::options::OptionKeys::packstat
max_chews : basic::options::OptionKeys::remodel::RemodelLoopMover
max_chunk_size : basic::options::OptionKeys::nonlocal
max_cluster_seeds : basic::options::OptionKeys::cluster
max_contact_pairs : basic::options::OptionKeys::mh::score
max_cpu : basic::options::OptionKeys::boinc
max_cst_dist : basic::options::OptionKeys::constraints
max_ddg_score : basic::options::OptionKeys::frags::nonlocal
max_depth : basic::options::OptionKeys::motifs
max_dis_all : basic::options::OptionKeys::crossmatch , basic::options::OptionKeys::willmatch
max_dis_any : basic::options::OptionKeys::crossmatch , 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::crossmatch , basic::options::OptionKeys::willmatch
max_disulf_allowed : basic::options::OptionKeys::remodel
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_inner_cycles : basic::options::OptionKeys::loops
MAX_ITER_SECANT : numeric::kinematic_closure
max_kic_build_attempts : basic::options::OptionKeys::loops
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_rebuild : basic::options::OptionKeys::cm
max_loophash_per_structure : basic::options::OptionKeys::lh
max_min_iter : basic::options::OptionKeys::run
max_nstruct : basic::options::OptionKeys::boinc
max_num_strands_to_deal : basic::options::OptionKeys::strand_assembly
max_O_N_dis : basic::options::OptionKeys::strand_assembly
max_poses : basic::options::OptionKeys::docking::ligand
max_radius : basic::options::OptionKeys::lh
max_registry_shift : basic::options::OptionKeys::cm::hybridize
max_repeats : basic::options::OptionKeys::docking
max_res_in_strand : basic::options::OptionKeys::strand_assembly
max_retry_job : basic::options::OptionKeys::run
max_rms : basic::options::OptionKeys::lh
max_rms_from_native : basic::options::OptionKeys::optE
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_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_strand_gap_allowed : basic::options::OptionKeys::jumps
max_struct : basic::options::OptionKeys::lh
max_struct_per_radius : basic::options::OptionKeys::lh
max_total_cluster : basic::options::OptionKeys::cluster
maxdist2 : basic::options::OptionKeys::mh::filter
MAXIT : numeric::kinematic_closure
maxruntime : basic::options::OptionKeys::run
mc : basic::options::OptionKeys::mc
mc_kt : 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
medium_range_seqsep : basic::options::OptionKeys::rigid
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 , basic::options::OptionKeys::relax
membrane_axis : basic::options::OptionKeys::edensity
membrane_center : basic::options::OptionKeys::membrane
membrane_chains : basic::options::OptionKeys::in::file
membrane_normal : basic::options::OptionKeys::membrane
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_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
mh : basic::options::OptionKeys::mh
Mhbond_depth : basic::options::OptionKeys::membrane
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_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_decoy_rms_to_native : basic::options::OptionKeys::optE
min_dis_hb : basic::options::OptionKeys::willmatch
min_fast_loops : basic::options::OptionKeys::fast_loops
min_frag_size : basic::options::OptionKeys::templates
min_gap_extend : basic::options::OptionKeys::cm
min_gap_open : basic::options::OptionKeys::cm
min_good_loops : basic::options::OptionKeys::fast_loops
min_helix_size : basic::options::OptionKeys::sewing
min_loop_size : basic::options::OptionKeys::cm
min_max_start_seq_sep : basic::options::OptionKeys::resample
min_nr_large_frags : basic::options::OptionKeys::templates
min_nr_small_frags : basic::options::OptionKeys::templates
min_num_strands_to_deal : basic::options::OptionKeys::strand_assembly
min_O_N_dis : basic::options::OptionKeys::strand_assembly
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_surface_accessibility : basic::options::OptionKeys::packstat
min_tol : basic::options::OptionKeys::james
min_tolerance : basic::options::OptionKeys::relax , basic::options::OptionKeys::run , basic::options::OptionKeys::stepwise::protein
min_type : basic::options::OptionKeys::dna::specificity , basic::options::OptionKeys::james , basic::options::OptionKeys::relax , basic::options::OptionKeys::run , basic::options::OptionKeys::stepwise::protein
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::motifs
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 , basic::options::OptionKeys::docking::symmetry
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_dna : basic::options::OptionKeys::motifs
minimize_ligand : basic::options::OptionKeys::docking::ligand
minimize_ligand_torsions : basic::options::OptionKeys::enzdes
minimize_res : basic::options::OptionKeys::in::file , basic::options::OptionKeys::stepwise::rna
minimize_rounds : basic::options::OptionKeys::rna
minimize_sidechains : basic::options::OptionKeys::docking::symmetry
minimize_single_res_frequency : basic::options::OptionKeys::stepwise::monte_carlo
minimize_tolerance : basic::options::OptionKeys::dna::specificity
minimizer : basic::options::OptionKeys::cp
minimizer_output_before_o2prime_pack : basic::options::OptionKeys::stepwise::rna
minimizer_perform_minimize : basic::options::OptionKeys::stepwise::rna
minimizer_perform_o2prime_pack : basic::options::OptionKeys::stepwise::rna
minimizer_rename_tag : basic::options::OptionKeys::stepwise::rna
minimizer_score_fxn : basic::options::OptionKeys::cp
minimizer_tol : basic::options::OptionKeys::cp
minimum_helix_contacts : basic::options::OptionKeys::sewing
minirelax_repeats : basic::options::OptionKeys::relax
minirelax_sdev : basic::options::OptionKeys::relax
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 : basic::options::OptionKeys::MM
mm_loop_file : basic::options::OptionKeys::loops
mode : basic::options::OptionKeys::dna::specificity , basic::options::OptionKeys::inout::dbms
model_B : basic::options::OptionKeys::patterson
model_h3 : basic::options::OptionKeys::antibody
monte_carlo : basic::options::OptionKeys::stepwise::monte_carlo
MonteCarlo : basic::options::OptionKeys::MonteCarlo
more_stats : basic::options::OptionKeys::dna::design
motif_begin : basic::options::OptionKeys::dna::specificity
motif_build_defs : basic::options::OptionKeys::motifs
motif_build_position_chain : 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_match_radius : basic::options::OptionKeys::mh
motif_out_file : basic::options::OptionKeys::mh
motif_output_directory : basic::options::OptionKeys::motifs
motif_size : basic::options::OptionKeys::dna::specificity
motifs : basic::options::OptionKeys::motifs
move : basic::options::OptionKeys::stepwise
move_anchor : basic::options::OptionKeys::cm::hybridize
move_anchor_frequency : basic::options::OptionKeys::fold_and_dock
move_anchor_points : basic::options::OptionKeys::fold_and_dock
move_jumps_between_chains : basic::options::OptionKeys::stepwise::protein
movemap : basic::options::OptionKeys::in::file
movemap_from_blueprint : basic::options::OptionKeys::flxbb
movie : basic::options::OptionKeys::out::path , basic::options::OptionKeys::run
moving_jump : basic::options::OptionKeys::dna::specificity
mpi_batch_relax_absolute_max : basic::options::OptionKeys::lh
mpi_batch_relax_chunks : basic::options::OptionKeys::lh
MPI_bcast : basic::options::OptionKeys::canonical_sampling::probabilities
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_split_size : basic::options::OptionKeys::lh
mpi_master_save_score_only : 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_rank_dir : basic::options::OptionKeys::out::path
mpi_resume : basic::options::OptionKeys::lh
mpi_save_state_interval : basic::options::OptionKeys::lh
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
msms_analysis : basic::options::OptionKeys::rescore
mtzfile : basic::options::OptionKeys::cryst
multi_cool_annealer : basic::options::OptionKeys::packing
multibody : basic::options::OptionKeys::docking
multifastrelax : basic::options::OptionKeys::abinitio
multiple_processes_writing_to_one_directory : basic::options::OptionKeys::run
murphp : basic::options::OptionKeys::murphp
mut : basic::options::OptionKeys::ddg
mut_file : basic::options::OptionKeys::ddg
mut_only : basic::options::OptionKeys::ddg
mutalyze : basic::options::OptionKeys::matdes::mutalyze
mutate_rate : basic::options::OptionKeys::ms
mutate_same_name3 : basic::options::OptionKeys::docking::ligand
mute : basic::options::OptionKeys::out