- m -

• M : core::kinematics::Stub
• m1_ : protocols::hybridization::TMalign
• m1_b1_Ktheta_ : protocols::branch_angle::BranchParam1
• m1_b1_theta0_ : protocols::branch_angle::BranchParam1
• m1_b2_Ktheta_ : protocols::branch_angle::BranchParam2
• m1_b2_theta0_ : protocols::branch_angle::BranchParam2
• m1_m2_Ktheta_ : protocols::branch_angle::BranchParam1
• m1_m2_theta0_ : protocols::branch_angle::BranchParam1
• m2_ : protocols::hybridization::TMalign
• m2_b1_Ktheta_ : protocols::branch_angle::BranchParam1
• m2_b1_theta0_ : protocols::branch_angle::BranchParam1
• m2_b2_Ktheta_ : protocols::branch_angle::BranchParam2
• m2_b2_theta0_ : protocols::branch_angle::BranchParam2
• m_ : core::scoring::constraints::CircularSigmoidalFunc
• m_done_all : protocols::simple_moves::TailsScoreMover
• m_hill_size : protocols::simple_moves::TailsScoreMover
• m_number_of_hill_points : protocols::simple_moves::TailsScoreMover
• m_Temperature : protocols::relax::ClassicRelax
• m_Temperature_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::LoopRebuild , protocols::rna::RNA_DeNovoProtocol
• m_term_ : core::scoring::SecondaryStructurePotential
• machine_letter_ : protocols::wum::MPI_WorkUnitManager
• MACQ_ : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• MACR_ : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• mag_rot_ : protocols::rigid::RigidBodyMotionMover
• mag_trans_ : protocols::rigid::RigidBodyMotionMover
• magnitude_ : protocols::rbsegment_relax::SequenceShiftMover , protocols::simple_moves::sidechain_moves::PerturbChiSidechainMover
• magnitude_last_surface_deltaE_ : core::pack::interaction_graph::SurfaceEdge< V, E, G > , core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G >
• main_chain_torsion_set_for_moving_residues_ : protocols::swa::protein::StepWiseProteinScreener , protocols::swa::StepWiseScreener
• main_chain_torsion_set_for_moving_residues_save_ : protocols::swa::protein::StepWiseProteinCCD_Closer
• main_chain_torsion_set_lists_ : protocols::swa::protein::StepWiseProteinMainChainSampleGenerator , protocols::swa::protein::StepWiseProteinResidueSampler , protocols::swa::StepWiseResidueSampler
• main_chain_torsion_sets_for_moving_residues_ : protocols::swa::protein::StepWiseProteinCCD_Closer , protocols::swa::protein::StepWiseProteinLoopBridger , protocols::swa::protein::StepWiseProteinScreener , protocols::swa::StepWiseScreener
• main_resonances_ : protocols::noesy_assign::NoesyModule
• mainchain_atoms_ : core::chemical::ResidueType
• mainchain_glycosidic_bond_acceptor_ : core::chemical::carbohydrates::CarbohydrateInfo
• mainchain_torsion_diff_threshold_ : protocols::dna::PDBOutput
• mainchain_torsions_ : core::conformation::Residue , core::io::silent::RNA_SilentStruct
• make_mistake_ : protocols::jd2::archive::DebugArchive
• make_pymol_script_ : protocols::flxbb::LayerDesignOperation
• make_rasmol_format_file_ : protocols::toolbox::SelectResiduesByLayer , protocols::toolbox::task_operations::LayerOperations
• manager : protocols::forge::remodel::WorkingRemodelSet
• manager_ : protocols::fldsgn::BluePrintBDR , protocols::forge::components::BDR , protocols::forge::components::VarLengthBuild , protocols::forge::remodel::RemodelMover , protocols::jd2::archive::AbstractArchiveBase , protocols::protein_interface_design::movers::VLB
• manual_jump_pairs_ : protocols::seeded_abinitio::SeedFoldTree
• map_ : protocols::comparative_modeling::StealSideChainsMover , protocols::noesy_assign::ResonanceList , core::fragment::MapCacheUnit< T > , core::id::CacheableAtomID_MapVector , core::scoring::constraints::ResidueConstraints , core::scoring::EMapVector
• map_cst_from_centroid_to_fa_ : protocols::abinitio::ResolutionSwitcher
• map_helix_pairings_ : protocols::fldsgn::topology::HelixPairingSet
• map_is_clean_ : core::sequence::AnnotatedSequence
• map_loaded : core::scoring::electron_density::ElecDensAllAtomCenEnergy , core::scoring::electron_density::ElecDensCenEnergy , core::scoring::electron_density::ElecDensEnergy , core::scoring::electron_density::FastDensEnergy , core::scoring::electron_density::PattersonCorrEnergy
• map_name_ : protocols::qsar::qsarMap
• map_reso : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• map_strand_pairings_ : protocols::fldsgn::topology::StrandPairingSet
• map_to_cen_atom_ : protocols::noesy_assign::PeakAssignmentParameters
• map_to_original_ : protocols::toolbox::AllowInsert
• mapping_ : core::id::SequenceMapping , core::scoring::constraints::SequenceProfileConstraint , protocols::abinitio::Template
• mapreso_ : core::scoring::electron_density::ElectronDensityOptions
• maps_ : protocols::frag_picker::scores::ABEGO_SS_Score
• markpsp_ : protocols::pockets::PocketGrid
• marksps_ : protocols::pockets::PocketGrid
• mask_reses_ : protocols::electron_density::SetupForDensityScoringMover
• mass : protocols::cartesian::CartesianAtom
• mass_ : core::chemical::Element
• mass_limit_ : protocols::ligand_docking::MolarMassFilter , protocols::ligand_docking::MolecularMassFilter
• master_ : core::conformation::ResidueKinWriter , core::conformation::ConformationKinWriter , protocols::match::Bool3DGridKinemageWriter , protocols::match::output::ResidueKinemageWriter , protocols::match::output::WriteUpstreamHitKinemage , protocols::match::output::SingleDownstreamResidueWriter , protocols::wum2::WorkUnit
• master_node_ : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD
• master_rank_ : protocols::inputter::InputterStream , protocols::jd2::MPIFileBufJobDistributor , protocols::loophash::MPI_LoopHashRefine_Master , protocols::wum::DatabaseQueryWorkUnitManager< T >
• master_weight_ : protocols::toolbox::pose_metric_calculators::EnergiesData
• masterlib_extra_ : protocols::loophash::EXCN_bbdb_Merge_Failed
• match_algorithm_ : protocols::match::output::WriteUpstreamCoordinateKinemage
• match_groups_ : protocols::match::output::MatchConsolidator
• match_groups_dshits_ : protocols::match::output::CloudPDBWriter
• match_groups_ushits_ : protocols::match::output::CloudPDBWriter
• match_params_ : protocols::enzdes::SecondaryMatchProtocol
• match_positions_ : protocols::match::MatcherMover
• match_processing_successful_ : protocols::match::output::MatchProcessor
• match_score_ : core::sequence::SimpleScoringScheme
• matchCount : protocols::sparta::Sparta::SpartaLib
• matcher_ : protocols::match::output::UpstreamHitCacher
• matches_output_count_ : protocols::match::output::WriteUpstreamHitKinemage
• matching_database_ : core::scoring::disulfides::DisulfideMatchingPotential
• matchingFrags_ : protocols::forge::remodel::RemodelMover::instruction_flags
• matrix_ : protocols::simple_moves::FavorSequenceProfile
• matrix_A : protocols::simple_moves::BBGaussianMover
• matrix_dRdPhi : protocols::simple_moves::BBGaussianMover
• matrix_G : protocols::simple_moves::BBGaussianMover
• max0_ : core::scoring::hbonds::FadeInterval
• max_ : core::id::DOF_ID_Range , core::id::TorsionID_Range , core::scoring::constraints::EtableFunc
• max_allowed_conserved_pos_mutations_ : protocols::simple_filters::ConservedPosMutationFilter
• max_angle_ : protocols::rigid::RollMover
• max_angle_disp_ : protocols::backrub::BackrubSegment
• max_angle_disp_4_ : protocols::backrub::BackrubMover
• max_angle_disp_7_ : protocols::backrub::BackrubMover
• max_angle_disp_slope_ : protocols::backrub::BackrubMover
• max_atom_depth_ : core::scoring::trie::RotamerTrie< AT, CPDATA >
• max_atom_types_ : core::scoring::packing::HolesParams
• max_atomic_interaction_distance_ : core::scoring::ScoreFunctionInfo
• max_atoms_ : protocols::backrub::BackrubMover
• max_atoms_per_rotamer_ : core::scoring::trie::RotamerTrie< AT, CPDATA >
• max_bbrms_ : protocols::loophash::LoopHashMoverWrapper , protocols::loophash::LoopHashSampler
• max_bfactor_ : protocols::match::BfactorMPM
• max_bin_ : core::scoring::PairEPotential , protocols::scoring::methods::saxs::PDDFEnergy
• max_branch_depth_ : core::scoring::trie::RotamerTrie< AT, CPDATA >
• MAX_C_SIZE_LIMIT : core::chemical::carbohydrates::CarbohydrateInfo
• max_cache_size_ : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• max_capacity_ : protocols::frag_picker::BoundedPriorityQueue< T, StrictWeakOrdering > , protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering >
• max_cav_ : protocols::simple_moves::AddCavitiesMover
• max_cb_cb_dist_ : protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::protein_interface_design::movers::PlaceSimultaneouslyMover , protocols::protein_interface_design::movers::PlaceStubMover
• max_ccd_cycles_ : protocols::antibody2::H3PerturbCCD
• max_chi_ : core::io::silent::ProteinSilentStruct_Template< T >
• max_chunk_size_ : protocols::frag_picker::scores::GunnCostScore
• max_com_vector_ang_cos_ : protocols::match::NumNeighborsMPM
• max_connpoints_for_residue_ : core::scoring::trie::CPDataCorrespondence
• max_context_neighbor_cutoff_ : core::scoring::Energies , core::scoring::ScoreFunctionInfo
• max_cst_seq_sep_ : core::scoring::methods::CustomAtomPairEnergy
• max_cycle_ : protocols::antibody2::ModelCDRH3
• max_cycle_close_trial_ : protocols::antibody2::H3RefineCCD
• max_ddg_score_ : protocols::frag_picker::nonlocal::NonlocalFrags
• max_decoys_ : protocols::swa::rna::StepWiseRNA_Clusterer , protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer , protocols::swa::StepWiseClusterer
• max_degrees_off_parallel_ : protocols::features::helixAssembly::HelixBundleFeatures
• max_del_grid : core::scoring::electron_density::ElectronDensity , core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• max_dis : core::scoring::etable::EtableOptions
• max_dis2 : core::scoring::etable::Etable , core::scoring::etable::MembEtable
• max_dis2_ : core::scoring::carbon_hbonds::CarbonHBondEnergy , core::scoring::hackelec::HackElecEnergy , protocols::sic_dock::LinkerScore
• max_dis_ : core::scoring::carbon_hbonds::CarbonHBondEnergy , core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy , core::scoring::etable::Etable , core::scoring::etable::MembEtable , core::scoring::hackelec::HackElecEnergy
• max_dist_ : core::kinematics::ShortestPathInFoldTree , core::scoring::carbon_hbonds::CarbonHBondPotential , core::scoring::mm::MMLJEnergyTable , core::scoring::saxs::DistanceHistogram , protocols::features::AtomAtomPairFeatures , protocols::simple_filters::ContactMapEvaluator
• max_dist_from_dot_to_intersection : core::pack::interaction_graph::InvRotamerDots
• max_dist_ndx_ : protocols::toolbox::KClusterElement
• max_dist_squared_ : core::scoring::orbitals::OrbitalsScore
• max_distance_ : protocols::hotspot_hashing::LSMSearchPattern , protocols::simple_moves::AddConstraintsToCurrentConformationMover , protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener , protocols::toolbox::KClusterElement
• max_e_ : protocols::frag_picker::quota::TorsionBinPool
• max_emperor_lib_round_ : protocols::loophash::MPI_LoopHashRefine_Emperor
• max_frag_length_ : core::fragment::FragSet
• max_frag_size_ : protocols::frag_picker::FragmentPicker , protocols::rna::RNA_Relaxer
• max_generations_ : protocols::genetic_algorithm::GeneticAlgorithm
• max_h_ : protocols::frag_picker::quota::TorsionBinPool
• max_heavy_hydrogen_cutoff_ : core::scoring::etable::Etable
• max_heavyatom_depth_ : core::scoring::trie::RotamerTrie< AT, CPDATA >
• max_helix_fraction_ : protocols::simple_filters::AbinitioBaseFilter
• max_helix_length_ : protocols::simple_filters::AbinitioBaseFilter
• MAX_HPATCH_AREA : core::pack::interaction_graph::SurfacePotential
• MAX_HPATCH_SCORE : core::pack::interaction_graph::SurfacePotential
• max_hphobes_ : core::pack::interaction_graph::HPatchNode< V, E, G >
• max_hydrogen_hydrogen_cutoff_ : core::scoring::etable::Etable
• max_hydrogen_lj_radius_ : core::scoring::etable::Etable , core::scoring::etable::MembEtable
• max_inner_cycles_ : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• max_inter_ss_bbrms_ : protocols::loophash::LoopHashDiversifier
• max_intra_ss_bbrms_ : protocols::loophash::LoopHashDiversifier
• max_iter_ : core::optimization::MinimizerOptions
• max_iterations_ : protocols::protein_interface_design::movers::LoopOver
• max_k48_cter_dist_ : protocols::ub_e2c::ubi_e2c_modeler
• max_kic_build_attempts_ : protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC
• max_l_ : protocols::frag_picker::quota::TorsionBinPool
• max_length_ : protocols::frag_picker::scores::PCS_FragDistance , protocols::protein_interface_design::movers::LoopFinder , protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• max_levels_ : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• max_lib_size_ : protocols::loophash::MPI_LoopHashRefine
• max_linear_chainbreak_ : protocols::fldsgn::BluePrintBDR , protocols::forge::components::BDR , protocols::forge::components::VarLengthBuild , protocols::forge::remodel::RemodelLoopMover , protocols::forge::remodel::RemodelMover
• max_loop_length_ : protocols::features::LoopAnchorFeatures
• max_loop_rebuild : protocols::comparative_modeling::LoopRelaxThreadingMover
• max_loop_size_ : protocols::loophash::FastGapMover , protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• max_loophash_per_structure_ : protocols::loophash::MPI_LoopHashRefine_Master
• max_memory_pose_num_ : protocols::swa::rna::StepWiseRNA_Clusterer
• max_neighbors_ : protocols::match::NumNeighborsMPM
• max_noe_distance_ : protocols::noesy_assign::CrossPeakInfo
• max_non_hydrogen_lj_radius_ : core::scoring::etable::Etable , core::scoring::etable::MembEtable
• max_nstr : protocols::simple_filters::SheetFilter
• max_nstruct_ : protocols::jd2::archive::ArchiveBase , protocols::loophash::LoopHashMoverWrapper , protocols::loophash::LoopHashSampler
• max_nstruct_list_ : protocols::abinitio::IterativeBase
• max_O_N_dis_ : protocols::features::strand_assembly::StrandBundleFeatures
• max_orbital_dist_squared_ : core::scoring::orbitals::OrbitalsScore
• max_out_queue_size_ : protocols::wum::MPI_Relax
• max_outgoing_wu_mem : protocols::wum2::StatusRequest
• max_overlap_dis_ : protocols::match::output::UpstreamDownstreamCollisionFilter
• max_packet_size_ : protocols::moves::UDPSocketClient
• MAX_PATCH_SURFACE_AREA : core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfacePotential
• max_penalty_ : protocols::simple_filters::ResidueIEFilter
• max_population_size_ : protocols::genetic_algorithm::GeneticAlgorithm
• max_pos_ : core::fragment::FragSet
• max_pose_data_list_size_ : protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer
• max_radius_ : protocols::hotspot_hashing::LSMSearchPattern , protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashMoverWrapper , protocols::loophash::LoopHashSampler
• max_rama_score_increase_ : protocols::loops::loop_closure::ccd::CcdLoopClosureMover
• max_rand_ : protocols::frag_picker::scores::ScoreEValuator
• max_registry_shift_ : protocols::hybridization::ChunkTrialMover , protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol
• max_registry_shift_input_ : protocols::hybridization::ChunkTrialMover
• max_repeats_ : protocols::ub_e2c::ubi_e2c_modeler , protocols::symmetric_docking::SymDockProtocol
• max_repulsion_energy_ : protocols::flxbb::InterlockAroma
• max_residue_count_ : protocols::simple_filters::ResidueCountFilter
• max_rms_ : protocols::loophash::FastGapMover , protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashMoverWrapper , protocols::loophash::LoopHashSampler
• max_rmsd_after_relax_ : protocols::frag_picker::nonlocal::NonlocalFrags
• max_rot_bumpenergy_ : core::pack::rotamer_set::BumpSelector
• max_rotbump_energy_ : core::pack::task::PackerTask_
• max_sample_iterations_ : protocols::loops::loop_closure::kinematic_closure::KinematicPerturber
• MAX_SAMPLE_ITS_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• max_seglen_ : protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC , protocols::loops::loop_mover::refine::LoopMover_Refine_KIC
• max_seq_sep_ : protocols::constraints_additional::ConstraintEvaluator , protocols::constraints_additional::MaxSeqSepConstraintSet
• max_seq_sep_fudge_ : protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints
• max_sheet_dis_ : protocols::features::strand_assembly::StrandBundleFeatures
• max_sheet_torsion_ : protocols::features::strand_assembly::StrandBundleFeatures
• max_sims_per_pt_ : protocols::cluster::APCluster
• max_small_angle_ : protocols::simple_moves::oop::OopRandomSmallMover
• max_strand_dist_cutoff_ : core::scoring::SecondaryStructureWeights
• max_strand_size_ : protocols::features::strand_assembly::StrandBundleFeatures
• max_struct_ : protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashMoverWrapper , protocols::loophash::LoopHashSampler
• max_struct_per_radius_ : protocols::loophash::LoopHashMoverWrapper , protocols::loophash::LoopHashSampler
• max_surface_deltaE_last_50_commits_ : core::pack::interaction_graph::SurfaceEdge< V, E, G > , core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G >
• max_surface_deltaE_recent_50_commits_ : core::pack::interaction_graph::SurfaceEdge< V, E, G > , core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G >
• MAX_SURFACE_ENERGY : core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfacePotential
• max_swap_buffer_size_ : protocols::wum::WorkUnitQueue_Swapped
• max_threads_ : protocols::frag_picker::FragmentPicker
• max_total_delta_helix_ : protocols::loops::loop_closure::ccd::CcdLoopClosureMover
• max_total_delta_loop_ : protocols::loops::loop_closure::ccd::CcdLoopClosureMover
• max_total_delta_strand_ : protocols::loops::loop_closure::ccd::CcdLoopClosureMover
• max_trials_ : protocols::enzdes::DiversifyStoredRBConfs
• max_tries_ : protocols::moves::FilterMover , protocols::simple_moves::DME_FilterMover
• max_type_ : protocols::noesy_assign::PeakCalibrator
• max_type_direct_ : protocols::noesy_assign::PeakCalibrator
• max_weight_ : protocols::optimize_weights::WeightRangeConstraint
• maxatoms_ : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• maxcycles_ : protocols::moves::IteratedConvergenceMover
• maxd2 : core::scoring::etable::EtableParamsOnePair
• maxDist : core::coarse::CoarseEtable
• maxID : core::coarse::CoarseEtable
• maxLen_ : protocols::pockets::PocketGrid
• MAXNEIGH : core::scoring::FACTSResidueInfo
• maxouteriterations : core::pack::annealer::SimAnnealerBase
• maxPockSize_ : protocols::pockets::PocketGrid
• maxtrials_ : protocols::simple_moves::GenericMonteCarloMover
• maxType : core::coarse::CoarseEtable
• maxX : protocols::pockets::PCluster
• maxY : protocols::pockets::PCluster
• maxZ : protocols::pockets::PCluster
• maxz_ : core::scoring::ResidualDipolarCoupling
• Mbhbond_ : core::scoring::hbonds::HBondOptions
• mc_ : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio , protocols::antibody2::H3PerturbCCD , protocols::antibody2::H3RefineCCD , protocols::antibody2::SnugDock , protocols::canonical_sampling::CanonicalSamplingMover , protocols::docking::DockingHighResLegacy , protocols::docking::DockingLowRes , protocols::docking::DockingProtocol , protocols::docking::DockMCMCycle , protocols::docking::DockMinMover , protocols::flexpep_docking::FlexPepDockingAbInitio , protocols::flexpep_docking::FlexPepDockingLowRes , protocols::flexpep_docking::FlexPepDockingProtocol , protocols::loops::loop_closure::ccd::LoopClosure , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::LoopRebuild , protocols::moves::CanonicalSamplingMover , protocols::moves::MCShowMover , protocols::moves::RampingMover , protocols::moves::MonteCarloUtil , protocols::moves::TrialMover , protocols::rbsegment_relax::RBSegmentRelax , protocols::relax::ClassicRelax , protocols::simple_moves::rational_mc::RationalMonteCarlo , protocols::simple_moves::EnergyCutRotamerTrialsMinMover , protocols::simple_moves::EnergyCutRotamerTrialsMover , protocols::simple_moves::symmetry::SymEnergyCutRotamerTrialsMover , protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockingLowRes , protocols::symmetric_docking::SymDockProtocol
• mc_accepted_ : protocols::moves::MonteCarlo , protocols::simple_moves::GenericMonteCarloMover
• mc_created : protocols::LoopRebuild
• mc_cycles_ : protocols::seeded_abinitio::SegmentHybridizer
• mc_filter_ : protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockRbTrialMover , protocols::symmetric_docking::SymFoldandDockRbTrialMover
• mc_kt_ : protocols::enzdes::BackboneSampler , protocols::protein_interface_design::movers::BackrubDDMover
• mc_kt_high_ : protocols::enzdes::EnzdesFlexBBProtocol
• mc_kt_low_ : protocols::enzdes::EnzdesFlexBBProtocol
• MC_mover_ : protocols::simple_moves::MonteCarloRecover , protocols::simple_moves::MonteCarloTest
• mc_temp : protocols::simple_moves::ShakeStructureMover
• mca_history_size_ : core::pack::task::PackerTask_
• mcfi_ : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• mcfi_lists_ : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• mcfis_ : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList
• mcfis_for_restype_ : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList
• mcm_cycles : protocols::flexpep_docking::FlexPepDockingFlags
• mean1_ : core::scoring::constraints::SoedingFunc
• mean2_ : core::scoring::constraints::SoedingFunc
• mean_ : core::chemical::AddChiRotamer , core::scoring::constraints::GaussianFunc , core::scoring::dna::DNA_BasePotential , protocols::ddg::ddGMover
• means_ : core::scoring::constraints::SOGFunc_Impl , core::scoring::constraints::USOGFunc , core::scoring::disulfides::Cb_Distance_Func
• measure_sp3acc_BAH_from_hvy_ : core::scoring::hbonds::HBondOptions
• median_ : core::pack::dunbrack::BBIndNRChiSample< P > , protocols::filters::ReplicateFilter
• median_rms_ : protocols::cluster::ClusterBase
• medium_fast_ : protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler , protocols::swa::rna::StepWiseRNA_ResidueSampler
• mem_cbeta_2TM_den12_ : core::scoring::MembranePotential
• mem_cbeta_2TM_den6_ : core::scoring::MembranePotential
• mem_cbeta_4TM_den12_ : core::scoring::MembranePotential
• mem_cbeta_4TM_den6_ : core::scoring::MembranePotential
• mem_cbeta_den12_ : core::scoring::MembranePotential
• mem_cbeta_den6_ : core::scoring::MembranePotential
• mem_env_log10_ : core::scoring::MembranePotential , core::scoring::methods::MembraneEnvSmoothEnergy
• mem_env_log6_ : core::scoring::MembranePotential
• mem_pair_log_ : core::scoring::MembranePotential
• memb_center_search_ : core::scoring::MembranePotential
• memb_dsolv1_ : core::scoring::etable::MembEtable , core::scoring::methods::Fa_MbsolvEnergy
• memb_dsolv2_ : core::scoring::etable::MembEtable , core::scoring::methods::Fa_MbsolvEnergy
• memb_dsolv_ : core::scoring::etable::BaseEtableEnergy< Derived >
• memb_etable_ : core::scoring::methods::Fa_MbenvEnergy , core::scoring::methods::Fa_MbsolvEnergy
• memb_etables_ : core::scoring::ScoringManager
• memb_lk_dgfree_ : core::scoring::etable::MembEtable
• memb_lk_dgrefce_ : core::scoring::etable::MembEtable , core::scoring::methods::Fa_MbenvEnergy
• memb_normal_search_ : core::scoring::MembranePotential
• memb_potential_ : core::scoring::hbonds::HBondEnergy
• memb_solv1_ : core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::etable::MembEtable , core::scoring::methods::Fa_MbsolvEnergy
• memb_solv2_ : core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::etable::MembEtable , core::scoring::methods::Fa_MbsolvEnergy
• Membed_init_ : core::scoring::MembranePotential
• member : protocols::cluster::Cluster
• member_ : core::scoring::constraints::SOGFunc
• member_atoms_ : core::scoring::constraints::MultiConstraint
• member_constraints_ : core::scoring::constraints::MultiConstraint
• member_residues_ : core::scoring::constraints::MultiConstraint
• membrane_center_magnitude_ : core::scoring::MembranePotential
• membrane_center_max_delta_ : core::scoring::MembranePotential
• membrane_fapotential_ : core::scoring::ScoringManager
• membrane_jumps_ : protocols::abinitio::AbrelaxApplication
• membrane_normal_cycles_ : core::scoring::MembranePotential
• membrane_normal_delta_angle_ : core::scoring::MembranePotential
• membrane_normal_magnitude_ : core::scoring::MembranePotential
• membrane_normal_max_angle_ : core::scoring::MembranePotential
• membrane_normal_start_angle_ : core::scoring::MembranePotential
• membrane_potential_ : core::scoring::Membrane_FAPotential , core::scoring::ScoringManager
• memory_limit_ : protocols::wum::WorkUnitQueue , protocols::wum::WorkUnitQueue_Swapped
• memory_max_for_rpes_ : core::pack::interaction_graph::DoubleLazyInteractionGraph
• memory_offset_ : protocols::canonical_sampling::mc_convergence_checks::TransferBuffer , protocols::canonical_sampling::mc_convergence_checks::DataBuffer
• Menv_penalties_ : core::scoring::MembranePotential
• message_ : core::pack::task::ResfileReaderException
• method_creator_map_ : core::scoring::ScoringManager
• method_weights_ : core::scoring::methods::EnergyMethodOptions
• methods_by_score_type_ : core::scoring::ScoreFunction
• methyl_names_ : protocols::noesy_assign::MethylNameLibrary
• metric_ : protocols::simple_filters::PoseMetricEvaluator< T >
• metric_calculators_ : core::pose::metrics::PoseMetricContainer
• metric_value_getters_ : protocols::multistate_design::MultiStateFitnessFunction
• metric_value_map_ : protocols::multistate_design::SingleStateEntityData
• metric_value_template_ : protocols::toolbox::pose_metric_calculators::MetricValueGetter
• metrics_ : core::pose::Pose
• metropolis_hastings_mover_ : protocols::simple_moves::sidechain_moves::SidechainMCMover
• mg_calculation_annotated_sequence_ : core::scoring::rna::RNA_ScoringInfo
• mid_dist_ : protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential
• mid_pos_ : protocols::fldsgn::topology::SS_Base
• middle_offset_ : protocols::swa::protein::StepWiseProteinLoopBridger
• middle_pack_min_ : protocols::antibody2::AntibodyModelerProtocol
• middle_res_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::swa::protein::StepWiseProteinLoopBridger
• might_be_designing_ : core::scoring::rna::RNA_PairwiseLowResolutionEnergy
• min0_ : core::scoring::hbonds::FadeInterval
• min_ : core::id::DOF_ID_Range , core::id::TorsionID_Range , core::scoring::constraints::EtableFunc , protocols::ddg::ddGMover
• min_aa_probability_ : protocols::toolbox::task_operations::SeqprofConsensusOperation
• min_after_repack_ : protocols::loops::loop_mover::refine::LoopMover_Refine_KIC
• min_all_jumps_ : protocols::enzdes::EnzdesBaseProtocol
• min_angle_ : protocols::rigid::RollMover
• min_atoms_ : protocols::backrub::BackrubMover
• min_base_relax_ : protocols::antibody::CDRH3Modeler
• min_bb_ : protocols::enzdes::EnzRepackMinimize , protocols::protein_interface_design::movers::PrepackMover , protocols::simple_moves::DesignRepackMover
• min_bb_set_ : protocols::simple_moves::DesignRepackMover
• min_bbrms_ : protocols::loophash::LoopHashMoverWrapper , protocols::loophash::LoopHashSampler
• min_bin_ : protocols::scoring::methods::saxs::PDDFEnergy
• min_breakout_fast_loops_ : protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure
• min_breakout_good_loops_ : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• MIN_C_SIZE_LIMIT : core::chemical::carbohydrates::CarbohydrateInfo
• min_cav_ball_radius : core::scoring::packstat::SasaOptions
• min_chi_ : protocols::MakeRotLib::RotData
• min_client_rank_ : protocols::jd2::MPIFileBufJobDistributor
• min_cluster_overlap : core::scoring::packstat::SasaOptions
• min_com_vector_ang_cos_ : protocols::match::NumNeighborsMPM
• min_contacts_per_res_ : protocols::frag_picker::nonlocal::NonlocalFrags
• min_contribution_symmetric_peaks_ : protocols::noesy_assign::PeakAssignmentParameters
• min_cst : protocols::simple_moves::ShakeStructureMover
• min_cst_ : protocols::ddg::ddGMover
• min_cst_mut_types_ : protocols::ddg::ddGMover
• min_cst_set_mut_ : protocols::ddg::ddGMover
• min_cst_set_wt_ : protocols::ddg::ddGMover
• min_cst_sfxn_ : protocols::ddg::ddGMover
• min_cst_sfxn_no_cst_weight_ : protocols::ddg::ddGMover
• min_cst_wt_types_ : protocols::ddg::ddGMover
• min_cycles_ : protocols::seeded_abinitio::SegmentHybridizer
• min_decoys_for_statistics_ : protocols::jd2::archive::NormalizedEvaluatedArchive
• min_dis : core::scoring::etable::Etable , core::scoring::etable::MembEtable
• min_dis2 : core::scoring::etable::Etable , core::scoring::etable::MembEtable
• min_dis2_ : core::scoring::hackelec::HackElecEnergy
• min_dis_ : core::scoring::hackelec::HackElecEnergy
• min_dis_score_ : core::scoring::hackelec::HackElecEnergy
• min_dist_ : protocols::features::AtomAtomPairFeatures , protocols::noesy_assign::FragsToAtomDist::DistanceRecord
• min_diversity_list_ : protocols::abinitio::IterativeBase
• min_edge_count : core::kinematics::FoldTree
• min_env_energy_ : protocols::flxbb::InterlockAroma
• min_epsilon_ : protocols::MakeRotLib::RotData
• min_error_ : core::optimization::GA_Minimizer
• min_fast_loops_ : protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure
• min_frag_length_ : protocols::simple_moves::ClassicFragmentMover
• min_good_loops_ : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• min_hbonds_ : protocols::swa::RigidBodySampler
• min_hole_radius : core::scoring::packstat::SasaOptions
• min_inter_ss_bbrms_ : protocols::loophash::LoopHashDiversifier
• min_interacting_set_fraction_ : protocols::features::helixAssembly::HelixBundleFeatures
• min_intra_ss_bbrms_ : protocols::loophash::LoopHashDiversifier
• min_length_ : protocols::protein_interface_design::movers::LoopFinder , protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• min_lig_ : protocols::enzdes::EnzRepackMinimize
• min_loop_length_ : protocols::features::LoopAnchorFeatures , protocols::jumping::JumpSelector
• min_loop_size_ : protocols::comparative_modeling::MultiThreadingMover , protocols::domain_assembly::AssembleLinkerMover , protocols::loophash::FastGapMover , protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure , protocols::comparative_modeling::ThreadingMover , protocols::topology_broker::RigidChunkClaimer
• min_map : protocols::cartesian::MolecularDynamics
• min_map_ : core::optimization::AtomTreeMultifunc , core::optimization::CartesianMultifunc
• min_move_ : protocols::abinitio::FoldConstraints
• min_movemap_ : protocols::dna::DnaInterfacePacker
• min_mover_ : protocols::relax::ClassicRelax , protocols::symmetric_docking::SymDockingHiRes
• min_nb_ : protocols::simple_moves::AddCavitiesMover
• min_neighbors_ : protocols::match::NumNeighborsMPM
• MIN_NUM_CONTACTS_ : protocols::swa::RigidBodySampler
• min_num_south_ribose_filter_ : protocols::swa::rna::StepWiseRNA_Clusterer
• min_O_N_dis_ : protocols::features::strand_assembly::StrandBundleFeatures
• min_occ_energy_ : core::scoring::geometric_solvation::DatabaseOccSolEne
• min_omega_ : protocols::MakeRotLib::RotData
• min_only : protocols::flexpep_docking::FlexPepDockingFlags
• min_options_ : protocols::simple_moves::MinMover , protocols::simple_moves::SaneMinMover , protocols::loops::loop_mover::refine::ShearMinCCDTrial
• min_orb_dist_enum_map_ : core::scoring::orbitals::OrbitalsScore
• min_overlap_ : protocols::simple_moves::ClassicFragmentMover
• min_params : protocols::relax::CentroidRelax::parameters
• min_params_ : core::scoring::packing::HolesEnergy
• min_per_residue_fa_attr_ : protocols::features::helixAssembly::HelixBundleFeatures
• min_pos_ : core::fragment::FragSet
• min_rb_ : protocols::enzdes::EnzRepackMinimize , protocols::simple_moves::DesignRepackMover
• min_rb_set_ : protocols::simple_moves::DesignRepackMover
• min_receptor_bb : protocols::flexpep_docking::FlexPepDockingFlags
• min_residue_count_ : protocols::simple_filters::ResidueCountFilter
• min_rms_ : protocols::enzdes::MinimizeStoredRBConfs , protocols::enzdes::DiversifyStoredRBConfs , protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashMoverWrapper , protocols::loophash::LoopHashSampler , protocols::loophash::FastGapMover
• min_sc_ : protocols::simple_moves::DesignRepackMover , protocols::enzdes::EnzRepackMinimize
• min_sc_set_ : protocols::simple_moves::DesignRepackMover
• min_score_ : core::scoring::MinScoreScoreFunction
• min_scorefxn : protocols::simple_moves::ShakeStructureMover
• min_scorefxn_ : protocols::hybridization::CartesianHybridize , protocols::seeded_abinitio::SegmentHybridizer
• min_sep_ : protocols::simple_moves::AddCavitiesMover
• min_sep_d2_from_upstream_atoms_ : protocols::match::downstream::RigidLigandBuilder , protocols::match::downstream::LigandConformerBuilder
• min_seq_sep_ : protocols::frag_picker::nonlocal::NonlocalFrags , protocols::simple_moves::AddConstraintsToCurrentConformationMover
• min_seq_separation_ : protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator
• min_seqsep_ : protocols::simple_filters::ContactMapEvaluator
• min_sheet_dis_ : protocols::features::strand_assembly::StrandBundleFeatures
• min_sheet_torsion_ : protocols::features::strand_assembly::StrandBundleFeatures
• min_size_ : protocols::simple_moves::AddCavitiesMover
• min_strand_size_ : protocols::features::strand_assembly::StrandBundleFeatures
• min_structures_for_acceptance_statistics_ : protocols::jd2::archive::ArchiveBase
• min_threshold_ : protocols::antibody2::LHRepulsiveRampLegacy
• min_tolerance : protocols::relax::ClassicRelax
• min_tolerance_ : protocols::ub_e2c::ubi_e2c_modeler , protocols::antibody2::CDRsMinPackMin , protocols::antibody2::H3RefineCCD , protocols::docking::DockMCMCycle , protocols::docking::DockMinMover , protocols::swa::protein::StepWiseProteinPoseMinimizer , protocols::docking::DockingHighResLegacy , protocols::symmetric_docking::SymDockingHiRes
• min_type : protocols::relax::ClassicRelax
• min_type_ : core::optimization::MinimizerOptions , protocols::anchored_design::AnchoredPerturbMover , protocols::ub_e2c::ubi_e2c_modeler , protocols::antibody2::CDRsMinPackMin , protocols::antibody2::LHRepulsiveRampLegacy , protocols::antibody2::LHSnugFitLegacy , protocols::docking::DockingHighResLegacy , protocols::docking::DockMCMCycle , protocols::docking::DockMinMover , protocols::rna::RNA_Minimizer , protocols::swa::protein::StepWiseProteinPoseMinimizer , protocols::symmetric_docking::SymDockingHiRes , protocols::relax::RelaxProtocolBase , protocols::anchored_design::AnchoredRefineMover
• min_value_ : protocols::simple_filters::MinValueEvaluator< T >
• min_VC_to_write_ : protocols::noesy_assign::PeakFileFormat_Base
• min_volume_ : protocols::noesy_assign::PeakAssignmentParameters
• min_weight_ : protocols::optimize_weights::WeightRangeConstraint
• mingap_ : protocols::protein_interface_design::movers::LoopFinder
• mini_pose_list_ : protocols::rna::ChunkSet
• minimization_edge_pool_ : core::scoring::MinimizationGraph
• minimization_graph_ : core::scoring::Energies
• minimization_movers_ : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• minimization_repeats_after_placement_ : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• minimization_repeats_before_placement_ : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• minimization_scorefxns_ : protocols::protein_interface_design::movers::MapHotspot
• minimization_type_ : protocols::antibody2::H3RefineCCD
• minimize_ : protocols::dna::DnaInterfacePacker , protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• minimize_all_ : protocols::rna::RNA_HelixAssembler
• minimize_all_ligand_torsions_ : protocols::enzdes::EnzdesBaseProtocol
• minimize_all_rsds_ : protocols::ligand_docking::LigandDockProtocol
• minimize_and_score_sugar_ : protocols::swa::rna::StepWiseRNA_Minimizer
• minimize_backbone_ : protocols::ligand_docking::LigandDockProtocol
• minimize_best_tensor_ : protocols::scoring::methods::pcs::PCS_Energy_parameters_manager
• minimize_best_tensor_stage1_ : protocols::topology_broker::PseudocontactShiftEnergyController
• minimize_best_tensor_stage2_ : protocols::topology_broker::PseudocontactShiftEnergyController
• minimize_best_tensor_stage3_ : protocols::topology_broker::PseudocontactShiftEnergyController
• minimize_best_tensor_stage4_ : protocols::topology_broker::PseudocontactShiftEnergyController
• minimize_bond_angles_ : protocols::relax::RelaxProtocolBase
• minimize_bond_lengths_ : protocols::relax::RelaxProtocolBase
• minimize_bondangle_subset_ : protocols::relax::RelaxProtocolBase
• minimize_bondlength_subset_ : protocols::relax::RelaxProtocolBase
• minimize_cats_ : protocols::enzdes::EnzdesFlexBBProtocol
• minimize_dna_ : protocols::motifs::MotifDnaPacker
• minimize_in_stages_ : protocols::enzdes::EnzRepackMinimize
• minimize_ligand_ : protocols::ligand_docking::LigandArea , protocols::ligand_docking::LigandDockProtocol
• minimize_ligand_chis_ : core::pack::RTMin
• minimize_ligand_jumps_ : core::pack::RTMin
• minimize_ligand_torsions_ : protocols::enzdes::EnzdesBaseProtocol
• minimize_options_ : protocols::dna::DnaInterfacePacker
• minimize_prot_jumps_ : protocols::enzdes::EnzRepackMinimize
• minimize_structure_ : protocols::rna::RNA_DeNovoProtocol
• minimize_tolerance_ : core::optimization::GA_Minimizer , core::optimization::MinimizerOptions
• minimize_toward_stub_ : protocols::protein_interface_design::movers::PlaceOnLoop
• minimize_trial_ : protocols::docking::DockMinMover
• minimize_water_ : protocols::ligand_docking::LigandDockProtocol , protocols::ligand_docking::MoveMapBuilder
• minimizer_ : protocols::flexpep_docking::FlexPepDockingAbInitio , protocols::loops::loop_mover::refine::ShearMinCCDTrial , protocols::loops::loop_mover::refine::SmallMinCCDTrial , protocols::star::StarAbinitio , protocols::flexpep_docking::FlexPepDockingLowRes
• minimizer_dofs_after_minimization_ : protocols::optimize_weights::IterativeOptEDriver
• minimizer_dofs_before_minimization_ : protocols::optimize_weights::IterativeOptEDriver
• minimizer_dofs_mixed_ : protocols::optimize_weights::IterativeOptEDriver
• minimizer_options_ : protocols::loops::loop_mover::refine::SmallMinCCDTrial
• minimum_width_ : protocols::cluster::EnsembleConstraints_Simple
• miniPose_ : protocols::jumping::ResiduePairJump
• minlen : protocols::hybridization::TMalign
• minmover_ : protocols::docking::SidechainMinMover , protocols::symmetric_docking::SymSidechainMinMover , protocols::simple_moves::TaskAwareMinMover
• MINMULT : core::scoring::electron_density::ElectronDensity
• minPockSize_ : protocols::pockets::PocketGrid
• minScoreAllowed_ : protocols::frag_picker::scores::DisulfideIdentity , protocols::frag_picker::scores::ProlinePhiScore , protocols::frag_picker::scores::RamaScore , protocols::frag_picker::scores::SequenceIdentity , protocols::frag_picker::scores::BFactor
• mintype_ : protocols::grafting::AnchoredGraftMover
• minX : protocols::pockets::PCluster
• minY : protocols::pockets::PCluster
• minZ : protocols::pockets::PCluster
• mismatch_score_ : core::sequence::SimpleScoringScheme
• missing_pt_ : protocols::pockets::DarcParticleSwarmMinimizer , protocols::pockets::FingerprintMultifunc
• mixing_factor_ : protocols::optimize_weights::IterativeOptEDriver
• mixture_param_ : core::scoring::constraints::MixtureFunc
• mm : protocols::cartesian::MolecularDynamics
• mm_ : protocols::simple_moves::ConstrainToIdealMover , protocols::swa::protein::StepWiseProteinCCD_Closer , protocols::protein_interface_design::movers::PrepackMover , protocols::seeded_abinitio::SegmentHybridizer
• mm_atom_pair_atr_deriv_table_ : core::scoring::mm::MMLJEnergyTable
• mm_atom_pair_atr_energy_table_ : core::scoring::mm::MMLJEnergyTable
• mm_atom_pair_atr_three_bond_deriv_table_ : core::scoring::mm::MMLJEnergyTable
• mm_atom_pair_atr_three_bond_energy_table_ : core::scoring::mm::MMLJEnergyTable
• mm_atom_pair_rep_deriv_table_ : core::scoring::mm::MMLJEnergyTable
• mm_atom_pair_rep_energy_table_ : core::scoring::mm::MMLJEnergyTable
• mm_atom_pair_rep_three_bond_deriv_table_ : core::scoring::mm::MMLJEnergyTable
• mm_atom_pair_rep_three_bond_energy_table_ : core::scoring::mm::MMLJEnergyTable
• mm_atom_set_ : core::scoring::mm::MMBondAngleLibrary , core::scoring::mm::MMLJLibrary , core::scoring::mm::MMBondLengthLibrary , core::scoring::mm::MMTorsionLibrary
• mm_atom_type_ : core::chemical::Adduct
• mm_atom_type_index_ : core::chemical::Atom
• mm_atom_type_name_ : core::chemical::SetMMAtomType , core::chemical::AddAtom , core::chemical::Adduct
• mm_atom_type_set_tag_ : core::chemical::ResidueLoaderOptions
• mm_atom_type_sets_ : core::chemical::ChemicalManager
• mm_atom_types_ : core::chemical::ResidueType
• mm_bondangle_library_ : protocols::branch_angle::BranchAngleOptimizer , core::scoring::mm::MMBondAngleResidueTypeParamSet , core::scoring::ScoringManager , core::scoring::mm::MMBondAngleScore
• mm_bondlength_library_ : core::scoring::mm::MMBondLengthLibrary , core::scoring::mm::MMBondLengthScore , core::scoring::ScoringManager
• mm_lj_energy_table_ : core::scoring::ScoringManager
• mm_lj_library_ : core::scoring::mm::MMLJLibrary , core::scoring::ScoringManager , core::scoring::mm::MMLJScore
• mm_lj_score_ : core::scoring::mm::MMLJEnergyTable
• mm_lj_three_bond_library_ : core::scoring::mm::MMLJLibrary
• mm_name_ : core::chemical::Atom
• mm_torsion_library_ : core::scoring::mm::MMTorsionScore , core::scoring::ScoringManager
• mm_type_ : core::conformation::Atom
• mmt_ : protocols::simple_moves::TorsionDOFMover
• mnx_ : core::scoring::packstat::Octree2D
• mny_ : core::scoring::packstat::Octree2D
• mod_segment_prod_ : protocols::fldsgn::MatchResidues
• mode_ : protocols::moves::MonteCarloUtil , protocols::toolbox::task_operations::SelectBySASAOperation , protocols::enzdes::ValueEvaluator , protocols::rosetta_scripts::ParsedProtocol
• mode_tokens_ : core::pack::task::ResidueLevelTask_
• model_and_remove_capping_residues_ : protocols::rna::RNA_HelixAssembler
• model_count : protocols::boinc::BoincSharedMemory
• model_count_ : protocols::canonical_sampling::TrajectoryRecorder
• model_h3_ : protocols::antibody2::AntibodyModelerProtocol , protocols::antibody::AntibodyModeler
• model_low_energy : protocols::boinc::BoincSharedMemory
• model_low_energy_rmsd : protocols::boinc::BoincSharedMemory
• model_weight_ : protocols::abinitio::PairingStatistics
• models_ : protocols::abinitio::PairingStatEntry
• models_per_file_ : protocols::contact_map::ContactMap
• modeltag : core::io::pdb::FileData
• modeltag_ : core::pose::PDBInfo
• modifiable_ : protocols::moves::ResId
• modify_after_jump_ : protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• modify_before_jump_ : protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• modify_was_successful_ : protocols::forge::build::BuildManager
• mol_data_ : core::chemical::sdf::ctabV2000Parser , core::chemical::sdf::CtabBase , core::chemical::ResidueType , core::chemical::sdf::MolFileParser , core::chemical::sdf::ctabV3000Parser
• mol_data_map_ : core::chemical::sdf::MolData
• mol_file_lines_ : core::chemical::sdf::MolFileParser
• mol_file_map_ : core::chemical::sdf::SDFParser
• molar_mass_ : core::chemical::ResidueType
• molecular_mass_ : core::chemical::ResidueType
• molecule : core::scoring::sc::Atom
• molecule_comments_ : core::chemical::sdf::MolFileParser
• molecule_container_ : core::chemical::sdf::CtabBase , core::chemical::sdf::ctabV2000Parser , core::chemical::sdf::MolFileParser , core::chemical::sdf::ctabV3000Parser , core::chemical::sdf::atomTyper
• molecule_info_ : core::chemical::sdf::MolFileParser
• molecule_map_ : core::chemical::sdf::SDFParser
• molecule_name_ : core::chemical::sdf::MolFileParser
• molecule_name_vector_ : core::chemical::sdf::SDFParser
• moltenres_2_flexseg_ : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• moltenres_2_resid_ : protocols::flexpack::rotamer_set::FlexbbRotamerSets , core::pack::rotamer_set::RotamerSubsets , core::pack::rotamer_set::RotamerSets , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
• moltenres_for_rotamer_ : protocols::flexpack::rotamer_set::FlexbbRotamerSets , core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubsets
• moltenres_for_sample_rot_ : core::pack::rotamer_set::ContinuousRotamerSets
• moltenres_sample_rot_offset_ : core::pack::rotamer_set::ContinuousRotamerSets
• moltenresid_2_resid_ : core::pack::scmin::AtomTreeCollection , core::pack::rotamer_set::ContinuousRotamerSets
• monoub_all_dof_map_ : protocols::ub_e2c::ubi_e2c_modeler
• monoub_ctr_of_mass_ : protocols::ub_e2c::ubi_e2c_modeler
• monoub_docking_map_ : protocols::ub_e2c::ubi_e2c_modeler
• monoub_end_ : protocols::ub_e2c::ubi_e2c_modeler
• monoub_flex_cter_map_ : protocols::ub_e2c::ubi_e2c_modeler
• monoub_mode_ : protocols::ub_e2c::ubi_e2c_modeler
• monte_carlo_ : protocols::rna::RNA_DeNovoProtocol , protocols::canonical_sampling::TemperatureController , protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::canonical_sampling::MetropolisHastingsMover
• monte_carlo_cycles_ : protocols::rna::RNA_DeNovoProtocol , protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• monte_carlo_cycles_max_default_ : protocols::rna::RNA_DeNovoProtocol
• monteCarlo_ : protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::FullatomRelaxMover
• more_ancient_ptr : core::pack::interaction_graph::history_queue_struct
• more_precise_base_pair_classification_ : core::scoring::rna::RNA_LowResolutionPotential
• more_recent_ptr : core::pack::interaction_graph::history_queue_struct
• motif_cuts : protocols::simple_filters::SymmetricMotifFilter
• motif_forward_ : protocols::motifs::IRCollection
• motif_library_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• motif_search_ : protocols::motifs::MotifDnaPacker , protocols::enzdes::AddLigandMotifRotamers
• motif_source_ : protocols::motifs::IRCollection
• motifAtomIDs : protocols::motifs::Motif
• motifcop_ : protocols::motifs::MotifHit
• movable_ : protocols::nonlocal::BiasedFragmentMover , protocols::nonlocal::SingleFragmentMover , protocols::nonlocal::Chunk
• movable_jumps_ : protocols::toolbox::task_operations::InterfaceTaskOperation , protocols::docking::RigidBodyInfo , protocols::docking::DockingHighRes , protocols::rigid::RigidBodyPerturbNoCenterMover , protocols::docking::DockMCMCycle , protocols::rigid::RigidBodyPerturbMover , protocols::symmetric_docking::SymDockProtocol , protocols::docking::DockSetupMover , protocols::docking::TemperedDocking , protocols::docking::DockingInitialPerturbation , protocols::docking::DockingLowRes , protocols::docking::DockingProtocol , protocols::docking::DockingHighResFilter
• move_distance : protocols::ligand_docking::Transform_info
• move_first_rigid_body_ : protocols::rna::RNA_Minimizer , protocols::rna::RNA_DeNovoProtocol
• move_jumps_between_chains_ : protocols::swa::protein::StepWiseProteinPoseMinimizer
• move_map_ : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• move_map_list_ : protocols::swa::rna::StepWiseRNA_Minimizer
• move_map_torsion_id_map_ : core::kinematics::MoveMap
• move_takeoff_torsions_ : protocols::swa::protein::StepWiseProteinPoseMinimizer
• move_tolerance_sqr_ : core::scoring::NeighborList
• moved_ : core::pack::interaction_graph::SimpleNode , core::scoring::EnergyNode
• movemap_ : protocols::flexpep_docking::FlexPepDockingProtocol , protocols::loops::loop_closure::ccd::CcdLoopClosureMover , protocols::symmetric_docking::SymDockingHiRes , protocols::abinitio::MembraneAbinitio , protocols::docking::DockingLowRes , protocols::symmetric_docking::SymSidechainMinMover , protocols::flexpep_docking::FlexPepDockingAbInitio , protocols::simple_moves::BackboneMover , protocols::docking::SidechainMinMover , protocols::flxbb::FlxbbDesign , protocols::grafting::GraftMoverBase , protocols::antibody2::CloseOneCDRLoop , protocols::floppy_tail::FloppyTailMover , protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure , protocols::topology_broker::FragmentClaimer , protocols::simple_moves::SaneMinMover , protocols::simple_moves::BBGaussianMover , protocols::loops::loop_closure::ccd::LoopClosure , protocols::simple_moves::FragmentMover , protocols::rbsegment_relax::CCDMoveWrapper , protocols::relax::CentroidRelax , protocols::antibody2::LHRepulsiveRamp , protocols::relax::RelaxProtocolBase , protocols::loops::loop_closure::ccd::CcdMover , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::rbsegment_relax::AutoRBMover , protocols::LoopRebuild , protocols::seeded_abinitio::SeedSetupMover , protocols::simple_moves::carbohydrates::RingConformationMover , protocols::flexpep_docking::FlexPepDockingLowRes , protocols::docking::DockMCMProtocol , protocols::loops::loop_closure::kinematic_closure::KinematicPerturber , protocols::abinitio::KinematicControl , protocols::docking::DockingHighResLegacy , protocols::simple_moves::MinMover , protocols::docking::DockMinMover , protocols::symmetric_docking::SymDockingLowRes , protocols::docking::DockMCMCycle , protocols::abinitio::ClassicAbinitio
• movemap_builder_ : protocols::ligand_docking::FinalMinimizer , protocols::ligand_docking::HighResDocker
• movemap_cen_all_ : protocols::anchored_design::AnchorMoversData
• movemap_fa_all_ : protocols::anchored_design::AnchorMoversData
• movemap_from_blueprint_ : protocols::flxbb::FlxbbDesign
• movemap_lesstail_ : protocols::floppy_tail::FloppyTailMover
• movemap_minimizer_ : protocols::flexpep_docking::FlexPepDockingProtocol
• movemap_reset_ : protocols::docking::DockMCMProtocol
• movemap_tag_ : protocols::relax::FastRelax
• moveMapOP_ : protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::FullatomRelaxMover
• mover_ : protocols::moves::RampingMover , protocols::topology_broker::FragmentClaimer , protocols::rotamer_recovery::RRProtocolMover , protocols::simple_moves::GenericMonteCarloMover , protocols::moves::WhileMover , protocols::protein_interface_design::movers::SubroutineMover , protocols::moves::RepeatMover , protocols::flxbb::DesignTask , protocols::simple_moves::rational_mc::RationalMonteCarlo , protocols::comparative_modeling::RecoverSideChainsMover , protocols::protein_interface_design::movers::LoopOver , protocols::moves::TrialMover , protocols::seeded_abinitio::PlaceFragments
• mover_creator_map_ : protocols::moves::MoverFactory
• mover_list_ : protocols::wum::MoverList
• mover_mc_trial_count : protocols::boinc::BoincSharedMemory
• mover_stopping_condition_ : protocols::simple_moves::GenericMonteCarloMover
• mover_tag_ : protocols::protein_interface_design::movers::Splice , protocols::topology_broker::FragmentClaimer , protocols::simple_moves::GenericMonteCarloMover
• mover_type_text : protocols::boinc::BoincSharedMemory
• movers_ : protocols::canonical_sampling::MetropolisHastingsMover , protocols::moves::CyclicMover , protocols::moves::MoverContainer , protocols::rosetta_scripts::ParsedProtocol , protocols::moves::CompositionMover
• moveset_phase1_ : protocols::relax::ClassicRelax
• moveset_phase2_ : protocols::relax::ClassicRelax
• moveset_phase3_ : protocols::relax::ClassicRelax
• moving_atoms_ : core::optimization::CartesianMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap
• moving_dofids_ : core::optimization::CartesianMinimizerMap
• moving_pos_ : protocols::swa::StepWiseJobParameters
• moving_res : protocols::swa::rna::FloatingBaseChainClosureJobParameter
• moving_res_ : protocols::swa::RigidBodySampler , protocols::swa::rna::StepWiseRNA_JobParameters , protocols::topology_broker::AsymFoldandDockClaimer , protocols::swa::rna::StepWiseRNA_JobParameters_Setup
• moving_res_base_state : protocols::swa::rna::FloatingBaseChainClosureJobParameter
• moving_res_contact_dist_cutoff_ : protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer
• moving_res_list_ : protocols::swa::rna::StepWiseRNA_JobParameters_Setup , protocols::swa::monte_carlo::SubToFullInfo , protocols::swa::StepWisePoseSetup
• moving_res_pucker_state : protocols::swa::rna::FloatingBaseChainClosureJobParameter
• moving_res_to_base_contact_only_ : protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer
• moving_residue_array_ : protocols::swa::protein::StepWiseProteinPoseSetup
• moving_residues_ : protocols::swa::StepWiseResidueSampler , protocols::swa::protein::StepWiseProteinPacker , protocols::swa::StepWiseScreener , protocols::swa::rna::StepWiseRNA_BaseCentroidScreener , protocols::swa::protein::StepWiseProteinScreener , protocols::swa::protein::StepWiseProteinResidueSampler , protocols::swa::protein::StepWiseProteinPoseMinimizer , protocols::swa::protein::StepWiseProteinCCD_Closer , protocols::swa::protein::StepWiseProteinPoseSetup
• moving_suite_ : protocols::swa::rna::StepWiseRNA_RotamerGenerator , protocols::swa::rna::RNA_LoopCloseSampler , protocols::swa::rna::RNA_AnalyticLoopCloser
• moving_suite_list_ : protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper
• moving_torsionids_ : core::optimization::CartesianMinimizerMap
• MPI_bcast_ : protocols::moves::CanonicalSamplingMover , protocols::canonical_sampling::CanonicalSamplingMover
• mpi_channel_ : protocols::jd2::SingleFileBuffer
• mpi_feedback_ : protocols::loophash::MPI_LoopHashRefine
• mpi_master_save_score_only_ : protocols::loophash::MPI_LoopHashRefine_Master
• mpi_metropolis_temp_ : protocols::loophash::MPI_LoopHashRefine
• MPI_nprocs_ : protocols::optimize_weights::IterativeOptEDriver
• mpi_nprocs_ : protocols::optimize_weights::OptEMultifunc
• MPI_nprocs_ : protocols::pmut_scan::PointMutScanDriver , protocols::pack_daemon::MPIMultistateFitnessFunction
• MPI_rank_ : protocols::optimize_weights::IterativeOptEDriver
• mpi_rank_ : protocols::optimize_weights::OptEMultifunc
• MPI_rank_ : protocols::pmut_scan::PointMutScanDriver
• mpi_resume_ : protocols::loophash::MPI_LoopHashRefine
• MPI_synchronize_pools_ : protocols::moves::CanonicalSamplingMover , protocols::canonical_sampling::CanonicalSamplingMover
• ms_whenfail_ : protocols::protein_interface_design::movers::LoopOver , protocols::moves::FilterMover
• msa_ : core::scoring::packstat::PackingScoreResData
• mseq_ : protocols::hybridization::DDomainParse
• msg_tag : protocols::jd2::archive::MPIArchiveJobDistributor::CompletionMessage
• mu0_ : core::scoring::methods::BBIndepCartBondedParameters
• multi_cool_annealer_ : core::pack::task::PackerTask_
• multi_relative_ : protocols::simple_filters::Operator
• multichain_constructor_ : protocols::analysis::InterfaceAnalyzerMover
• multicomp_ : protocols::simple_filters::ShapeComplementarityFilter
• multifunc_ : protocols::optimize_weights::WrappedOptEExpressionCreator , protocols::optimize_weights::WrapperOptEMultifunc
• multiple_domain_mover_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• multiple_jumps_ : protocols::docking::DockingInitialPerturbation
• MultiplicitiveFactor_ : core::scoring::FACTSPotential
• multiplier_ : protocols::inputter::FastaInputter , protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler , protocols::inputter::PDBInputter , protocols::optimize_weights::PNatLigPoseOptEData , protocols::swa::rna::StepWiseRNA_ResidueSampler , protocols::inputter::SilentFileInputter
• multiply_over_all_ : protocols::inputter::SilentFileInputter , protocols::inputter::PDBInputter , protocols::inputter::FastaInputter
• multistate_packer_ : protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover , protocols::dna::DnaInterfaceMultiStateDesign
• mus_spline_ : core::scoring::methods::BBDepCartBondedParameters
• mut_aa_ : protocols::optimize_weights::DDGMutationOptEData , protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover
• mut_residue_ : protocols::pmut_scan::MutationData
• mut_unfolded_energies_emap_ : protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData
• mutant_complexes_ : protocols::optimize_weights::DDGBindOptEData
• mutant_components_ : protocols::ddg::ddGMover
• mutant_unbound_components_ : protocols::ddg::ddGMover
• mutant_unbounds_ : protocols::optimize_weights::DDGBindOptEData
• mutants_ : protocols::ddg::ddGMover
• mutants_list_ : protocols::pmut_scan::PointMutScanDriver
• mutants_list_file_ : protocols::pmut_scan::PointMutScanDriver
• mutate_rate_ : protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover , protocols::dna::DnaInterfaceMultiStateDesign
• mutate_to_glycine_ : protocols::simple_moves::RepulsiveOnlyMover
• mutation_ddGs_ : core::io::PositionDdGInfo::PositionDdGInfo
• mutation_probability_ : core::optimization::GA_Minimizer
• mutation_rate_ : protocols::genetic_algorithm::EntityRandomizer
• mutation_threshold_ : protocols::protein_interface_design::filters::SequenceRecoveryFilter
• mutations_ : protocols::optimize_weights::DDGBindOptEData , protocols::pmut_scan::Mutant , protocols::protein_interface_design::filters::SequenceRecoveryFilter
• muts_ : protocols::optimize_weights::DDGMutationOptEData
• mxr_ : core::scoring::packstat::Octree2D
• mxx_ : core::scoring::packstat::Octree2D
• mxy_ : core::scoring::packstat::Octree2D
• my_AA_ : core::coarse::Rule
• my_constraints_ : protocols::ligand_docking::ResidueTorsionRestraints
• my_csts_ : core::scoring::constraints::BigBinConstraint
• my_emperor_ : protocols::loophash::MPI_LoopHashRefine_Master , protocols::wum::DatabaseQueryWorkUnitManager< T >
• my_filter_ : protocols::moves::FilterMover
• my_frag_id_ : core::fragment::FragID_Iterator
• my_hits_for_target_hit_map_ : protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• my_master_ : protocols::wum::MPI_WorkUnitManager_Slave
• my_mover_ : protocols::moves::FilterMover , protocols::simple_moves::DME_FilterMover
• my_provider_ : protocols::frag_picker::VallChunk
• my_rank_ : protocols::jd2::MpiFileBuffer
• my_window_ : protocols::viewer::ConformationViewer