- m -

• M : core::kinematics::Stub
• m_ : core::scoring::func::CircularSigmoidalFunc
• m_AtomTypesByDecreasingStability : core::chemical::gasteiger::PossibleAtomTypesForAtom
• m_FinalizeFunction : core::chemical::gasteiger::PossibleAtomTypesForAtom
• m_NumberAtomTypesWithHybridization : core::chemical::gasteiger::PossibleAtomTypesForAtom
• m_NumberConjugatedTypes : core::chemical::gasteiger::PossibleAtomTypesForAtom
• m_term_ : core::scoring::SecondaryStructurePotential
• MACQ_ : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• MACR_ : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• magnitude_last_surface_deltaE_ : core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G > , core::pack::interaction_graph::SurfaceEdge< V, E, G >
• main_group_ : core::chemical::Element
• mainchain_atoms_ : core::chemical::ResidueType
• mainchain_atoms_indices_ : core::chemical::ResidueType
• mainchain_glycosidic_bond_acceptor_ : core::chemical::carbohydrates::CarbohydrateInfo
• mainchain_torsions_ : core::conformation::Residue , core::io::silent::RNA_SilentStruct
• map_ : core::fragment::MapCacheUnit< T > , core::id::CacheableAtomID_MapVector , core::scoring::constraints::ResidueConstraints , core::scoring::EMapVector
• map_is_clean_ : core::sequence::AnnotatedSequence
• map_loaded : core::scoring::electron_density::PattersonCorrEnergy
• map_reso : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• map_type_ : core::scoring::cryst::PhenixInterface
• mapping_ : core::id::SequenceMapping , core::io::pdb::GeometricRenameIsomorphismCallback , core::scoring::constraints::SequenceProfileConstraint
• mapreso_ : core::scoring::electron_density::ElectronDensityOptions
• maskbits_ : core::scoring::sasa::LeGrandSasa
• masks_ : core::scoring::sasa::LeGrandSasa
• mass_ : core::chemical::ResidueType
• master_ : core::conformation::ConformationKinWriter , core::conformation::ResidueKinWriter
• match_aa1_ : core::scoring::motif::ResPairMotifQuery
• match_aa2_ : core::scoring::motif::ResPairMotifQuery
• match_chi_rmsd_ : core::scoring::motif::ResPairMotifQuery
• match_index : core::indexed_structure_store::FragmentLookupResult
• match_radius_ : core::scoring::motif::ResPairMotifQuery
• match_rmsd : core::indexed_structure_store::FragmentLookupResult
• match_rmsd_threshold : core::indexed_structure_store::FragmentLookupResult
• match_score : core::indexed_structure_store::FragmentLookupResult
• match_score_ : core::sequence::SimpleScoringScheme
• match_ss1_ : core::scoring::motif::ResPairMotifQuery
• match_ss2_ : core::scoring::motif::ResPairMotifQuery
• matching_database_ : core::scoring::disulfides::DisulfideMatchingPotential
• matrix_finalized_ : core::scoring::bin_transitions::BinTransitionData
• 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
• 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_per_rotamer_ : core::scoring::trie::RotamerTrie< AT, CPDATA >
• max_bin_ : core::scoring::PairEPotential
• max_branch_depth_ : core::scoring::trie::RotamerTrie< AT, CPDATA >
• MAX_C_SIZE_LIMIT : core::chemical::carbohydrates::CarbohydrateInfo
• max_ca_dis2_ : core::scoring::motif::ResPairMotifQuery
• max_chi_ : core::io::silent::ProteinSilentStruct_Template< T >
• 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_del_grid : 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::etable::coulomb::Coulomb
• max_dis_ : core::scoring::carbon_hbonds::CarbonHBondEnergy , core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy , core::scoring::etable::coulomb::Coulomb , core::scoring::etable::Etable , core::scoring::etable::MembEtable , 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
• max_dist_from_dot_to_intersection : core::pack::interaction_graph::InvRotamerDots
• max_dist_squared_ : core::scoring::orbitals::OrbitalsScore
• max_e_contribution_to_pi_system_ : core::chemical::gasteiger::GasteigerAtomTypeData
• max_frag_length_ : core::fragment::FragSet
• max_heavy_hydrogen_cutoff_ : core::scoring::etable::Etable
• max_heavyatom_depth_ : core::scoring::trie::RotamerTrie< AT, CPDATA >
• 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_iter_ : core::optimization::MinimizerOptions
• max_non_hydrogen_lj_radius_ : core::scoring::etable::Etable , core::scoring::etable::MembEtable
• max_orbital_dist_squared_ : core::scoring::orbitals::OrbitalsScore
• 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_pos_ : core::fragment::FragSet
• 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_rotbump_energy_ : core::pack::task::PackerTask_
• max_strand_dist_cutoff_ : core::scoring::SecondaryStructureWeights
• 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
• maxatoms_ : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• maxd2 : core::scoring::etable::EtableParamsOnePair
• maxouteriterations : core::pack::annealer::SimAnnealerBase
• maxsub : core::scoring::TMscoreStore
• maxsub_max : core::scoring::TMscoreStore
• maxsub_sum : core::scoring::TMscoreStore
• maxz_ : core::scoring::ResidualDipolarCoupling
• Mbhbond_ : core::scoring::hbonds::HBondOptions
• mca_history_size_ : core::pack::task::PackerTask_
• 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
• means_ : core::scoring::disulfides::Cb_Distance_Func , core::scoring::func::SOGFunc_Impl , core::scoring::func::USOGFunc
• measure_sp3acc_BAH_from_hvy_ : core::scoring::hbonds::HBondOptions
• median_ : core::pack::dunbrack::BBIndNRChiSample< P >
• 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_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_ : 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
• 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_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_num_ : core::conformation::membrane::MembraneInfo
• memory_max_for_rpes_ : core::pack::interaction_graph::DoubleLazyInteractionGraph
• Menv_penalties_ : core::scoring::MembranePotential
• 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
• method_ : core::scoring::sasa::SasaCalc
• method_creator_map_ : core::scoring::ScoringManager
• method_type_ : core::scoring::sasa::SasaCalc
• method_weights_ : core::scoring::methods::EnergyMethodOptions
• methods_by_score_type_ : core::scoring::ScoreFunction
• methyl_probe_dist_ : core::scoring::rna::data::RNA_DMS_Potential
• metric_calculators_ : core::pose::metrics::PoseMetricContainer
• metrics_ : core::pose::Pose
• mg_calculation_annotated_sequence_ : core::scoring::rna::RNA_ScoringInfo
• 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
• MIN_C_SIZE_LIMIT : core::chemical::carbohydrates::CarbohydrateInfo
• min_cav_ball_radius : core::scoring::packstat::SasaOptions
• min_cluster_overlap : core::scoring::packstat::SasaOptions
• min_dis : core::scoring::etable::Etable , core::scoring::etable::MembEtable
• min_dis2 : core::scoring::etable::Etable , core::scoring::etable::MembEtable
• min_dis2_ : core::scoring::etable::coulomb::Coulomb
• min_dis_ : core::scoring::etable::coulomb::Coulomb
• min_dis_score_ : core::scoring::etable::coulomb::Coulomb
• min_edge_count : core::kinematics::FoldTree
• min_error_ : core::optimization::GA_Minimizer
• min_hole_radius : core::scoring::packstat::SasaOptions
• min_map_ : core::optimization::AtomTreeMultifunc , core::optimization::CartesianMultifunc
• min_occ_energy_ : core::scoring::geometric_solvation::DatabaseOccSolEne
• min_orb_dist_enum_map_ : core::scoring::orbitals::OrbitalsScore
• min_params_ : core::scoring::packing::HolesEnergy
• min_pos_ : core::fragment::FragSet
• MIN_ROT_PROB : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary
• min_score_ : core::scoring::MinScoreScoreFunction
• MIN_SEQ_SEPARATIONS : core::scoring::methods::GoapEnergy
• min_type_ : core::optimization::MinimizerOptions
• minimization_edge_pool_ : core::scoring::MinimizationGraph
• minimization_graph_ : core::scoring::Energies
• minimize_tolerance_ : core::optimization::GA_Minimizer , core::optimization::MinimizerOptions
• minimumB : core::scoring::electron_density::ElectronDensity
• MINMULT : core::scoring::electron_density::ElectronDensity
• misc1_ : core::scoring::motif::ResPairMotif
• mismatch_score_ : core::sequence::SimpleScoringScheme
• missing_dens_as_jump_ : core::io::pdb::FileDataOptions
• mixture_param_ : core::scoring::func::MixtureFunc
• ml : core::scoring::cryst::XtalMLEnergy
• 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::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
• 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
• mm_type_ : core::conformation::Atom
• mnx_ : core::scoring::packstat::Octree2D
• mny_ : core::scoring::packstat::Octree2D
• mode_tokens_ : core::pack::task::ResidueLevelTask_
• modeltag : core::io::pdb::FileData
• modeltag_ : core::pose::PDBInfo
• modifications_ : core::chemical::carbohydrates::CarbohydrateInfo
• molecule : core::scoring::sc::Atom
• molecule_string_data_ : core::chemical::sdf::MolFileIOMolecule
• molgraph_ : core::chemical::sdf::MolFileIOMolecule
• moltenres_2_resid_ : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubsets
• moltenres_for_rotamer_ : 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 : core::pack::annealer::RotSub
• moltenresid_2_resid_ : core::pack::rotamer_set::ContinuousRotamerSets , core::pack::scmin::AtomTreeCollection
• 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
• 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_set_names_ : core::scoring::motif::MotifHashManager
• motif_umap_ : core::scoring::motif::MotifHash
• motifs_by_fname_ : core::scoring::motif::MotifHashManager
• move_map_torsion_id_map_ : core::kinematics::MoveMap
• move_tolerance_sqr_ : core::scoring::NeighborList
• moved_ : core::pack::interaction_graph::SimpleNode , core::scoring::EnergyNode
• mover_ : core::environment::DofPassport
• moving_atoms_ : core::optimization::CartesianMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap
• moving_dofids_ : core::optimization::CartesianMinimizerMap
• moving_torsionids_ : core::optimization::CartesianMinimizerMap
• mp_base_potential_ : core::scoring::ScoringManager
• 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
• mpose_ : core::scoring::motif::MotifHit
• msa_ : core::scoring::packstat::PackingScoreResData
• mtzfile_ : core::scoring::cryst::PhenixInterface
• mu0_ : core::scoring::methods::BBIndepCartBondedParameters
• multi_cool_annealer_ : core::pack::task::PackerTask_
• MultiplicitiveFactor_ : core::scoring::FACTSPotential
• mus_spline_ : core::scoring::methods::BBDepCartBondedParameters
• mutation_ddGs_ : core::io::PositionDdGInfo::PositionDdGInfo
• mutation_probability_ : core::optimization::GA_Minimizer
• mxr_ : core::scoring::packstat::Octree2D
• mxx_ : core::scoring::packstat::Octree2D
• mxy_ : core::scoring::packstat::Octree2D
• my_csts_ : core::scoring::constraints::BigBinConstraint
• my_frag_id_ : core::fragment::FragID_Iterator