- 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::func::CircularSigmoidalFunc
• m_AtomTypesByDecreasingStability : core::chemical::gasteiger::PossibleAtomTypesForAtom
• m_done_all : protocols::simple_moves::TailsScoreMover
• m_FinalizeFunction : core::chemical::gasteiger::PossibleAtomTypesForAtom
• m_hill_size : protocols::simple_moves::TailsScoreMover
• m_number_of_hill_points : protocols::simple_moves::TailsScoreMover
• m_NumberAtomTypesWithHybridization : core::chemical::gasteiger::PossibleAtomTypesForAtom
• m_NumberConjugatedTypes : core::chemical::gasteiger::PossibleAtomTypesForAtom
• m_Temperature : protocols::relax::ClassicRelax
• m_Temperature_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::LoopRebuild
• 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::abinitio::abscript::StructPerturberCM , protocols::kinematic_closure::perturbers::WalkingBondAnglePerturber , protocols::kinematic_closure::perturbers::WalkingPerturber , protocols::rbsegment_relax::SequenceShiftMover , protocols::simple_moves::sidechain_moves::PerturbChiSidechainMover
• magnitude_last_surface_deltaE_ : core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G > , core::pack::interaction_graph::SurfaceEdge< V, E, G >
• main_chain_torsion_set_ : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer
• main_chain_torsion_set_for_moving_residues_ : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• main_chain_torsion_set_lists_ : protocols::stepwise::sampler::protein::ProteinMainChainStepWiseSampler
• main_chain_torsion_set_save_ : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer
• main_chain_torsion_sets_ : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_MultiPoseCloser
• main_chain_torsion_sets_for_moving_residues_ : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger , protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• main_group_ : core::chemical::Element
• main_mover_ : protocols::simple_moves::ChangeAndResetFoldTreeMover
• main_task_factory_ : protocols::backrub::BackrubProtocol
• mainchain_atoms_ : core::chemical::ResidueType
• mainchain_atoms_indices_ : 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
• maintain_cap_ : protocols::simple_moves::RepeatPropagationMover
• make_bundle_ : protocols::helical_bundle::BundleGridSampler
• make_bundle_helix_movers_ : protocols::helical_bundle::MakeBundle
• make_movie_ : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• make_pymol_script_ : protocols::flxbb::LayerDesignOperation
• make_rasmol_format_file_ : core::select::util::SelectResiduesByLayer
• MALARKEY : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• manager : protocols::forge::remodel::RemodelWorkingSet
• 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_ : core::fragment::MapCacheUnit< T > , core::id::CacheableAtomID_MapVector , core::scoring::constraints::ResidueConstraints , core::scoring::EMapVector , protocols::comparative_modeling::StealSideChainsMover , protocols::noesy_assign::ResonanceList
• map_BB_to_DOF_ : protocols::ncbb::SecStructMinimizeMultiFunc
• map_cst_from_centroid_to_fa_ : protocols::abinitio::ResolutionSwitcher
• map_DOF_to_BB_ : protocols::ncbb::SecStructMinimizeMultiFunc
• map_DOF_to_NM_ : protocols::normalmode::NormalModeMultifunc
• map_from_reference_ : protocols::toolbox::AtomID_Mapper
• map_helix_pairings_ : protocols::fldsgn::topology::HelixPairingSet
• map_is_clean_ : core::sequence::AnnotatedSequence
• map_name_ : protocols::qsar::qsarMap
• map_NM_to_DOF_ : protocols::normalmode::NormalModeMultifunc
• 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_reference_ : protocols::toolbox::AtomID_Mapper
• map_type_ : core::scoring::cryst::PhenixInterface , protocols::cryst::SetRefinementOptionsMover
• map_var_to_DOF_ : protocols::normalmode::NormalModeMultifunc
• map_var_to_modeno_ : protocols::normalmode::NormalModeMultifunc
• mapfile_ : protocols::cryst::LoadDensityMapMover
• mapfile_activated_ : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• mapout_ : protocols::electron_density::VoxelSpacingRefinementMover
• mapping_ : core::id::SequenceMapping , core::io::pose_from_sfr::GeometricRenameIsomorphismCallback , core::scoring::constraints::SequenceProfileConstraint , protocols::abinitio::Template , protocols::simple_moves::symmetry::NCSResMapping
• mapreso_ : core::scoring::electron_density::ElectronDensityOptions
• maps_ : protocols::frag_picker::scores::ABEGO_SS_Score
• markpsp_ : protocols::pockets::PocketGrid
• marksps_ : protocols::pockets::PocketGrid
• mask_ : protocols::electron_density::ReportFSC , protocols::electron_density::ScaleMapIntensities
• mask_output_ : protocols::electron_density::ScaleMapIntensities
• mask_reses_ : protocols::electron_density::SetupForDensityScoringMover
• maskbits_ : core::scoring::sasa::LeGrandSasa
• masks_ : core::scoring::sasa::LeGrandSasa
• mass : protocols::cartesian::CartesianAtom
• mass_ : core::chemical::ResidueType , protocols::md::MDBase
• mass_limit_ : protocols::ligand_docking::MolarMassFilter , protocols::ligand_docking::MolecularMassFilter
• master_ : core::conformation::ConformationKinWriter , core::conformation::ResidueKinWriter , protocols::match::Bool3DGridKinemageWriter , protocols::match::output::ResidueKinemageWriter , protocols::match::output::SingleDownstreamResidueWriter , protocols::match::output::WriteUpstreamHitKinemage
• master_mover_ : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• master_node_ : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD
• master_packer_ : protocols::stepwise::modeler::StepWiseConnectionSampler , protocols::stepwise::modeler::StepWiseModeler
• master_rank_ : protocols::jd2::MPIFileBufJobDistributor , protocols::loophash::MPI_LoopHashRefine_Master , protocols::mpi_refinement::MPI_Refine_Master
• master_weight_ : protocols::toolbox::pose_metric_calculators::EnergiesData
• masters_done_ : protocols::mpi_refinement::MPI_Refine_Emperor
• match_aa1_ : core::scoring::motif::ResPairMotifQuery
• match_aa2_ : core::scoring::motif::ResPairMotifQuery
• match_algorithm_ : protocols::match::output::WriteUpstreamCoordinateKinemage
• match_chi_rmsd_ : core::scoring::motif::ResPairMotifQuery
• match_groups_ : protocols::match::output::MatchConsolidator
• match_groups_dshits_ : protocols::match::output::CloudPDBWriter
• match_groups_ushits_ : protocols::match::output::CloudPDBWriter
• match_index : core::indexed_structure_store::FragmentLookupResult
• match_names_ : protocols::match::output::MatchScoreWriter
• match_params_ : protocols::enzdes::SecondaryMatchProtocol
• match_positions_ : protocols::match::MatcherMover
• match_processing_successful_ : protocols::match::output::MatchProcessor
• match_radius_ : core::scoring::motif::ResPairMotifQuery
• match_rmsd : core::indexed_structure_store::FragmentLookupResult
• match_rmsd_threshold : core::indexed_structure_store::FragmentLookupResult
• match_rt_limit_ : protocols::denovo_design::DisulfidizeMover
• match_score : core::indexed_structure_store::FragmentLookupResult
• match_score_ : core::sequence::SimpleScoringScheme
• match_score_writer_ : protocols::match::output::MatchProcessor
• match_scores_ : protocols::match::output::MatchScoreWriter
• match_segments_ : protocols::sewing::AppendAssemblyMover
• match_ss1_ : core::scoring::motif::ResPairMotifQuery
• match_ss2_ : core::scoring::motif::ResPairMotifQuery
• matchCount : protocols::sparta::Sparta::SpartaLib
• matched_residues_ : protocols::sewing::SewResidue
• 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_finalized_ : core::scoring::bin_transitions::BinTransitionData
• matrix_G : protocols::simple_moves::BBGaussianMover
• matrix_initialized_ : core::scoring::bin_transitions::BinTransitionData
• max0_ : core::scoring::hbonds::FadeInterval
• max_ : core::id::DOF_ID_Range , core::id::TorsionID_Range , core::scoring::func::EtableFunc , protocols::simple_filters::RepeatParameterFilter
• max_abs_inter_strand_dihedral_to_not_be_same_direction_strands_ : protocols::features::strand_assembly::SandwichFeatures
• max_allowed_conserved_pos_mutations_ : protocols::simple_filters::ConservedPosMutationFilter
• max_angle_ : protocols::rigid::RollMover , protocols::simple_filters::AngleToVector , protocols::simple_moves::RandomTorsionMover
• max_angle_dev_ : protocols::membrane::FlipMover
• 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 , protocols::backrub::BackrubProtocol
• max_atoms_per_rotamer_ : core::scoring::trie::RotamerTrie< AT, CPDATA >
• max_attempts_ : protocols::loop_modeling::LoopBuilder , protocols::rosetta_scripts::MultipleOutputWrapper
• 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_buried_sasa_ : protocols::toolbox::task_operations::CrystalContactsOperation
• MAX_C_SIZE_LIMIT : core::chemical::carbohydrates::CarbohydrateInfo
• max_CA_CA_dis_ : protocols::features::strand_assembly::SandwichFeatures
• max_ca_dis2_ : core::scoring::motif::ResPairMotifQuery
• max_cache_size_ : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• max_capacity_ : 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::antibody::H3PerturbCCD
• max_chainbreak_ : protocols::analysis::LoopAnalyzerMover
• max_chi_ : core::io::silent::ProteinSilentStruct_Template< T >
• max_chi_considered_ : protocols::rotamer_recovery::RRComparerChiDiff
• max_chunk_size_ : protocols::frag_picker::scores::GunnCostScore
• max_cluster_size_ : protocols::pose_selectors::ClusterPoseSelector
• max_clusters_ : protocols::pose_selectors::ClusterPoseSelector
• 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_contig_insertion_ : protocols::hybridization::CartesianHybridize , protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol
• max_coord_ : protocols::canonical_sampling::HamiltonianExchange
• max_cst_seq_sep_ : core::scoring::methods::CustomAtomPairEnergy
• max_cycle_ : protocols::antibody::ModelCDRH3
• max_cycle_close_trial_ : protocols::antibody::H3RefineCCD
• max_cycles_ : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• max_ddg_score_ : protocols::frag_picker::nonlocal::NonlocalFrags
• max_decoys_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::modeler::align::StepWiseClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased , protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• max_del_grid : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• max_dis : core::scoring::etable::EtableOptions
• max_dis2_ : core::scoring::carbon_hbonds::CarbonHBondEnergy , core::scoring::etable::coulomb::Coulomb , core::scoring::etable::Etable
• max_dis_ : core::scoring::carbon_hbonds::CarbonHBondEnergy , core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy , core::scoring::etable::coulomb::Coulomb , core::scoring::etable::Etable , core::scoring::methods::FACTSEnergy , core::scoring::methods::GoapEnergy , core::scoring::methods::LK_PolarNonPolarEnergy
• 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_sq_ : protocols::denovo_design::DisulfidizeMover
• max_dist_squared_ : core::scoring::orbitals::OrbitalsScore , protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker
• max_distance_ : protocols::hotspot_hashing::LSMSearchPattern , protocols::simple_moves::AddConstraintsToCurrentConformationMover , protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange , protocols::toolbox::KClusterElement
• max_distance_squared_ : protocols::stepwise::modeler::StepWiseConnectionSampler , protocols::stepwise::screener::CentroidDistanceScreener , protocols::stepwise::screener::StubDistanceScreener
• max_disulf_score_ : protocols::denovo_design::DisulfidizeMover
• max_disulfides_ : protocols::denovo_design::DisulfidizeMover
• max_e_contribution_to_pi_system_ : core::chemical::gasteiger::GasteigerAtomTypeData
• max_E_in_extracted_sw_loop_ : protocols::features::strand_assembly::SandwichFeatures
• max_edges_per_node_ : protocols::sewing::GreedyAssemblyMover
• max_emperor_lib_round_ : protocols::loophash::MPI_LoopHashRefine_Emperor , protocols::mpi_refinement::MPI_Refine_Emperor
• max_ending_loop_size_ : protocols::features::strand_assembly::SandwichFeatures
• max_env_enrichment_ : core::scoring::dna::DNA_EnvPairPotential
• max_flanking_residues_ : protocols::sewing::LoophashAssemblyMover
• max_frag_length_ : core::fragment::FragSet
• max_frag_size_ : protocols::farna::movers::RNA_Relaxer , protocols::frag_picker::FragmentPicker
• max_gaplength_to_model_ : protocols::hybridization::MRMover
• max_generations_ : protocols::genetic_algorithm::GeneticAlgorithmBase
• max_H_in_extracted_sw_loop_ : protocols::features::strand_assembly::SandwichFeatures
• 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::fldsgn::filters::SecondaryStructureCountFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter , 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_input_poses_ : protocols::rosetta_scripts::MultiplePoseMover
• max_insertion_rms_ : protocols::sewing::LoophashAssemblyMover
• max_inter_sheet_dis_CA_CA_ : protocols::features::strand_assembly::SandwichFeatures
• max_inter_ss_bbrms_ : protocols::loophash::LoopHashDiversifier
• max_inter_strand_angle_to_not_be_same_direction_strands_ : protocols::features::strand_assembly::SandwichFeatures
• max_intra_ss_bbrms_ : protocols::loophash::LoopHashDiversifier
• max_iter_ : core::optimization::MinimizerOptions , protocols::electron_density::BfactorFittingMover , protocols::electron_density::VoxelSpacingRefinementMover , protocols::relax::LocalRelax , protocols::relax::RelaxProtocolBase
• 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_length_ : protocols::antibody::CDRSetOptions , protocols::frag_picker::scores::PCS_FragDistance , protocols::ncbb::SecStructFinder , protocols::protein_interface_design::movers::LoopFinder , protocols::sewing::sampling::requirements::GlobalLengthRequirement , protocols::sewing::sampling::requirements::SegmentLengthRequirement , protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• max_levels_ : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• max_lib_size_ : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• max_linear_chainbreak_ : protocols::fldsgn::BluePrintBDR , protocols::forge::components::BDR , protocols::forge::components::VarLengthBuild , protocols::forge::remodel::RemodelLoopMover , protocols::forge::remodel::RemodelMover
• max_loop_distance_ : protocols::sewing::LoophashAssemblyMover , protocols::sewing::RehashAssemblyMover
• max_loop_length_ : protocols::features::LoopAnchorFeatures , protocols::fldsgn::filters::SecondaryStructureCountFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter
• max_loop_rebuild : protocols::comparative_modeling::LoopRelaxThreadingMover
• max_loop_segments_to_build_ : protocols::sewing::LoophashAssemblyMover
• 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::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• max_missing_weight_ : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions , protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• max_nbrs_ : core::scoring::dna::DNA_EnvPairPotential
• 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_ntries_ : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_MultiPoseCloser , protocols::stepwise::StepWiseSampleAndScreen
• max_num_strands_to_deal_ : protocols::features::strand_assembly::SandwichFeatures , protocols::features::strand_assembly::StrandBundleFeatures
• max_num_sw_per_pdb_ : protocols::features::strand_assembly::SandwichFeatures
• max_O_N_dis_ : protocols::features::strand_assembly::StrandBundleFeatures
• max_omega_ : protocols::analysis::LoopAnalyzerMover
• max_orbital_dist_squared_ : core::scoring::orbitals::OrbitalsScore
• max_output_poses_ : protocols::rosetta_scripts::MultiplePoseMover
• max_overlap_dis_ : protocols::match::output::UpstreamDownstreamCollisionFilter
• max_packet_size_ : protocols::moves::UDPSocketClient
• max_pair_enrichment_ : core::scoring::dna::DNA_EnvPairPotential
• MAX_PATCH_SURFACE_AREA : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::interaction_graph::SurfacePotential
• max_path_length_ : protocols::simple_filters::AveragePathLengthFilter
• max_pbond_ : protocols::analysis::LoopAnalyzerMover
• max_penalty_ : protocols::simple_filters::ResidueIEFilter
• max_per_move_torsion_delta_ : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• max_population_size_ : protocols::genetic_algorithm::GeneticAlgorithmBase
• max_pos_ : core::fragment::FragSet
• max_pose_data_list_size_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• max_poses_ : protocols::rosetta_scripts::AdditionalOutputWrapper , protocols::rosetta_scripts::MultipleOutputWrapper
• max_radius_ : protocols::hotspot_hashing::LSMSearchPattern , protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashMoverWrapper , protocols::loophash::LoopHashSampler
• max_rama_ : protocols::analysis::LoopAnalyzerMover
• max_rama_score_increase_ : protocols::loops::loop_closure::ccd::RamaCheckBase
• max_rand_ : protocols::frag_picker::scores::ScoreEValuator
• max_range_ : protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler
• max_ref_lib_size_ : protocols::mpi_refinement::MPI_Refinement
• max_registry_shift_ : protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol
• max_registry_shift_global_ : protocols::hybridization::ChunkTrialMover
• max_repeats_ : protocols::symmetric_docking::SymDockProtocol , protocols::ub_e2c::ubi_e2c_modeler
• max_repulsion_energy_ : protocols::flxbb::InterlockAroma
• max_res_in_strand_ : protocols::features::strand_assembly::StrandBundleFeatures
• max_residue_count_ : protocols::simple_filters::ResidueCountFilter
• max_rms_ : protocols::enzdes::ResidueConformerFilter , 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_ROT_ENERGY : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary
• max_rot_num : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary
• max_rot_per_trans_ : protocols::electron_density::DockIntoDensityMover
• max_rotbump_energy_ : core::pack::task::PackerTask_
• max_sample_iterations_ : protocols::loops::loop_closure::kinematic_closure::KinematicPerturber
• max_sample_per_structure_ : protocols::mpi_refinement::MPI_Refine_Master
• max_samples_ : protocols::helical_bundle::BackboneGridSampler , protocols::helical_bundle::BundleGridSampler
• max_seglen_ : protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC , protocols::loops::loop_mover::refine::LoopMover_Refine_KIC
• max_segments_ : protocols::sewing::sampling::requirements::RequirementSet
• max_seq_sep_ : protocols::constraints_additional::ConstraintEvaluator , protocols::constraints_additional::MaxSeqSepConstraintSet
• max_seq_sep_fudge_ : protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints
• max_sheet_angle_ : protocols::features::strand_assembly::StrandBundleFeatures
• max_sheet_angle_by_four_term_cen_res_ : protocols::features::strand_assembly::SandwichFeatures
• max_sheet_angle_with_cen_res_in_smaller_sheet_and_two_terminal_res_in_larger_sheet_ : protocols::features::strand_assembly::SandwichFeatures
• max_sheet_dis_ : protocols::features::strand_assembly::SandwichFeatures , protocols::features::strand_assembly::StrandBundleFeatures
• max_sheet_length_ : protocols::fldsgn::filters::SecondaryStructureCountFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter
• max_sheet_torsion_ : protocols::features::strand_assembly::StrandBundleFeatures
• max_sheet_torsion_cen_res_ : protocols::features::strand_assembly::SandwichFeatures
• max_shift_ : protocols::rbsegment_relax::OptimizeThreadingMover
• max_sims_per_pt_ : protocols::cluster::APCluster
• max_small_angle_ : protocols::simple_moves::a3b_hbs::A3BHbsRandomSmallMover , protocols::simple_moves::oop::OopRandomSmallMover , protocols::simple_moves::triazolamer::TriazolamerRandomSmallMover
• max_ss_cluster_size_ : protocols::features::ModelFeatures
• max_starting_loop_size_ : protocols::features::strand_assembly::SandwichFeatures
• max_strand_dist_cutoff_ : core::scoring::SecondaryStructureWeights
• max_struct_ : protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashMoverWrapper , protocols::loophash::LoopHashSampler , protocols::simple_moves::CombinePoseMover
• max_struct_per_radius_ : protocols::loophash::LoopHashMoverWrapper , protocols::loophash::LoopHashSampler
• max_struct_try_ : protocols::simple_moves::CombinePoseMover
• max_structures_ : protocols::pose_selectors::ClusterPoseSelector
• max_surface_deltaE_last_50_commits_ : core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G > , core::pack::interaction_graph::SurfaceEdge< V, E, G >
• max_surface_deltaE_recent_50_commits_ : core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G > , core::pack::interaction_graph::SurfaceEdge< V, E, G >
• MAX_SURFACE_ENERGY : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::interaction_graph::SurfacePotential
• max_swap_buffer_size_ : protocols::wum::WorkUnitQueue_Swapped
• MAX_TARGETS : protocols::pockets::PocketGrid
• max_temperature_ : protocols::sewing::MonteCarloAssemblyMover
• max_threads_ : protocols::frag_picker::FragmentPicker
• max_total_torsion_delta_ : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• max_trans_ : protocols::topology_broker::RigidBodyRandomTMHMover
• max_trials_ : protocols::enzdes::DiversifyStoredRBConfs
• max_tries_ : protocols::moves::FilterMover , protocols::simple_moves::DME_FilterMover , protocols::stepwise::sampler::rna::RNA_KIC_Sampler
• max_tries_for_random_sugar_setup_ : protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler
• max_tries_multiplier_for_ccd_ : protocols::stepwise::options::StepWiseBasicOptions
• max_type_ : protocols::noesy_assign::PeakCalibrator
• max_type_direct_ : protocols::noesy_assign::PeakCalibrator
• max_value_ : protocols::simple_moves::PSSM2BfactorMover
• max_vdw_change_ : protocols::pose_length_moves::FixAllLoopsMover , protocols::pose_length_moves::NearNativeLoopCloser
• 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
• maxfrac_ : protocols::mpi_refinement::WorkUnit_CombinePose
• maxfrac_crossover_ : protocols::simple_moves::CombinePoseMover
• maxiter_ : protocols::md::Rattle
• maxLen_ : protocols::pockets::PocketGrid
• maxouteriterations : core::pack::annealer::SimAnnealerBase
• maxPockSize_ : protocols::pockets::PocketGrid
• maxsub : core::scoring::TMscoreStore
• maxsub_max : core::scoring::TMscoreStore
• maxsub_sum : core::scoring::TMscoreStore
• maxtrials_ : protocols::simple_moves::GenericMonteCarloMover
• maxX : protocols::pockets::CCluster , protocols::pockets::PCluster
• maxY : protocols::pockets::CCluster , protocols::pockets::PCluster
• maxZ : protocols::pockets::CCluster , protocols::pockets::PCluster
• maxz_ : core::scoring::ResidualDipolarCoupling
• Mbhbond_ : core::scoring::hbonds::HBondOptions
• mc_ : protocols::abinitio::abscript::AbscriptMover , protocols::abinitio::abscript::AbscriptMover::StageTracker , protocols::abinitio::abscript::AbscriptStageMover , protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio , protocols::antibody::design::AntibodyDesignMover , protocols::antibody::GraftedStemOptimizer , protocols::antibody::H3PerturbCCD , protocols::antibody::H3RefineCCD , protocols::antibody::SnugDock , protocols::canonical_sampling::CanonicalSamplingMover , protocols::carbohydrates::GlycanRelaxMover , 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::LoopRebuild , protocols::loops::loop_closure::ccd::LoopClosure , protocols::loops::loop_mover::refine::LoopRefineInnerCycle
• MC_ : protocols::moves::DualMonteCarlo
• mc_ : protocols::moves::MCShowMover , protocols::moves::MonteCarloUtil , protocols::moves::RampingMover , protocols::moves::TrialMover , protocols::rbsegment_relax::RBSegmentRelax , protocols::relax::ClassicRelax , protocols::simple_moves::EnergyCutRotamerTrialsMinMover , protocols::simple_moves::EnergyCutRotamerTrialsMover , protocols::simple_moves::rational_mc::RationalMonteCarlo , 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_initial_pose_ : protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• mc_kt_ : protocols::backrub::BackrubProtocol , 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::MonteCarloReset , protocols::simple_moves::MonteCarloTest
• mc_scorefxn_ : protocols::hybridization::CartesianSampler
• mc_temp : protocols::simple_moves::ShakeStructureMover
• mc_temp_ : protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• 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
• md_energy_report_stepsize_ : protocols::md::MDBase
• md_report_stepsize_ : protocols::md::MDBase
• md_rsr_update_stepsize_ : protocols::md::MDBase
• mdsch_ : protocols::md::MDBase
• mean1_ : core::scoring::func::SoedingFunc
• mean2_ : core::scoring::func::SoedingFunc
• mean_ : core::chemical::AddChiRotamer , core::scoring::dna::DNA_BasePotential , core::scoring::func::GaussianFunc , core::scoring::methods::D2H_SA_Energy , protocols::ddg::ddGMover
• mean_backbone_torsion_ : core::scoring::dna::DNA_DihedralPotential
• mean_sd : core::chemical::carbohydrates::LinkageConformerData
• mean_sugar_torsion_ : core::scoring::dna::DNA_DihedralPotential
• means_ : core::scoring::disulfides::Cb_Distance_Func , core::scoring::func::SOGFunc_Impl , core::scoring::func::USOGFunc
• measure : core::io::CisPeptideInformation
• measure_sp3acc_BAH_from_hvy_ : core::scoring::hbonds::HBondOptions
• median_ : core::pack::dunbrack::BBIndNRChiSample< P > , protocols::filters::ReplicateFilter
• median_rms_ : protocols::cluster::ClusterBase
• mem_cbeta_2TM_den12_ : core::scoring::membrane::MembraneData , core::scoring::MembranePotential
• mem_cbeta_2TM_den6_ : core::scoring::membrane::MembraneData , core::scoring::MembranePotential
• mem_cbeta_4TM_den12_ : core::scoring::membrane::MembraneData , core::scoring::MembranePotential
• mem_cbeta_4TM_den6_ : core::scoring::membrane::MembraneData , core::scoring::MembranePotential
• mem_cbeta_den12_ : core::scoring::membrane::MembraneData , core::scoring::MembranePotential
• mem_cbeta_den6_ : core::scoring::membrane::MembraneData , core::scoring::MembranePotential
• mem_env_log10_ : core::scoring::membrane::FaMPEnvSmoothEnergy , core::scoring::membrane::MembraneData , core::scoring::MembranePotential , core::scoring::methods::MembraneEnvSmoothEnergy
• mem_env_log6_ : core::scoring::membrane::MembraneData , core::scoring::MembranePotential
• mem_from_topo_ : protocols::membrane::MPQuickRelaxMover
• mem_pair_log_ : core::scoring::membrane::MembraneData , core::scoring::MembranePotential
• memb_center_search_ : core::scoring::MembranePotential
• memb_dsolv1_ : core::scoring::etable::MembEtable , core::scoring::membrane::FaMPSolvEnergy , core::scoring::methods::Fa_MbsolvEnergy
• memb_dsolv2_ : core::scoring::etable::MembEtable , core::scoring::membrane::FaMPSolvEnergy , core::scoring::methods::Fa_MbsolvEnergy
• memb_etable_ : core::scoring::membrane::FaMPEnvEnergy , core::scoring::membrane::FaMPSolvEnergy , 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::membrane::FaMPEnvEnergy , core::scoring::methods::Fa_MbenvEnergy
• memb_normal_search_ : core::scoring::MembranePotential
• memb_solv1_ : core::scoring::etable::MembEtable , core::scoring::membrane::FaMPSolvEnergy , core::scoring::methods::Fa_MbsolvEnergy
• memb_solv2_ : core::scoring::etable::MembEtable , core::scoring::membrane::FaMPSolvEnergy , core::scoring::methods::Fa_MbsolvEnergy
• Membed_init_ : core::scoring::MembranePotential
• member : protocols::cluster::Cluster
• member_ : core::scoring::func::SOGFunc
• member_atoms_ : core::scoring::constraints::MultiConstraint
• member_constraints_ : core::scoring::constraints::MultiConstraint
• member_residues_ : core::scoring::constraints::MultiConstraint
• membrane_ : core::import_pose::ImportPoseOptions , protocols::docking::DockingPrepackProtocol
• membrane_center_magnitude_ : core::scoring::MembranePotential
• membrane_center_max_delta_ : core::scoring::MembranePotential
• membrane_fapotential_ : core::scoring::ScoringManager
• membrane_info_ : core::conformation::Conformation
• membrane_jump_ : core::conformation::membrane::MembraneInfo
• 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
• membrane_rsd_ : protocols::membrane::AddMembraneMover
• membrane_rsd_num_ : core::conformation::membrane::MembraneInfo
• 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::DataBuffer , protocols::canonical_sampling::mc_convergence_checks::TransferBuffer
• Menv_penalties_ : core::scoring::MembranePotential
• merge_atom_maps_ : core::io::pose_from_sfr::PoseFromSFRBuilder
• merge_behavior_manager_ : core::chemical::ResidueTypeSet
• merge_behaviors_ : core::chemical::MergeBehaviorManager , core::io::pose_from_sfr::PoseFromSFRBuilder
• meridian_angle_degrees_ : protocols::sewing::Model
• meridian_range_ : protocols::sewing::NodeConstraint
• message_ : protocols::denovo_design::connection::EXCN_ConnectionFailed
• mest_ : core::scoring::disulfides::FullatomDisulfidePotential
• metal_binding_atoms_ : core::chemical::ResidueType
• metal_bond_angle_constraint_multiplier_ : core::import_pose::ImportPoseOptions
• metal_bond_dist_constraint_multiplier_ : core::import_pose::ImportPoseOptions
• metal_bond_LJ_multiplier_ : core::import_pose::ImportPoseOptions
• metal_set_ : core::io::NomenclatureManager
• metal_site_ : protocols::metal_interface::ZincHeterodimerMover
• metal_to_mobile_ : protocols::metal_interface::ZincHeterodimerMover
• metalbinding_constraint_energy_ : core::scoring::constraints::ConstraintEdge
• metapatch_map_ : core::chemical::ResidueTypeSet
• metapatch_names_ : protocols::residue_optimization::MetapatchEnumeration
• metapatches_ : core::chemical::ResidueTypeSet
• method_ : core::scoring::sasa::SasaCalc , protocols::mpi_refinement::Clusterer
• method_creator_map_ : core::scoring::ScoringManager
• method_type_ : core::scoring::sasa::SasaCalc
• method_weights_ : core::scoring::methods::EnergyMethodOptions
• methodname_ : protocols::mpi_refinement::Scheduler
• methods_by_score_type_ : core::scoring::ScoreFunction
• methods_picked_ : protocols::mpi_refinement::Scheduler
• methyl_names_ : protocols::noesy_assign::MethylNameLibrary
• methyl_probe_dist_ : core::scoring::rna::data::RNA_DMS_Potential
• 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
• mg_coord_cst_dist_ : protocols::magnesium::MgMinimizer
• mg_lig_interaction_cutoff_ : core::scoring::magnesium::MgEnergy
• mg_lig_knowledge_based_potential_ : core::scoring::magnesium::MgEnergy
• mg_lj_radius_ : core::scoring::magnesium::MgEnergy
• mg_lk_coeff : core::scoring::magnesium::MgEnergy
• mg_lk_dgfree_ : core::scoring::magnesium::MgEnergy
• mg_lk_lambda_ : core::scoring::magnesium::MgEnergy
• mg_map_ : protocols::denovo_design::components::SolutionSorter
• mg_poses : protocols::magnesium::MgScanner
• mg_poses_ : protocols::magnesium::MgScanner
• mg_ref_score_ : core::scoring::magnesium::MgEnergy
• mg_res_ : protocols::magnesium::MgMinimizer
• mg_res_list_ : protocols::magnesium::MgHydrater , protocols::magnesium::MgWaterHydrogenPacker
• mg_sol_fade_func_ : core::scoring::magnesium::MgEnergy
• mg_sol_fade_zone_ : core::scoring::magnesium::MgEnergy
• mg_sol_interaction_cutoff_ : core::scoring::magnesium::MgEnergy
• mg_water_hydrogen_packer_ : protocols::magnesium::MgHydrater
• mg_water_pairs_ : protocols::magnesium::MgWaterHydrogenPacker
• mh_ : protocols::sic_dock::scores::MotifHashRigidScore
• mid_ : protocols::pockets::PocketGrid
• mid_dist_ : protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential
• mid_pos_ : protocols::fldsgn::topology::SS_Base
• middle_offset_ : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger
• middle_pack_min_ : protocols::antibody::AntibodyModelerProtocol
• middle_res_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger
• midway_dist_ : core::scoring::etable::count_pair::CountPair2B< CrossoverBehavior >
• might_be_designing_ : core::scoring::rna::RNA_PairwiseLowResolutionEnergy , core::scoring::rna::StackElecEnergy
• min0_ : core::scoring::hbonds::FadeInterval
• min_ : core::id::DOF_ID_Range , core::id::TorsionID_Range , core::scoring::func::EtableFunc , protocols::ddg::ddGMover , protocols::simple_filters::RepeatParameterFilter
• min_aa_probability_ : protocols::toolbox::task_operations::SeqprofConsensusOperation
• min_after_repack_ : protocols::loops::loop_mover::refine::LoopMover_Refine_KIC
• min_after_stage1_ : protocols::hybridization::HybridizeProtocol
• min_all_jumps_ : protocols::enzdes::EnzdesBaseProtocol
• min_angle_ : protocols::rigid::RollMover , protocols::simple_filters::AngleToVector
• min_assembly_score_ : protocols::sewing::EnumerateAssemblyMover , protocols::sewing::MonteCarloAssemblyMover
• min_at_end_ : protocols::hybridization::FoldTreeHybridize
• min_atoms_ : protocols::backrub::BackrubMover , protocols::backrub::BackrubProtocol
• min_backbone_ : protocols::electron_density::DockIntoDensityMover
• min_base_relax_ : protocols::antibody_legacy::CDRH3Modeler
• min_bb_ : protocols::enzdes::EnzRepackMinimize , protocols::protein_interface_design::movers::PrepackMover , protocols::simple_moves::DesignRepackMover , protocols::simple_moves::symmetry::TaskAwareSymMinMover
• min_bb_set_ : protocols::simple_moves::DesignRepackMover
• min_bbrms_ : protocols::loophash::LoopHashMoverWrapper , protocols::loophash::LoopHashSampler
• min_bin_ : protocols::scoring::methods::saxs::PDDFEnergy
• min_bpy_contacts_ : protocols::sic_dock::scores::TrisBpyScore
• min_breakout_fast_loops_ : protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure
• min_breakout_good_loops_ : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• min_C_O_N_angle_ : protocols::features::strand_assembly::SandwichFeatures
• MIN_C_SIZE_LIMIT : core::chemical::carbohydrates::CarbohydrateInfo
• min_CA_CA_dis_ : protocols::features::strand_assembly::SandwichFeatures
• min_cav_ball_radius : core::scoring::packstat::SasaOptions
• min_chi_ : protocols::make_rot_lib::RotData , protocols::simple_moves::symmetry::TaskAwareSymMinMover
• 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::relax::RangeRelaxMover , protocols::seeded_abinitio::SegmentHybridizer
• min_decoys_for_statistics_ : protocols::jd2::archive::NormalizedEvaluatedArchive
• min_dis2_ : core::scoring::etable::coulomb::Coulomb , core::scoring::etable::Etable
• min_dis_ : core::scoring::etable::coulomb::Coulomb , core::scoring::etable::Etable
• min_dis_score_ : core::scoring::etable::coulomb::Coulomb
• min_dist_ : protocols::features::AtomAtomPairFeatures , protocols::noesy_assign::FragsToAtomDist::DistanceRecord
• min_dist_squared_ : protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker
• min_distance_grid_ : protocols::magnesium::SampleGrid
• min_disulfides_ : protocols::denovo_design::DisulfidizeMover
• min_diversity_list_ : protocols::abinitio::IterativeBase
• min_edge_count : core::kinematics::FoldTree
• min_env_energy_ : protocols::flxbb::InterlockAroma
• min_env_enrichment_ : core::scoring::dna::DNA_EnvPairPotential
• min_epsilon_ : protocols::make_rot_lib::RotData
• min_error_ : core::optimization::GA_Minimizer
• min_everything_ : protocols::ncbb::SecStructFinder
• min_fast_loops_ : protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure
• min_final_hbonds_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• min_flanking_residues_ : protocols::sewing::LoophashAssemblyMover
• min_frag_length_ : protocols::simple_moves::ClassicFragmentMover
• min_genkic_hbonds_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• min_good_loops_ : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• min_helix_length_ : protocols::fldsgn::filters::SecondaryStructureCountFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter
• min_helix_size_ : protocols::features::helixAssembly::HelixBundleFeatures , protocols::features::ModelFeatures
• min_hole_radius : core::scoring::packstat::SasaOptions
• min_inter_sheet_dis_CA_CA_ : protocols::features::strand_assembly::SandwichFeatures
• min_inter_ss_bbrms_ : protocols::loophash::LoopHashDiversifier
• min_interacting_set_fraction_ : protocols::features::helixAssembly::HelixBundleFeatures
• min_intra_ss_bbrms_ : protocols::loophash::LoopHashDiversifier
• min_len_helix_ : protocols::frags::TorsionFragmentMover
• min_len_strand_ : protocols::frags::TorsionFragmentMover
• min_length_ : protocols::antibody::CDRSetOptions , protocols::ncbb::SecStructFinder , protocols::protein_interface_design::movers::LoopFinder , protocols::sewing::sampling::requirements::GlobalLengthRequirement , protocols::sewing::sampling::requirements::SegmentLengthRequirement , protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• min_lig_ : protocols::enzdes::EnzRepackMinimize
• min_loop_ : protocols::denovo_design::DisulfidizeMover
• min_loop_length_ : protocols::features::LoopAnchorFeatures , protocols::fldsgn::filters::SecondaryStructureCountFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter , protocols::jumping::JumpSelector
• min_loop_size_ : protocols::comparative_modeling::MultiThreadingMover , protocols::comparative_modeling::ThreadingMover , protocols::domain_assembly::AssembleLinkerMover , protocols::loophash::FastGapMover , protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure , protocols::topology_broker::RigidChunkClaimer
• min_map : protocols::cartesian::MolecularDynamics
• min_map_ : core::optimization::AtomTreeMultifunc , core::optimization::CartesianMultifunc , protocols::md::CartesianMD , protocols::ncbb::SecStructMinimizeMultiFunc , protocols::normalmode::NormalModeMultifunc
• min_move_ : protocols::abinitio::FoldConstraints
• min_movemap_ : protocols::dna::DnaInterfacePacker
• min_mover_ : protocols::carbohydrates::GlycanRelaxMover , protocols::relax::ClassicRelax , protocols::symmetric_docking::SymDockingHiRes
• min_N_H_O_angle_between_two_sheets_ : protocols::features::strand_assembly::SandwichFeatures
• min_N_O_dis_between_two_sheets_ : protocols::features::strand_assembly::SandwichFeatures
• min_nb_ : protocols::simple_moves::AddCavitiesMover
• min_neighbor_sc_ : protocols::antibody::design::CDRGraftDesignOptions
• min_neighbors_ : protocols::match::NumNeighborsMPM
• min_num_south_sugar_filter_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• min_num_strands_in_sheet_ : protocols::features::strand_assembly::SandwichFeatures
• min_num_strands_to_deal_ : protocols::features::strand_assembly::SandwichFeatures , protocols::features::strand_assembly::StrandBundleFeatures
• min_O_N_dis_ : protocols::features::strand_assembly::StrandBundleFeatures
• min_occ_energy_ : core::scoring::geometric_solvation::DatabaseOccSolEne
• min_omega_ : protocols::make_rot_lib::RotData
• min_only : protocols::flexpep_docking::FlexPepDockingFlags
• min_options_ : protocols::loop_modeling::refiners::MinimizationRefiner , protocols::loops::loop_mover::refine::ShearMinCCDTrial , protocols::simple_moves::MinMover , protocols::simple_moves::SaneMinMover
• min_orb_dist_enum_map_ : core::scoring::orbitals::OrbitalsScore
• min_overlap_ : protocols::simple_moves::ClassicFragmentMover
• min_pair_enrichment_ : core::scoring::dna::DNA_EnvPairPotential
• 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_primary_seq_distance_diff_for_electrostatic_interactions_ : protocols::features::strand_assembly::SandwichFeatures
• min_rb_ : protocols::antibody::design::CDRGraftDesignOptions , protocols::enzdes::EnzRepackMinimize , protocols::simple_moves::DesignRepackMover , protocols::simple_moves::symmetry::TaskAwareSymMinMover
• min_rb_set_ : protocols::simple_moves::DesignRepackMover
• min_receptor_bb : protocols::flexpep_docking::FlexPepDockingFlags
• min_res_in_strand_ : protocols::features::strand_assembly::SandwichFeatures , protocols::features::strand_assembly::StrandBundleFeatures
• min_residue_count_ : protocols::simple_filters::ResidueCountFilter
• min_rms_ : protocols::enzdes::DiversifyStoredRBConfs , protocols::enzdes::MinimizeStoredRBConfs , protocols::loophash::FastGapMover , protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashMoverWrapper , protocols::loophash::LoopHashSampler
• MIN_ROT_PROB : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary
• min_sc_ : protocols::antibody::design::CDRGraftDesignOptions , protocols::enzdes::EnzRepackMinimize , protocols::simple_moves::DesignRepackMover
• min_sc_set_ : protocols::simple_moves::DesignRepackMover
• min_score_ : core::scoring::MinScoreScoreFunction
• min_scorefxn : protocols::simple_moves::ShakeStructureMover
• min_scorefxn_ : protocols::antibody::design::GeneralAntibodyModeler , protocols::hybridization::CartesianHybridize , protocols::seeded_abinitio::SegmentHybridizer
• min_segments_ : protocols::sewing::sampling::requirements::RequirementSet
• min_sep_ : protocols::simple_moves::AddCavitiesMover
• min_sep_d2_from_upstream_atoms_ : protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder
• min_seq_sep_ : protocols::frag_picker::nonlocal::NonlocalFrags , protocols::simple_moves::AddConstraintsToCurrentConformationMover
• min_seq_separation_ : protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator
• MIN_SEQ_SEPARATIONS : core::scoring::methods::GoapEnergy
• min_seqsep_ : protocols::simple_filters::ContactMapEvaluator
• min_sfxn_ : protocols::relax::LocalRelax
• min_sheet_angle_ : protocols::features::strand_assembly::StrandBundleFeatures
• min_sheet_angle_by_four_term_cen_res_ : protocols::features::strand_assembly::SandwichFeatures
• min_sheet_dis_ : protocols::features::strand_assembly::SandwichFeatures , protocols::features::strand_assembly::StrandBundleFeatures
• min_sheet_length_ : protocols::fldsgn::filters::SecondaryStructureCountFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter
• min_sheet_torsion_ : protocols::features::strand_assembly::StrandBundleFeatures
• min_sheet_torsion_cen_res_ : protocols::features::strand_assembly::SandwichFeatures
• min_shortest_dis_sidechain_inter_sheet_ : protocols::features::strand_assembly::StrandBundleFeatures
• min_size_ : protocols::simple_moves::AddCavitiesMover
• min_solution_count_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• min_ss_cluster_size_ : protocols::features::ModelFeatures
• min_strand_size_ : protocols::features::ModelFeatures
• min_structures_for_acceptance_statistics_ : protocols::jd2::archive::ArchiveBase
• min_temperature_ : protocols::sewing::MonteCarloAssemblyMover
• min_threshold_ : protocols::antibody::LHRepulsiveRampLegacy
• min_tolerance : protocols::relax::ClassicRelax
• min_tolerance_ : protocols::antibody::CDRsMinPackMin , protocols::antibody::H3RefineCCD , protocols::docking::DockingHighResLegacy , protocols::docking::DockMCMCycle , protocols::docking::DockMinMover , protocols::helical_bundle::FitSimpleHelix , protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer , protocols::stepwise::options::StepWiseBasicOptions , protocols::symmetric_docking::SymDockingHiRes , protocols::ub_e2c::ubi_e2c_modeler
• min_type : protocols::relax::ClassicRelax
• min_type_ : core::optimization::MinimizerOptions , protocols::anchored_design::AnchoredPerturbMover , protocols::anchored_design::AnchoredRefineMover , protocols::antibody::CDRsMinPackMin , protocols::antibody::LHRepulsiveRampLegacy , protocols::antibody::LHSnugFitLegacy , protocols::docking::DockingHighResLegacy , protocols::docking::DockMCMCycle , protocols::docking::DockMinMover , protocols::farna::movers::RNA_Minimizer , protocols::helical_bundle::FitSimpleHelix , protocols::relax::RelaxProtocolBase , protocols::simple_moves::symmetry::TaskAwareSymMinMover , protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer , protocols::stepwise::options::StepWiseBasicOptions , protocols::symmetric_docking::SymDockingHiRes , protocols::ub_e2c::ubi_e2c_modeler
• min_type_to_enum_ : protocols::antibody::design::AntibodyDesignEnumManager
• min_type_to_string_ : protocols::antibody::design::AntibodyDesignEnumManager
• min_value_ : protocols::simple_moves::PSSM2BfactorMover
• min_VC_to_write_ : protocols::noesy_assign::PeakFileFormat_Base
• min_volume_ : protocols::noesy_assign::PeakAssignmentParameters
• min_weight_ : protocols::optimize_weights::WeightRangeConstraint
• minfrac_ : protocols::mpi_refinement::WorkUnit_CombinePose
• minfrac_crossover_ : protocols::simple_moves::CombinePoseMover
• mingap_ : protocols::protein_interface_design::movers::LoopFinder
• mini_pose_list_ : protocols::farna::libraries::ChunkSet
• mini_pose_lists_ : protocols::farna::libraries::BasePairStepLibrary
• minimization_edge_pool_ : core::scoring::MinimizationGraph
• minimization_graph_ : core::scoring::Energies
• minimization_mode_ : protocols::helical_bundle::FitSimpleHelixMultiFunc
• minimization_movers_ : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• minimization_rebuild_rounds_ : protocols::simple_moves::CyclizationMover
• 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::antibody::H3RefineCCD
• minimize_ : protocols::dna::DnaInterfacePacker , protocols::magnesium::MgScanner , protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch , protocols::mpi_refinement::StructAvrgMover , protocols::simple_moves::CyclizationMover
• minimize_after_delete_ : protocols::stepwise::monte_carlo::mover::DeleteMover , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• minimize_all_ : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• minimize_all_ligand_torsions_ : protocols::enzdes::EnzdesBaseProtocol
• minimize_all_rsds_ : protocols::ligand_docking::LigandDockProtocol
• minimize_and_score_native_pose_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• minimize_and_score_sugar_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• minimize_backbone_ : protocols::ligand_docking::LigandDockProtocol
• minimize_best_tensor_ : protocols::scoring::methods::pcs::PCS_Energy_parameters_manager , protocols::scoring::methods::pcsTs1::PCS_Energy_parameters_manager_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_parameters_manager_Ts4
• minimize_best_tensor_stage1_ : protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• minimize_best_tensor_stage2_ : protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• minimize_best_tensor_stage3_ : protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• minimize_best_tensor_stage4_ : protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• 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_bps_ : protocols::farna::options::RNA_MinimizerOptions
• minimize_cats_ : protocols::enzdes::EnzdesFlexBBProtocol
• minimize_dna_ : protocols::motifs::MotifDnaPacker
• minimize_during_scoring_ : protocols::magnesium::MgScanner
• minimize_in_stages_ : protocols::enzdes::EnzRepackMinimize
• minimize_jump_ : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• minimize_ligand_ : protocols::ligand_docking::LigandArea , protocols::ligand_docking::LigandDockProtocol
• minimize_ligand_torsions_ : protocols::enzdes::EnzdesBaseProtocol
• minimize_mg_coord_constraint_distance_ : protocols::magnesium::MgScanner
• minimize_options_ : protocols::dna::DnaInterfacePacker
• minimize_prot_jumps_ : protocols::enzdes::EnzRepackMinimize
• minimize_res_ : protocols::stepwise::monte_carlo::mover::TransientCutpointHandler
• minimize_rounds_ : protocols::farna::options::RNA_MinimizerOptions
• minimize_scorefxn_ : protocols::magnesium::MgMinimizer , protocols::stepwise::modeler::StepWiseMinimizer
• minimize_single_res_ : protocols::stepwise::monte_carlo::mover::AddMover , protocols::stepwise::monte_carlo::mover::ResampleMover , protocols::stepwise::monte_carlo::mover::StepWiseMasterMover
• minimize_single_res_frequency_ : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• minimize_structure_ : protocols::farna::options::RNA_FragmentMonteCarloOptions
• 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
• minimized_pose_list_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer
• minimizer_ : protocols::electron_density::BfactorFittingMover , protocols::electron_density::VoxelSpacingRefinementMover , protocols::flexpep_docking::FlexPepDockingAbInitio , protocols::flexpep_docking::FlexPepDockingLowRes , protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionSampler , protocols::loop_modeling::LoopBuilder , protocols::loops::loop_mover::refine::ShearMinCCDTrial , protocols::loops::loop_mover::refine::SmallMinCCDTrial , protocols::star::StarAbinitio , protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• 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 , protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler , protocols::stepwise::modeler::StepWiseMinimizer
• minimizer_rename_tag_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• minimizer_use_coordinate_constraints_ : protocols::farna::options::RNA_MinimizerOptions
• minimum_peak_intensity_ : protocols::noesy_assign::PeakFileFormat_Base
• minimum_width_ : protocols::cluster::EnsembleConstraints_Simple
• minimumB : core::scoring::electron_density::ElectronDensity
• miniPose_ : protocols::jumping::ResiduePairJump
• minlen : protocols::hybridization::TMalign
• minmover_ : protocols::docking::SidechainMinMover , protocols::simple_moves::symmetry::TaskAwareSymMinMover , protocols::simple_moves::TaskAwareMinMover , protocols::symmetric_docking::SymSidechainMinMover
• MINMULT : core::scoring::electron_density::ElectronDensity
• minoption_ : protocols::normalmode::NormalModeRelaxMover
• minPockSize_ : protocols::pockets::PocketGrid
• minscorefxn_ : protocols::hybridization::FoldTreeHybridize
• mintolerance_ : protocols::cyclic_peptide::TryDisulfPermutations
• mintype_ : protocols::antibody::design::CDRGraftDesignOptions , protocols::cyclic_peptide::TryDisulfPermutations , protocols::grafting::AnchoredGraftMover
• minX : protocols::pockets::CCluster , protocols::pockets::PCluster
• minY : protocols::pockets::CCluster , protocols::pockets::PCluster
• minZ : protocols::pockets::CCluster , protocols::pockets::PCluster
• mirror_z_ : core::conformation::symmetry::SymmetryTransform
• mirror_Z_ : core::conformation::symmetry::VirtualCoordinate
• mirror_z_transform : core::kinematics::Jump
• misc1_ : core::scoring::motif::ResPairMotif
• mismatch_probability_ : protocols::denovo_design::filters::SSPredictionFilter
• mismatch_score_ : core::sequence::SimpleScoringScheme
• missing_ : core::io::pose_from_sfr::PoseFromSFRBuilder
• missing_dens_as_jump_ : core::io::StructFileRepOptions
• missing_pt_ : protocols::pockets::DarcParticleSwarmMinimizer , protocols::pockets::FingerprintMultifunc
• missing_weight_ : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• missing_weight_interval_ : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• mixing_factor_ : protocols::optimize_weights::IterativeOptEDriver
• mixture_param_ : core::scoring::func::MixtureFunc
• ml : core::scoring::cryst::XtalMLEnergy
• mm : protocols::cartesian::MolecularDynamics
• mm_ : protocols::cryst::SetCrystWeightMover , protocols::frags::TorsionFragmentMover , protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionSampler , protocols::normalmode::NormalModeRelaxMover , protocols::protein_interface_design::movers::PrepackMover , protocols::residue_optimization::MetapatchEnumeration , protocols::seeded_abinitio::SegmentHybridizer , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer
• mm_atom_set_ : core::scoring::mm::MMBondAngleLibrary , core::scoring::mm::MMBondLengthLibrary , core::scoring::mm::MMLJLibrary , core::scoring::mm::MMTorsionLibrary
• mm_atom_type_index_ : core::chemical::Atom
• mm_atom_type_name_ : core::chemical::AddAtom , core::chemical::Adduct , core::chemical::SetMMAtomType
• mm_atom_type_set_tag_ : core::chemical::ResidueLoaderOptions
• mm_atom_type_sets_ : core::chemical::ChemicalManager
• mm_atom_types_ : core::chemical::ResidueType , core::chemical::ResidueTypeSet
• mm_bondangle_library_ : core::scoring::mm::MMBondAngleResidueTypeParamSet , core::scoring::mm::MMBondAngleScore , core::scoring::ScoringManager , protocols::branch_angle::BranchAngleOptimizer
• 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::mm::MMLJScore , core::scoring::ScoringManager
• 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 , protocols::simple_moves::CyclizationMover
• mm_type_ : core::conformation::Atom
• mman_ : core::scoring::methods::CenPairMotifDegreeEnergy , core::scoring::methods::CenPairMotifEnergy , core::scoring::methods::SSElementMotifContactEnergy , protocols::sewing::scoring::MotifScorer , protocols::simple_filters::MotifScoreFilter , protocols::simple_filters::SSElementMotifContactFilter
• mmt_ : protocols::simple_moves::TorsionDOFMover
• mnx_ : core::scoring::packstat::Octree2D
• mny_ : core::scoring::packstat::Octree2D
• mobile_label_ : protocols::rigid::UniformRigidBodyCM
• mobile_residues_ : protocols::environment::CoMTrackerCM
• mobile_selector_ : protocols::environment::CoMTrackerCM
• mod_segment_prod_ : protocols::fldsgn::MatchResidues
• mode_ : protocols::enzdes::ValueEvaluator , protocols::ligand_docking::ComputeLigandRDF , protocols::matdes::SymUnsatHbondFilter , protocols::moves::MonteCarloUtil , protocols::normalmode::NormalMode , protocols::pose_reporters::RMSDReporter , protocols::rbsegment_relax::MakeStarTopologyMover , protocols::residue_optimization::MetapatchEnumeration , protocols::rosetta_scripts::ParsedProtocol , protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::toolbox::task_operations::SelectBySASAOperation , protocols::toolbox::task_operations::StoreCompoundTaskMover
• mode_lowres_ : protocols::docking::membrane::MPFindInterfaceMover
• mode_scale_ : protocols::normalmode::NormalModeRelaxMover
• mode_tokens_ : core::pack::task::ResidueLevelTask_
• mode_using_ : protocols::normalmode::NormalModeRelaxMover
• model_ : protocols::sewing::ModelNode
• model_and_remove_capping_residues_ : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• model_cdrs_ : protocols::antibody::design::GeneralAntibodyModeler
• model_count : protocols::boinc::BoincSharedMemory
• model_count_ : protocols::canonical_sampling::TrajectoryRecorder
• model_h3_ : protocols::antibody::AntibodyModelerProtocol , protocols::antibody_legacy::AntibodyModeler
• model_id : protocols::sewing::Basis , protocols::sewing::HashValue
• model_id_ : protocols::sewing::Model , protocols::sewing::sampling::requirements::ResidueRetentionRequirement , protocols::sewing::SewSegment
• model_ids_ : protocols::sewing::GivenPathAssemblyMover
• model_indices_ : protocols::sewing::SewGraph
• model_low_energy : protocols::boinc::BoincSharedMemory
• model_low_energy_rmsd : protocols::boinc::BoincSharedMemory
• model_tag_ : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• model_weight_ : protocols::abinitio::PairingStatistics
• modeler_ : protocols::antibody::design::AntibodyDesignMover
• modeler_scorefxn_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection
• models : protocols::sewing::EnumerateAssemblyMover
• models_ : protocols::abinitio::PairingStatEntry , protocols::sewing::AppendAssemblyMover
• models_per_file_ : protocols::contact_map::ContactMap
• modeltag_ : core::io::StructFileRep , core::pose::PDBInfo
• modes_using_ : protocols::normalmode::NormalModeMinimizer , protocols::normalmode::NormalModeMultifunc
• modifiable_ : protocols::moves::ResId
• modifications_ : core::chemical::carbohydrates::CarbohydrateInfo
• modify_after_jump_ : protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• modify_before_jump_ : protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• modify_unselected_residues_ : protocols::toolbox::task_operations::SelectResiduesWithinChainOperation
• modify_was_successful_ : protocols::forge::build::BuildManager
• modres_map_ : core::io::StructFileRep
• molecule : core::scoring::sc::Atom
• molecule_string_data_ : core::chemical::sdf::MolFileIOMolecule
• molgraph_ : core::chemical::sdf::MolFileIOMolecule
• molName : protocols::pockets::SmallMol
• moltenres_2_flexseg_ : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• moltenres_2_resid_ : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubsets , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::flexpack::rotamer_set::FlexbbRotamerSets
• moltenres_for_rotamer_ : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubsets , protocols::flexpack::rotamer_set::FlexbbRotamerSets
• moltenres_for_sample_rot_ : core::pack::rotamer_set::ContinuousRotamerSets
• moltenres_sample_rot_offset_ : core::pack::rotamer_set::ContinuousRotamerSets
• moltenresid : core::pack::annealer::RotSub
• moltenresid_2_resid_ : core::pack::rotamer_set::ContinuousRotamerSets , core::pack::scmin::AtomTreeCollection
• monomer_bump_ : protocols::cryst::DockLatticeMover
• monopole_ : core::scoring::MultipoleElecResidueInfo , core::scoring::MultipoleParameter
• 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::canonical_sampling::MetropolisHastingsMover , protocols::canonical_sampling::TemperatureController , protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::RNA_FragmentMonteCarlo , protocols::loop_modeling::LoopProtocol , protocols::loop_modeling::utilities::AcceptanceCheck , protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::FullatomRelaxMover
• monte_carlo_cycles_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::options::RNA_FragmentMonteCarloOptions , protocols::farna::RNA_FragmentMonteCarlo
• monte_carlo_cycles_max_default_ : protocols::farna::RNA_FragmentMonteCarlo
• 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 : core::scoring::motif::MotifHit , protocols::denovo_design::connection::Connection::ConnectionInfo
• motif_ : protocols::denovo_design::connection::BridgeChains
• motif_cuts : protocols::simple_filters::SymmetricMotifFilter
• motif_forward_ : protocols::motifs::IRCollection
• motif_fragments_RMSD : protocols::motif_grafting::movers::motif2scaffold_data , protocols::motif_grafting::movers::MotifMatch
• motif_hash_BB_BB_ : core::scoring::motif::MotifHashManager
• motif_hash_BB_PH_ : core::scoring::motif::MotifHashManager
• motif_hash_BB_PO_ : core::scoring::motif::MotifHashManager
• motif_hash_SC_BB_ : core::scoring::motif::MotifHashManager
• motif_hash_SC_SC_ : core::scoring::motif::MotifHashManager
• motif_library_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• motif_match_results_ : protocols::motif_grafting::movers::MotifGraftMover
• motif_search_ : protocols::enzdes::AddLigandMotifRotamers , protocols::motifs::MotifDnaPacker
• motif_set_names_ : core::scoring::motif::MotifHashManager
• motif_sets_ : protocols::matdes::SchemePlaceMotifsMover
• motif_source_ : protocols::motifs::IRCollection
• motif_umap_ : core::scoring::motif::MotifHash
• motifAtomIDs : protocols::motifs::Motif
• motifcop_ : protocols::motifs::MotifHit
• motifHigh : protocols::motif_grafting::movers::motif2scaffold_indexes
• motifLow : protocols::motif_grafting::movers::motif2scaffold_indexes
• motifs_ : protocols::denovo_design::connection::Connection
• motifs_by_fname_ : core::scoring::motif::MotifHashManager
• movable_ : protocols::nonlocal::BiasedFragmentMover , protocols::nonlocal::Chunk , protocols::nonlocal::SingleFragmentMover
• movable_group : protocols::denovo_design::components::Segment
• movable_jumps_ : protocols::docking::DockingHighRes , protocols::docking::DockingHighResFilter , protocols::docking::DockingInitialPerturbation , protocols::docking::DockingLowRes , protocols::docking::DockingProtocol , protocols::docking::DockMCMCycle , protocols::docking::DockSetupMover , protocols::docking::RigidBodyInfo , protocols::docking::TemperedDocking , protocols::protein_interface_design::filters::FNatFilter , protocols::protein_interface_design::filters::IRmsdFilter , protocols::protein_interface_design::filters::LRmsdFilter , protocols::rigid::RigidBodyPerturbMover , protocols::rigid::RigidBodyPerturbNoCenterMover , protocols::symmetric_docking::SymDockProtocol , protocols::toolbox::task_operations::InterfaceTaskOperation
• move_ : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• move_apart_first_ : protocols::docking::SlideIntoContact
• move_distance : protocols::ligand_docking::Transform_info
• move_element_ : protocols::stepwise::monte_carlo::mover::StepWiseMove
• move_first_rigid_body_ : protocols::farna::options::RNA_BasicOptions
• move_jump_points_away_ : protocols::stepwise::monte_carlo::mover::TransientCutpointHandler
• move_jumps_between_chains_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer , protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• move_map_ : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::simple_moves::CyclizationMover , protocols::simple_moves::RandomOmegaFlipMover , protocols::simple_moves::RandomTorsionMover , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer , protocols::surface_docking::FullatomRelaxMover
• move_map_torsion_id_map_ : core::kinematics::MoveMap
• move_takeoff_torsions_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer
• move_tolerance_sqr_ : core::scoring::NeighborList
• move_type_ : protocols::stepwise::monte_carlo::mover::StepWiseMove
• move_type_string_ : protocols::stepwise::monte_carlo::mover::StepWiseMasterMover
• moved_ : core::pack::interaction_graph::SimpleNode , core::scoring::EnergyNode , protocols::md::Rattle
• movemap_ : protocols::abinitio::abscript::AbscriptLoopCloserCM , protocols::abinitio::ClassicAbinitio , protocols::abinitio::KinematicControl , protocols::abinitio::MembraneAbinitio , protocols::antibody::CloseOneCDRLoop , protocols::antibody::LHRepulsiveRamp , protocols::carbohydrates::LinkageConformerMover , protocols::docking::DockingHighResLegacy , protocols::docking::DockingLowRes , protocols::docking::DockMCMCycle , protocols::docking::DockMCMProtocol , protocols::docking::DockMinMover , protocols::docking::SidechainMinMover , protocols::flexpep_docking::FlexPepDockingAbInitio , protocols::flexpep_docking::FlexPepDockingLowRes , protocols::flexpep_docking::FlexPepDockingProtocol , protocols::floppy_tail::FloppyTailMover , protocols::flxbb::FlxbbDesign , protocols::grafting::AnchoredGraftMover , protocols::LoopRebuild , protocols::loops::loop_closure::ccd::CCDLoopClosureMover , protocols::loops::loop_closure::ccd::LoopClosure , protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure , protocols::loops::loop_closure::kinematic_closure::KinematicPerturber , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::md::MDBase , protocols::membrane::MPQuickRelaxMover , protocols::normalmode::NormalModeMinimizer , protocols::rbsegment_relax::AutoRBMover , protocols::rbsegment_relax::CCDMoveWrapper , protocols::relax::CentroidRelax , protocols::relax::RangeRelaxMover , protocols::relax::RelaxProtocolBase , protocols::seeded_abinitio::SeedSetupMover , protocols::simple_moves::BackboneMover , protocols::simple_moves::BBDihedralSamplerMover , protocols::simple_moves::BBGaussianMover , protocols::simple_moves::DisulfideInsertionMover , protocols::simple_moves::FragmentMover , protocols::simple_moves::MinMover , protocols::simple_moves::RingConformationMover , protocols::simple_moves::SaneMinMover , protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockingLowRes , protocols::symmetric_docking::SymSidechainMinMover , protocols::toolbox::task_operations::RestrictToMoveMapChiOperation , protocols::topology_broker::FragmentClaimer
• 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_preminimization_ : protocols::backrub::BackrubProtocol
• movemap_reset_ : protocols::docking::DockMCMProtocol
• movemap_residues_ : protocols::carbohydrates::LinkageConformerMover
• movemap_set_ : protocols::toolbox::task_operations::RestrictToMoveMapChiOperation
• movemap_smallmover_ : protocols::backrub::BackrubProtocol
• movemap_tag_ : protocols::relax::FastRelax
• mover_ : core::environment::DofPassport , protocols::abinitio::abscript::FragmentCM , protocols::comparative_modeling::RecoverSideChainsMover , protocols::enzdes::RemoveLigandFilter , protocols::flxbb::DesignTask , protocols::jd3::MoverAndPoseJob , protocols::loop_modeling::samplers::LegacyKicSampler , protocols::loops::loop_mover::LoopCM , protocols::moves::FilterReporterMover , protocols::moves::RampingMover , protocols::moves::RepeatMover , protocols::moves::TrialMover , protocols::moves::WhileMover , protocols::protein_interface_design::movers::LoopOver , protocols::protein_interface_design::movers::SubroutineMover , protocols::rigid::UniformRigidBodyCM , protocols::rosetta_scripts::MultipleOutputWrapper , protocols::rotamer_recovery::RRProtocolMover , protocols::simple_moves::ContingentAcceptMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::rational_mc::RationalMonteCarlo , protocols::topology_broker::FragmentClaimer
• mover_creator_map_ : protocols::moves::MoverFactory
• mover_cycles_ : protocols::loop_modeling::LoopProtocol
• mover_list_ : protocols::wum::MoverList
• mover_mc_trial_count : protocols::boinc::BoincSharedMemory
• mover_stopping_condition_ : protocols::simple_moves::GenericMonteCarloMover
• mover_tag_ : protocols::rosetta_scripts::AdditionalOutputWrapper , protocols::rosetta_scripts::MultipleOutputWrapper , protocols::simple_moves::GenericMonteCarloMover , protocols::topology_broker::FragmentClaimer
• mover_type_text : protocols::boinc::BoincSharedMemory
• moverkey_ : protocols::abinitio::abscript::FragmentJumpCM , protocols::abinitio::abscript::JumpSampleData
• movers_ : protocols::abinitio::abscript::AbscriptStageMover , protocols::canonical_sampling::MetropolisHastingsMover , protocols::environment::EnvMover , protocols::loop_modeling::LoopProtocol , protocols::moves::CompositionMover , protocols::moves::CyclicMover , protocols::moves::MoverContainer , protocols::rosetta_scripts::ParsedProtocol
• movers_and_passes_ : protocols::environment::EnvClaimBroker
• movers_setup_ : protocols::docking::DockingEnsemblePrepackProtocol , protocols::docking::DockingPrepackProtocol
• movertype : protocols::mpi_refinement::MethodParams
• moves_ : protocols::membrane::MPQuickRelaxMover , protocols::relax::RangeRelaxMover
• moveset_phase1_ : protocols::relax::ClassicRelax
• moveset_phase2_ : protocols::relax::ClassicRelax
• moveset_phase3_ : protocols::relax::ClassicRelax
• movie_file_accepted_ : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• movie_file_trial_ : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• moving_atom_name_ : protocols::stepwise::screener::AnchorSugarScreener
• moving_atoms_ : core::optimization::CartesianMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , protocols::electron_density::BfactorMultifunc
• moving_distance_ : protocols::normalmode::NormalModeRelaxMover
• moving_dofids_ : core::optimization::CartesianMinimizerMap
• moving_lattice_ : protocols::cryst::MakeLayerMover
• moving_partition_res_ : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler , protocols::stepwise::modeler::StepWiseConnectionSampler , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler
• moving_phosphate_virtualized_ : protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler
• moving_res : protocols::stepwise::modeler::rna::sugar::SugarModeling
• moving_res_ : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup , protocols::stepwise::modeler::rna::bulge::BulgeApplyMover , protocols::stepwise::modeler::rna::bulge::BulgeUnApplyMover , protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker , protocols::stepwise::modeler::rna::o2prime::O2PrimePacker , protocols::stepwise::modeler::rna::sugar::SugarInstantiateMover , protocols::stepwise::modeler::rna::sugar::SugarVirtualizeMover , protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator , protocols::stepwise::modeler::StepWiseConnectionSampler , protocols::stepwise::modeler::StepWiseModeler , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler , protocols::stepwise::screener::CentroidDistanceScreener , protocols::stepwise::screener::FastForwardToNextResidueAlternative , protocols::stepwise::screener::SugarInstantiator , protocols::stepwise::screener::TagDefinition , protocols::stepwise::screener::VDW_BinScreener , protocols::topology_broker::AsymFoldandDockClaimer
• moving_res_base_state : protocols::stepwise::modeler::rna::sugar::SugarModeling
• moving_res_base_stub_ : protocols::stepwise::modeler::StepWiseConnectionSampler , protocols::stepwise::screener::BaseCentroidScreener , protocols::stepwise::screener::RNA_ChainClosableGeometryStubBasedScreener , protocols::stepwise::screener::StubDistanceScreener , protocols::stepwise::screener::VDW_BinScreener
• moving_res_contact_dist_cutoff_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• moving_res_legacy_ : protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator
• moving_res_list_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup , protocols::stepwise::legacy::screener::SimplePoseSelection , protocols::stepwise::modeler::protein::checker::ProteinAtrRepChecker , protocols::stepwise::modeler::StepWiseConnectionSampler , protocols::stepwise::modeler::StepWiseModeler , protocols::stepwise::screener::AlignRMSD_Screener , protocols::stepwise::screener::PartitionContactScreener
• moving_res_pucker_state : protocols::stepwise::modeler::rna::sugar::SugarModeling
• moving_res_stub_ : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler
• moving_res_to_base_contact_only_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• moving_residue_at_origin_ : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler
• moving_residues_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_MultiPoseCloser , protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler , protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• moving_residues_input_ : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• moving_rsd_at_origin : protocols::stepwise::screener::SampleApplier
• moving_rsd_at_origin_ : protocols::stepwise::screener::RNA_ChainClosableGeometryStubBasedScreener
• moving_rsd_at_origin_list : protocols::stepwise::screener::SampleApplier
• moving_rsd_at_origin_list_ : protocols::stepwise::screener::RNA_ChainClosableGeometryStubBasedScreener
• moving_suite_ : protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser , protocols::stepwise::sampler::rna::RNA_KIC_Sampler , protocols::stepwise::sampler::rna::RNA_KinematicCloser
• moving_torsionids_ : core::optimization::CartesianMinimizerMap
• mp_base_potential_ : core::scoring::ScoringManager
• mp_param_ : core::scoring::MultipoleElecResidueInfo
• mpdata_ : core::scoring::membrane::MPCbetaEnergy , core::scoring::membrane::MPEnvEnergy , core::scoring::membrane::MPLipoEnergy , core::scoring::membrane::MPNonHelixPenalty , core::scoring::membrane::MPPairEnergy , core::scoring::membrane::MPTerminiPenalty , core::scoring::membrane::MPTMProjPenalty
• mphbond_ : core::scoring::hbonds::HBondOptions
• MPI_bcast_ : protocols::canonical_sampling::CanonicalSamplingMover
• mpi_channel_ : protocols::jd2::SingleFileBuffer
• mpi_feedback_ : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• mpi_master_save_score_only_ : protocols::loophash::MPI_LoopHashRefine_Master , protocols::mpi_refinement::MPI_Refine_Master
• mpi_metropolis_temp_ : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• MPI_nprocs_ : protocols::optimize_weights::IterativeOptEDriver
• mpi_nprocs_ : protocols::optimize_weights::OptEMultifunc
• MPI_nprocs_ : protocols::pack_daemon::MPIMultistateFitnessFunction , protocols::pmut_scan::PointMutScanDriver
• MPI_rank_ : protocols::optimize_weights::IterativeOptEDriver
• mpi_rank_ : protocols::optimize_weights::OptEMultifunc
• MPI_rank_ : protocols::pmut_scan::PointMutScanDriver
• mpi_resume_ : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• MPI_synchronize_pools_ : protocols::canonical_sampling::CanonicalSamplingMover
• mpose_ : core::scoring::motif::MotifHit
• mrlod_ : protocols::make_rot_lib::MakeRotLibJob , protocols::make_rot_lib::MakeRotLibJobInputter
• ms_whenfail_ : protocols::moves::FilterMover , protocols::protein_interface_design::movers::LoopOver
• msa_ : core::scoring::packstat::PackingScoreResData
• mseq_ : protocols::hybridization::DDomainParse
• msg_ : protocols::denovo_design::components::EXCN_Apply , protocols::denovo_design::components::EXCN_Setup , protocols::rpc::JSON_RPC
• msg_tag : protocols::jd2::archive::MPIArchiveJobDistributor::CompletionMessage
• msr_ : protocols::metal_interface::AddZincSiteConstraints , protocols::metal_interface::ZincSiteFinder
• mtzfile_ : core::scoring::cryst::PhenixInterface
• mu0_ : core::scoring::methods::BBIndepCartBondedParameters
• mulfactor_ : protocols::mpi_refinement::StructAvrgMover
• multi_cool_annealer_ : core::pack::task::PackerTask_
• multi_origin_list_ : protocols::pockets::FingerprintBase
• multi_relative_ : protocols::simple_filters::Operator
• multi_use_ : protocols::protein_interface_design::movers::SaveAndRetrieveSidechains
• multi_water_fade_ : core::scoring::lkball::LK_BallEnergy
• multicomp_ : protocols::matdes::InterfacePackingFilter , protocols::matdes::OligomericAverageDegreeFilter , protocols::simple_filters::ShapeComplementarityFilter
• multicomponent_ : protocols::matdes::BuildingBlockInterfaceOperation
• 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::optimize_weights::PNatLigPoseOptEData , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection
• multipole_elec_potential_ : core::scoring::ScoringManager
• multipole_info_ : core::scoring::MultipoleElecPotential
• multistate_packer_ : protocols::dna::DnaInterfaceMultiStateDesign , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• mus_spline_ : core::scoring::methods::BBDepCartBondedParameters
• must_switch_bins_ : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber , protocols::simple_moves::bin_transitions::PerturbByBins
• 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_file_ : protocols::membrane::MPMutateRelaxMover
• mutant_info_ : protocols::antibody::design::MutateFrameworkForCluster
• mutant_unbound_components_ : protocols::ddg::ddGMover
• mutant_unbounds_ : protocols::optimize_weights::DDGBindOptEData
• mutants_ : protocols::ddg::ddGMover
• mutants_allowed_ : protocols::antibody::design::MutantPosition
• mutants_list_ : protocols::pmut_scan::PointMutScanDriver
• mutants_list_file_ : protocols::pmut_scan::PointMutScanDriver
• mutate_framework_for_cluster_ : protocols::antibody::design::AntibodyDesignMover
• mutate_gly_ : protocols::denovo_design::DisulfidizeMover
• mutate_pro_ : protocols::denovo_design::DisulfidizeMover
• mutate_rate_ : protocols::dna::DnaInterfaceMultiStateDesign , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• 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_sets_ : protocols::toolbox::task_operations::MutationSetDesignOperation
• mutation_threshold_ : protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::simple_filters::MutationsFilter
• mutations_ : protocols::optimize_weights::DDGBindOptEData , protocols::pmut_scan::Mutant , protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::simple_filters::MutationsFilter
• muts_ : protocols::optimize_weights::DDGMutationOptEData
• mxr_ : core::scoring::packstat::Octree2D
• mxx_ : core::scoring::packstat::Octree2D
• mxy_ : core::scoring::packstat::Octree2D
• my_constraints_ : protocols::ligand_docking::ResidueTorsionRestraints
• my_csts_ : core::scoring::constraints::BigBinConstraint
• my_emperor_ : protocols::loophash::MPI_LoopHashRefine_Master , protocols::mpi_refinement::MPI_Refine_Master
• my_filter_ : protocols::moves::FilterMover
• my_frag_id_ : core::fragment::FragID_Iterator
• my_group_ : core::scoring::MultipoleElecResidueInfo
• my_hits_for_target_hit_map_ : protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• my_local_coord_frame_ : core::scoring::MultipoleElecResidueInfo
• 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
• myslaves_ : protocols::mpi_refinement::MPI_Refine_Master