- m -

• m_term_initializer() : core::scoring::SecondaryStructurePotential
• magentic_anisotropy_q_coeff() : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• magentic_anisotropy_r_coeff() : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• mainchain_atom() : core::chemical::ResidueType , core::conformation::Residue
• mainchain_atoms() : core::chemical::ResidueType , core::conformation::Residue
• mainchain_glycosidic_bond_acceptor() : core::chemical::carbohydrates::CarbohydrateInfo
• mainchain_torsion() : core::conformation::Residue , core::io::silent::RNA_SilentStruct
• mainchain_torsions() : core::conformation::Residue , core::io::silent::RNA_SilentStruct
• make_assymetric_movemap() : core::optimization::symmetry::SymAtomTreeMinimizer
• make_edge_vector_current() : core::graph::UEVertex< V, E >
• make_jump() : core::kinematics::Jump , core::kinematics::RT
• make_multifunc() : core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::SCMinMinimizerMap
• make_orbital_element_name() : core::chemical::orbitals::AssignOrbitals
• make_orbital_type_name() : core::chemical::orbitals::AssignOrbitals
• make_pairenergy_table() : core::scoring::etable::Etable , core::scoring::etable::MembEtable
• make_semisymmetric_movemap() : core::optimization::symmetry::SymAtomTreeMinimizer
• map() : core::id::CacheableAtomID_MapVector
• map_atom_to_bead() : core::coarse::Translator
• map_orbital_name_to_enum() : core::chemical::orbitals::OrbitalTypeMapper
• map_symmetric_res_pairs() : core::conformation::symmetry::SymmetryInfo
• map_to_CEN() : core::scoring::constraints::AmbiguousNMRDistanceConstraint
• mapping() : core::id::SequenceMapping
• mapStringToRecord() : core::io::pdb::PDB_DReader
• mapto() : core::scoring::constraints::Obsolet_NamedAtomPairConstraint
• mark_energies_computed() : core::scoring::EnergyEdge
• mark_energies_uncomputed() : core::scoring::EnergyEdge
• mark_energy_computed() : core::scoring::constraints::CstResNeighbIterator , core::scoring::DenseNeighborIterator , core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::CentroidDisulfideNeighborIterator , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::DisulfideMatchingNeighborIterator , core::scoring::disulfides::DisulfResNeighbIterator , core::scoring::disulfides::FullatomDisulfideEnergyContainer , core::scoring::OneToAllNeighborIterator , core::scoring::PeptideBondedNeighborIterator , core::scoring::ResidueNeighborIterator
• mark_energy_uncomputed() : core::scoring::constraints::CstResNeighbIterator , core::scoring::DenseNeighborIterator , core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::CentroidDisulfideNeighborIterator , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::DisulfideMatchingNeighborIterator , core::scoring::disulfides::DisulfResNeighbIterator , core::scoring::disulfides::FullatomDisulfideEnergyContainer , core::scoring::OneToAllNeighborIterator , core::scoring::PeptideBondedNeighborIterator , core::scoring::ResidueNeighborIterator
• mark_incomplete() : core::chemical::ResConnID
• mark_residue_moved() : core::kinematics::ResidueCoordinateChangeList
• mark_revision_id_expired() : core::scoring::constraints::ConstraintSet
• mark_rotwell_exists() : core::pack::dunbrack::SingleResidueDunbrackLibrary
• maskDensityMap() : core::scoring::electron_density::ElectronDensity
• maskResidues() : core::scoring::electron_density::ElectronDensity
• mass() : core::chemical::ResidueType
• master() : core::conformation::ConformationKinWriter , core::conformation::ResidueKinWriter
• match_fragment() : core::scoring::electron_density::ElectronDensity
• match_score() : core::sequence::SimpleScoringScheme
• match_variants() : core::chemical::ResidueSelector
• matchCentroidPose() : core::scoring::electron_density::ElectronDensity
• matched_tags() : core::io::silent::SilentFileData
• matches() : core::scoring::constraints::CstEnergyContainer
• matchPose() : core::scoring::electron_density::ElectronDensity
• matchPoseToPatterson() : core::scoring::electron_density::ElectronDensity
• matchRes() : core::scoring::electron_density::ElectronDensity
• matchResFast() : core::scoring::electron_density::ElectronDensity
• MatrixScoringScheme() : core::sequence::MatrixScoringScheme
• max() : core::id::DOF_ID_Range , core::id::TorsionID_Range
• max_atom_depth() : core::scoring::trie::RotamerTrie< AT, CPDATA >
• max_atom_radius() : core::pack::interaction_graph::RotamerDots
• max_atom_types() : core::scoring::packing::HolesParams
• max_atomic_interaction_cutoff() : core::scoring::ScoreFunction
• max_atomic_interaction_distance() : core::scoring::ScoreFunctionInfo
• max_branch_depth() : core::scoring::trie::RotamerTrie< AT, CPDATA >
• 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_dis() : core::scoring::carbon_hbonds::CarbonHBondPotential , core::scoring::custom_pair_distance::DistanceFunc , core::scoring::etable::coulomb::Coulomb , core::scoring::etable::Etable , core::scoring::etable::MembEtable , core::scoring::methods::GoapEnergy
• max_dis2() : core::scoring::etable::coulomb::Coulomb
• max_dist() : core::kinematics::ShortestPathInFoldTree , core::scoring::mm::MMLJEnergyTable
• max_frag_length() : core::fragment::FragSet
• max_gap_percentage() : core::sequence::SequenceAlignment
• max_heavy_heavy_cutoff() : core::scoring::etable::Etable
• max_heavy_hydrogen_cutoff() : core::scoring::etable::Etable
• max_heavyatom_depth() : core::scoring::trie::RotamerTrie< AT, CPDATA >
• max_hphobe_atoms_any_restype() : 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_pos() : core::fragment::FragSet
• max_rotbump_energy() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• max_valence_electrons_sp() : core::chemical::ElectronConfiguration
• maxNominalRes() : core::scoring::electron_density::ElectronDensity
• Mbhbond() : core::scoring::hbonds::HBondOptions
• MCAligner() : core::sequence::MCAligner
• mean() : core::scoring::dna::DNA_BasePotential
• measure_chi4() : core::scoring::methods::ProClosureEnergy
• measure_sp3acc_BAH_from_hvy() : core::scoring::hbonds::HBondOptions
• mem_footprint() : core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::SilentStruct
• memb_atom_pair_energy() : core::scoring::etable::BaseEtableEnergy< Derived >
• memb_atom_pair_energy_() : core::scoring::etable::BaseEtableEnergy< Derived >
• memb_dsolv1() : core::scoring::etable::MembEtable
• memb_dsolv2() : core::scoring::etable::MembEtable
• memb_etable() : core::scoring::ScoringManager
• memb_eval_dE_dR_over_r() : core::scoring::etable::BaseEtableEnergy< Derived >
• memb_eval_dE_dR_over_r_() : core::scoring::etable::BaseEtableEnergy< Derived >
• memb_lk_dgfree() : core::scoring::etable::MembEtable
• memb_lk_dgrefce() : core::scoring::etable::MembEtable
• memb_solv1() : core::scoring::etable::MembEtable
• memb_solv2() : core::scoring::etable::MembEtable
• Membed_init() : core::scoring::MembranePotential
• member_constraints() : core::scoring::constraints::MultiConstraint
• MembEtable() : core::scoring::etable::MembEtable
• membrane() : core::conformation::Conformation , core::conformation::membrane::MembraneInfo
• membrane_center() : core::conformation::membrane::MembraneInfo
• Membrane_FAEmbed() : core::scoring::Membrane_FAEmbed
• Membrane_FAEmbed_from_pose() : core::scoring::methods::Fa_MbenvEnergy , core::scoring::methods::Fa_MbsolvEnergy
• Membrane_FAPotential() : core::scoring::Membrane_FAPotential
• membrane_normal() : core::conformation::membrane::MembraneInfo
• membrane_thickness() : core::conformation::membrane::MembraneInfo
• MembraneCbetaEnergy() : core::scoring::methods::MembraneCbetaEnergy
• MembraneCenPairEnergy() : core::scoring::methods::MembraneCenPairEnergy
• MembraneEmbed() : core::scoring::MembraneEmbed
• MembraneEmbed_from_pose() : core::scoring::methods::Fa_MbenvEnergy
• MembraneEnvEnergy() : core::scoring::methods::MembraneEnvEnergy
• MembraneEnvPenalties() : core::scoring::methods::MembraneEnvPenalties
• MembraneEnvSmoothEnergy() : core::scoring::methods::MembraneEnvSmoothEnergy
• MembraneInfo() : core::conformation::membrane::MembraneInfo
• MembraneLipo() : core::scoring::methods::MembraneLipo
• MembranePotential() : core::scoring::MembranePotential
• MembraneProteinFactory() : core::membrane::MembraneProteinFactory
• MembraneProtocolConfigLib() : core::membrane::config::MembraneProtocolConfigLib
• MembraneResidueFactory() : core::membrane::geometry::MembraneResidueFactory
• MembraneTopology() : core::scoring::MembraneTopology
• MembraneTopology_from_pose() : core::scoring::methods::Fa_MbenvEnergy , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::methods::MembraneCbetaEnergy , core::scoring::methods::MembraneCenPairEnergy , core::scoring::methods::MembraneEnvEnergy
• memory_usage_dynamic() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T > , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T > , core::pack::dunbrack::SingleResidueDunbrackLibrary
• memory_usage_in_bytes() : core::pack::dunbrack::SingleResidueDunbrackLibrary
• memory_usage_static() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T > , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T > , core::pack::dunbrack::SingleResidueDunbrackLibrary
• Menv_penalties() : core::scoring::MembranePotential
• merge() : core::fragment::Frame , core::scoring::dssp::StrandPairing , core::scoring::dssp::StrandPairingSet , core::scoring::ScoreFunction
• mergeable() : core::scoring::dssp::StrandPairing
• 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
• MetalloPlacementEnergy() : core::scoring::methods::MetalloPlacementEnergy
• MetaPoseInputStream() : core::import_pose::pose_stream::MetaPoseInputStream
• method_type() : core::scoring::methods::ContextDependentLRTwoBodyEnergy , core::scoring::methods::ContextDependentOneBodyEnergy , core::scoring::methods::ContextDependentTwoBodyEnergy , core::scoring::methods::ContextIndependentLRTwoBodyEnergy , core::scoring::methods::ContextIndependentOneBodyEnergy , core::scoring::methods::ContextIndependentTwoBodyEnergy , core::scoring::methods::EnergyMethod , core::scoring::methods::WholeStructureEnergy
• method_weights() : core::scoring::methods::EnergyMethodOptions
• metric() : core::pose::Pose
• mg_calculation_annotated_sequence() : core::scoring::rna::RNA_ScoringInfo
• min() : core::id::DOF_ID_Range , core::id::TorsionID_Range
• min_dis() : core::scoring::custom_pair_distance::DistanceFunc , core::scoring::etable::coulomb::Coulomb
• min_dis2() : core::scoring::etable::coulomb::Coulomb
• min_dist() : core::scoring::mm::MMLJScore
• min_map() : core::optimization::AtomTreeMultifunc , core::optimization::CartesianMultifunc
• min_pos() : core::fragment::FragSet
• min_type() : core::optimization::MinimizerOptions
• mindata_from_pose() : core::scoring::methods::RG_Energy_Fast , core::scoring::methods::RG_LocalEnergy
• MinDebug() : core::optimization::symmetry::MinDebug
• mine() : core::graph::ArrayPool< T > , core::pack::interaction_graph::InteractionGraphBase
• minimization_graph() : core::scoring::Energies
• MinimizationEdge() : core::scoring::MinimizationEdge
• MinimizationGraph() : core::scoring::MinimizationGraph
• MinimizationNode() : core::scoring::MinimizationNode
• minimize_in_whole_structure_context() : core::pack::dunbrack::cenrot::CenRotDunEnergy , core::pack::dunbrack::DunbrackEnergy , core::scoring::carbon_hbonds::CarbonHBondEnergy , core::scoring::constraints::ConstraintsEnergy , core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy , core::scoring::disulfides::FullatomDisulfideEnergy , core::scoring::elec::FA_ElecEnergy , core::scoring::elec::FA_ElecEnergyAroAll , core::scoring::elec::FA_ElecEnergyAroAro , core::scoring::elec::RNA_FA_ElecEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::geometric_solvation::GeometricSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy , core::scoring::hbonds::HBondEnergy , core::scoring::methods::CartesianBondedEnergy , core::scoring::methods::EnergyMethod , core::scoring::methods::GoapEnergy , core::scoring::methods::LK_BallEnergy , core::scoring::methods::NMerPSSMEnergy , core::scoring::methods::NMerRefEnergy , core::scoring::methods::NMerSVMEnergy , core::scoring::methods::OmegaTetherEnergy , core::scoring::methods::P_AA_pp_Energy , core::scoring::methods::PairEnergy , core::scoring::methods::ProClosureEnergy , core::scoring::methods::Rama2BOffsetEnergy , core::scoring::methods::RamachandranEnergy , core::scoring::methods::ReferenceEnergy , core::scoring::methods::SequenceDependentRefEnergy , core::scoring::methods::YHHPlanarityEnergy , core::scoring::orbitals::OrbitalsScore , core::scoring::rna::StackElecEnergy
• minimize_tolerance() : core::optimization::MinimizerOptions
• Minimizer() : core::optimization::Minimizer
• MinimizerMap() : core::optimization::MinimizerMap
• MinimizerMapBase() : core::kinematics::MinimizerMapBase
• MinimizerOptions() : core::optimization::MinimizerOptions
• MiniPose() : core::pose::MiniPose
• MinMultiHarmonicFunc() : core::scoring::func::MinMultiHarmonicFunc
• MinScoreScoreFunction() : core::scoring::MinScoreScoreFunction
• mismatch_score() : core::sequence::SimpleScoringScheme
• missing_dens_as_jump() : core::io::pdb::FileDataOptions
• MissingEnergy() : core::scoring::methods::MissingEnergy
• MixtureFunc() : core::scoring::func::MixtureFunc
• mm_atom_name() : core::conformation::Residue
• mm_atom_set() : core::scoring::mm::MMLJLibrary
• mm_atom_type() : core::chemical::ResidueType , core::scoring::mm::mmtrie::MMEnergyTableAtom
• mm_atom_type_index() : core::chemical::Atom
• mm_atom_type_name() : core::chemical::Adduct
• mm_atom_type_set() : core::chemical::ChemicalManager , core::chemical::ResidueTypeSet
• mm_atom_type_set_tag() : core::chemical::ResidueLoaderOptions
• mm_bondangle_library() : core::scoring::mm::MMBondAngleResidueTypeParamSet
• mm_lj_library() : core::scoring::mm::MMLJScore
• mm_lj_score() : core::scoring::mm::MMLJEnergyTable
• mm_name() : core::chemical::Atom
• mm_type() : core::conformation::Atom
• MMAtomType() : core::chemical::MMAtomType
• MMAtomTypeSet() : core::chemical::MMAtomTypeSet
• MMBondAngleEnergy() : core::scoring::methods::MMBondAngleEnergy
• MMBondAngleLibrary() : core::scoring::mm::MMBondAngleLibrary
• MMBondAngleResidueTypeParam() : core::scoring::mm::MMBondAngleResidueTypeParam
• MMBondAngleResidueTypeParamSet() : core::scoring::mm::MMBondAngleResidueTypeParamSet
• MMBondAngleScore() : core::scoring::mm::MMBondAngleScore
• MMBondLengthEnergy() : core::scoring::methods::MMBondLengthEnergy
• MMBondLengthLibrary() : core::scoring::mm::MMBondLengthLibrary
• MMBondLengthScore() : core::scoring::mm::MMBondLengthScore
• MMEnergyTableAtom() : core::scoring::mm::mmtrie::MMEnergyTableAtom
• MMLJEnergyInter() : core::scoring::methods::MMLJEnergyInter
• MMLJEnergyIntra() : core::scoring::methods::MMLJEnergyIntra
• MMLJEnergyTable() : core::scoring::mm::MMLJEnergyTable
• MMLJLibrary() : core::scoring::mm::MMLJLibrary
• MMLJScore() : core::scoring::mm::MMLJScore
• MMTorsionEnergy() : core::scoring::methods::MMTorsionEnergy
• MMTorsionLibrary() : core::scoring::mm::MMTorsionLibrary
• MMTorsionScore() : core::scoring::mm::MMTorsionScore
• MNBRAK() : core::optimization::BrentLineMinimization
• modeltag() : core::pose::PDBInfo
• modify_pot() : core::scoring::etable::MembEtable
• modify_pot_one_pair() : core::scoring::etable::Etable
• modify_task() : core::pack::task::TaskFactory
• MolData() : core::chemical::sdf::MolData
• MolecularSurfaceCalculator() : core::scoring::sc::MolecularSurfaceCalculator
• MolFileParser() : core::chemical::sdf::MolFileParser
• moltenres_2_resid() : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSetsBase , core::pack::rotamer_set::RotamerSubsets
• moltenres_2_resid_vector() : core::pack::rotamer_set::FixbbRotamerSets , core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubsets
• moltenres_atomtree_collection() : core::pack::scmin::AtomTreeCollection
• moltenres_for_rotamer() : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSetsBase , core::pack::rotamer_set::RotamerSubsets
• moltenres_for_sample_rot() : core::pack::rotamer_set::ContinuousRotamerSets
• moltenres_rotid_2_rotid() : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSetsBase , core::pack::rotamer_set::RotamerSubsets
• moltenresid_2_resid() : core::pack::rotamer_set::ContinuousRotamerSets
• MolWriter() : core::chemical::sdf::MolWriter
• momento_for_moltenres() : core::pack::scmin::SidechainStateAssignment
• monomer_test() : core::scoring::elec::FA_ElecEnergy
• more_precise_base_pair_classification() : core::scoring::rna::RNA_LowResolutionPotential
• moved() : core::pack::interaction_graph::SimpleNode , core::scoring::EnergyNode
• MoveMap() : core::kinematics::MoveMap
• movemap_torsion_id_begin() : core::kinematics::MoveMap
• movemap_torsion_id_end() : core::kinematics::MoveMap
• mover() : core::environment::DofPassport
• moves_residue() : core::fragment::Frame , core::fragment::NonContinuousFrame
• moving_res_in_full_model() : core::pose::full_model_info::FullModelInfo
• msa() : core::scoring::packstat::PackingScoreResData
• mu() : core::scoring::methods::BBDepCartBondedParameters , core::scoring::methods::BBIndepCartBondedParameters , core::scoring::methods::CartBondedParameters
• multi_cool_annealer() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• multi_cool_annealer_history_size() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• MultiConstraint() : core::scoring::constraints::MultiConstraint
• MultiConstraintCreator() : core::scoring::constraints::MultiConstraintCreator
• MultiCoolAnnealer() : core::pack::annealer::MultiCoolAnnealer
• Multifunc() : core::optimization::Multifunc
• MultiplicitiveFactor() : core::scoring::FACTSPotential
• multiplicity() : core::scoring::constraints::AmbiguousNMRDistanceConstraint
• MultiProbePerSphereAccumulator() : core::scoring::packstat::MultiProbePerSphereAccumulator
• MultiProbePoseAccumulator() : core::scoring::packstat::MultiProbePoseAccumulator
• mutate() : core::optimization::GA_Minimizer
• mutation_ddGs() : core::io::PositionDdGInfo::PositionDdGInfo
• my_residue_pair_energy() : core::scoring::methods::DirectReadoutEnergy