- m -

• main() : options
• make_compound_statement() : basic::database
• make_consensus_mutations() : basic::options::OptionKeys::enzdes , enzdes
• make_ensemble_cst() : basic::options::OptionKeys::cluster , cluster
• make_map() : utility::tools
• make_movie() : stepwise::monte_carlo
• make_pdb() : basic::options::OptionKeys::holes , holes
• make_points() : numeric::kdtree
• make_tag() : utility
• make_tag_with_dashes() : utility
• make_vector() : utility::tools
• make_vector0() : utility::tools
• make_vector1() : utility::tools
• make_voids() : basic::options::OptionKeys::holes , holes
• MakeVector() : numeric
• map_to_obj() : utility::json_spirit
• mapfile() : basic::options::OptionKeys::edensity , edensity
• mapreso() : basic::options::OptionKeys::edensity , edensity
• master_wu_per_send() : basic::options::OptionKeys::els , els
• match() : basic::options::OptionKeys::match , match
• match_grouper() : basic::options::OptionKeys::match , match
• match_overlap_ang() : willmatch
• match_overlap_dis() : willmatch
• match_rt_limit() : remodel
• matdes() : basic::options::OptionKeys::matdes , matdes
• MatrixMult() : numeric::model_quality
• max() : numeric , utility
• max_align_pos() : templates
• max_ang_metal() : 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_ca_ca_dist() : rigid
• max_cav_ball_radius() : packstat
• max_chews() : remodel::RemodelLoopMover
• max_chunk_size() : basic::options::OptionKeys::nonlocal , nonlocal
• max_cluster_seeds() : basic::options::OptionKeys::cluster , cluster
• max_contact_pairs() : basic::options::OptionKeys::mh::score , mh::score
• max_cpu() : basic::options::OptionKeys::boinc , boinc
• max_cst_dist() : basic::options::OptionKeys::constraints , constraints
• max_ddg_score() : basic::options::OptionKeys::frags::nonlocal , frags::nonlocal
• max_depth() : basic::options::OptionKeys::motifs , motifs
• max_dis_all() : basic::options::OptionKeys::crossmatch , crossmatch , willmatch
• max_dis_any() : basic::options::OptionKeys::crossmatch , crossmatch , willmatch
• max_dis_hb() : willmatch
• max_dis_hb_colinear() : willmatch
• max_dis_metal() : basic::options::OptionKeys::crossmatch , crossmatch , willmatch
• max_disulf_allowed() : remodel
• 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() : qsar
• max_inner_cycles() : basic::options::OptionKeys::loops , loops
• max_kic_build_attempts() : basic::options::OptionKeys::loops , loops
• max_kic_perturber_samples() : basic::options::OptionKeys::loops , loops
• max_lib_size() : basic::options::OptionKeys::lh , lh
• max_linear_chainbreak() : remodel::RemodelLoopMover
• max_loop_rebuild() : basic::options::OptionKeys::cm , cm
• max_loophash_per_structure() : basic::options::OptionKeys::lh , lh
• max_min_iter() : run
• max_nstruct() : basic::options::OptionKeys::boinc , boinc
• max_num_strands_to_deal() : strand_assembly
• max_O_N_dis() : strand_assembly
• max_poses() : basic::options::OptionKeys::docking::ligand , docking::ligand
• max_radius() : basic::options::OptionKeys::lh , lh
• max_registry_shift() : basic::options::OptionKeys::cm::hybridize , cm::hybridize
• max_repeats() : basic::options::OptionKeys::docking , docking
• max_res_in_strand() : strand_assembly
• max_retry_job() : run
• max_rms() : basic::options::OptionKeys::lh , lh
• max_rms_from_native() : basic::options::OptionKeys::optE , optE
• max_rmsd_after_relax() : basic::options::OptionKeys::frags::nonlocal , frags::nonlocal
• max_rmsd_against_known_structures() : basic::options::OptionKeys::mc , mc
• max_rotbump_energy() : packing
• max_sheet_angle() : strand_assembly
• max_sheet_dis() : strand_assembly
• max_sheet_torsion() : strand_assembly
• max_shrink() : templates
• max_strand_gap_allowed() : basic::options::OptionKeys::jumps , jumps
• max_struct() : basic::options::OptionKeys::lh , lh
• max_struct_per_radius() : basic::options::OptionKeys::lh , lh
• max_total_cluster() : basic::options::OptionKeys::cluster , cluster
• maxdist2() : basic::options::OptionKeys::mh::filter , mh::filter
• maxruntime() : run
• maxsub() : numeric::model_quality
• mc() : basic::options::OptionKeys::mc , mc
• mc_kt() : 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
• 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
• medium_range_seqsep() : rigid
• Membed_init() : basic::options::OptionKeys::membrane , membrane
• membrane() : abinitio , basic::options::OptionKeys::abinitio , basic::options::OptionKeys::in , basic::options::OptionKeys::membrane , in , membrane , ProQ , relax
• membrane_axis() : basic::options::OptionKeys::edensity , edensity
• membrane_center() : basic::options::OptionKeys::membrane , membrane
• membrane_chains() : basic::options::OptionKeys::in::file , in::file
• membrane_normal() : basic::options::OptionKeys::membrane , membrane
• memory_limit() : wum
• memory_test_cycles() : run
• 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_similar_motifs() : basic::options::OptionKeys::mh , mh
• 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
• method() : sasa
• methylate() : basic::options::OptionKeys::dna::specificity , dna::specificity
• mh() : basic::options::OptionKeys::mh , mh
• Mhbond_depth() : basic::options::OptionKeys::membrane , membrane
• midpoint() : numeric
• min() : basic::options::OptionKeys::ddg , ddg , numeric , rot_anl , utility
• min_align_pos() : templates
• min_all_jumps() : basic::options::OptionKeys::enzdes , enzdes
• min_atoms() : backrub , basic::options::OptionKeys::backrub
• min_bbrms() : basic::options::OptionKeys::lh , lh
• 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() : packstat
• min_cluster_overlap() : 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_decoy_rms_to_native() : basic::options::OptionKeys::optE , optE
• min_dis_hb() : willmatch
• min_fast_loops() : basic::options::OptionKeys::fast_loops , fast_loops
• min_frag_size() : templates
• min_gap_extend() : basic::options::OptionKeys::cm , cm
• min_gap_open() : basic::options::OptionKeys::cm , cm
• min_good_loops() : basic::options::OptionKeys::fast_loops , fast_loops
• min_helix_size() : sewing
• min_loop_size() : basic::options::OptionKeys::cm , cm
• min_max_start_seq_sep() : resample
• min_nr_large_frags() : templates
• min_nr_small_frags() : templates
• min_num_strands_to_deal() : strand_assembly
• min_O_N_dis() : strand_assembly
• min_padding() : templates
• min_rb() : basic::options::OptionKeys::matdes::mutalyze , matdes::mutalyze
• min_receptor_bb() : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• min_res_in_strand() : strand_assembly
• min_rms() : basic::options::OptionKeys::docking::ligand , basic::options::OptionKeys::lh , docking::ligand , lh
• min_score() : score::saxs
• min_score_score() : score
• min_seq_sep() : basic::options::OptionKeys::frags::contacts , frags::contacts
• min_seqsep() : basic::options::OptionKeys::james , james
• min_sequence_separation() : pose_metrics
• min_sheet_angle() : strand_assembly
• min_sheet_dis() : strand_assembly
• min_sheet_torsion() : strand_assembly
• min_shortest_dis_sidechain_inter_sheet() : strand_assembly
• min_surface_accessibility() : packstat
• min_tol() : basic::options::OptionKeys::james , james
• min_tolerance() : relax , run , stepwise::protein
• min_type() : basic::options::OptionKeys::dna::specificity , basic::options::OptionKeys::james , dna::specificity , james , relax , run , stepwise::protein
• min_unaligned_len() : abinitio::star , basic::options::OptionKeys::abinitio::star
• min_with_cst() : basic::options::OptionKeys::ddg , ddg
• minbb() : smhybrid
• mindist2() : basic::options::OptionKeys::mh::filter , mh::filter
• mini() : 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::motifs , dna::design , holes , motifs
• minimize_all_ligand_torsions() : basic::options::OptionKeys::enzdes , enzdes
• minimize_and_score_native_pose() : stepwise::rna
• minimize_and_score_sugar() : stepwise::rna
• minimize_backbone() : basic::options::OptionKeys::docking::ligand , basic::options::OptionKeys::docking::symmetry , docking::ligand , docking::symmetry
• minimize_bond_angles() : relax
• minimize_bond_lengths() : relax
• minimize_bondangle_subset() : relax
• minimize_bondlength_subset() : relax
• minimize_dna() : basic::options::OptionKeys::motifs , motifs
• minimize_ligand() : basic::options::OptionKeys::docking::ligand , docking::ligand
• minimize_ligand_torsions() : basic::options::OptionKeys::enzdes , enzdes
• minimize_res() : basic::options::OptionKeys::in::file , in::file , stepwise::rna
• minimize_rounds() : rna
• minimize_sidechains() : basic::options::OptionKeys::docking::symmetry , docking::symmetry
• minimize_single_res_frequency() : stepwise::monte_carlo
• minimize_tolerance() : basic::options::OptionKeys::dna::specificity , dna::specificity
• minimizer() : basic::options::OptionKeys::cp , cp
• minimizer_output_before_o2prime_pack() : stepwise::rna
• minimizer_perform_minimize() : stepwise::rna
• minimizer_perform_o2prime_pack() : stepwise::rna
• minimizer_rename_tag() : stepwise::rna
• minimizer_score_fxn() : basic::options::OptionKeys::cp , cp
• minimizer_tol() : basic::options::OptionKeys::cp , cp
• minimum_helix_contacts() : sewing
• minirelax_repeats() : relax
• minirelax_sdev() : relax
• minpack_disable_bumpcheck() : packing
• minpack_inner_iteration_scale() : packing
• minpack_temp_schedule() : packing
• missing_density_to_jump() : basic::options::OptionKeys::in , in
• missing_res() : stepwise::rna
• missing_res2() : stepwise::rna
• mistakes() : basic::options::OptionKeys::mistakes , mistakes
• MM() : basic::options::OptionKeys::MM , MM
• mm_loop_file() : basic::options::OptionKeys::loops , loops
• mod() : numeric
• mode() : basic::options::OptionKeys::dna::specificity , basic::options::OptionKeys::inout::dbms , dna::specificity , inout::dbms
• model_B() : patterson
• model_h3() : antibody , basic::options::OptionKeys::antibody
• modp() : numeric::kinematic_closure
• modrf() : numeric::kinematic_closure
• modulo() : numeric
• monte_carlo() : stepwise::monte_carlo
• MonteCarlo() : basic::options::OptionKeys::MonteCarlo , MonteCarlo
• more_stats() : basic::options::OptionKeys::dna::design , dna::design
• motif_begin() : basic::options::OptionKeys::dna::specificity , dna::specificity
• motif_build_defs() : basic::options::OptionKeys::motifs , motifs
• motif_build_position_chain() : 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_match_radius() : basic::options::OptionKeys::mh , mh
• motif_out_file() : basic::options::OptionKeys::mh , mh
• motif_output_directory() : basic::options::OptionKeys::motifs , motifs
• motif_size() : basic::options::OptionKeys::dna::specificity , dna::specificity
• motifs() : basic::options::OptionKeys::motifs , motifs
• move() : stepwise
• move_anchor() : basic::options::OptionKeys::cm::hybridize , cm::hybridize
• 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_jumps_between_chains() : stepwise::protein
• movemap() : basic::options::OptionKeys::in::file , in::file
• movemap_from_blueprint() : basic::options::OptionKeys::flxbb , flxbb
• movie() : out::path , run
• moving_jump() : basic::options::OptionKeys::dna::specificity , dna::specificity
• mpi_batch_relax_absolute_max() : basic::options::OptionKeys::lh , lh
• mpi_batch_relax_chunks() : basic::options::OptionKeys::lh , lh
• MPI_bcast() : basic::options::OptionKeys::canonical_sampling::probabilities , canonical_sampling::probabilities
• mpi_fast_nonblocking_output() : basic::options::OptionKeys::jd2 , jd2
• mpi_feedback() : basic::options::OptionKeys::lh , lh
• mpi_file_buf_job_distributor() : basic::options::OptionKeys::jd2 , jd2
• mpi_filebuf_jobdistributor() : basic::options::OptionKeys::jd2 , jd2
• mpi_loophash_split_size() : basic::options::OptionKeys::lh , lh
• mpi_master_save_score_only() : basic::options::OptionKeys::lh , lh
• mpi_metropolis_temp() : basic::options::OptionKeys::lh , lh
• mpi_nowait_for_remaining_jobs() : basic::options::OptionKeys::jd2 , jd2
• mpi_nprocs() : utility
• mpi_outbound_wu_buffer_size() : basic::options::OptionKeys::lh , lh
• mpi_rank() : utility
• mpi_rank_dir() : out::path
• mpi_resume() : basic::options::OptionKeys::lh , lh
• mpi_safe_std_err() : utility::options
• mpi_save_state_interval() : basic::options::OptionKeys::lh , lh
• MPI_sync_pools() : basic::options::OptionKeys::canonical_sampling::probabilities , canonical_sampling::probabilities
• mpi_timeout_factor() : basic::options::OptionKeys::jd2 , jd2
• mpi_tracer_to_file() : out
• mpi_weight_minimization() : basic::options::OptionKeys::optE , optE
• mpi_work_partition_job_distributor() : basic::options::OptionKeys::jd2 , jd2
• ms() : basic::options::OptionKeys::ms , ms
• msg_name() : utility
• msms_analysis() : rescore
• mtzfile() : basic::options::OptionKeys::cryst , cryst
• multi_cool_annealer() : packing
• multibody() : basic::options::OptionKeys::docking , docking
• multifastrelax() : abinitio , basic::options::OptionKeys::abinitio
• multiple_processes_writing_to_one_directory() : run
• multiply() : numeric
• multMatrix() : numeric::kinematic_closure
• multTransMatrix() : numeric::kinematic_closure
• murphp() : basic::options::OptionKeys::murphp , murphp
• mut() : basic::options::OptionKeys::ddg , ddg
• mut_file() : basic::options::OptionKeys::ddg , ddg
• mut_only() : basic::options::OptionKeys::ddg , ddg
• mutalyze() : basic::options::OptionKeys::matdes::mutalyze , matdes::mutalyze
• mutate_rate() : basic::options::OptionKeys::ms , ms
• mutate_same_name3() : basic::options::OptionKeys::docking::ligand , docking::ligand
• mute() : out