- m -

• 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_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_inv_gen() : protocols::frag_picker::scores::RDCScore
• 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
• magnitude_rotation() : protocols::rigid::RigidBodyMotionMover
• magnitude_translation() : protocols::rigid::RigidBodyMotionMover
• main_atom() : protocols::noesy_assign::CrossPeakInfo
• main_chain_torsion_set_lists() : protocols::swa::protein::StepWiseProteinCCD_Closer , protocols::swa::protein::StepWiseProteinLoopBridger , protocols::swa::protein::StepWiseProteinScreener , protocols::swa::StepWiseScreener
• main_chain_torsion_set_lists_real() : protocols::swa::protein::StepWiseProteinScreener
• 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 , core::conformation::Residue
• MainChainTorsionSet() : protocols::swa::MainChainTorsionSet , protocols::swa::protein::MainChainTorsionSet
• make() : protocols::frag_picker::scores::MakePartialSecondarySimilarity , protocols::frag_picker::scores::MakePCS_FragDistance , protocols::frag_picker::scores::MakePhi , protocols::frag_picker::scores::MakePhiPsiRmsd , protocols::frag_picker::scores::MakePhiPsiSquareWell , protocols::frag_picker::scores::MakeProfileScore , protocols::frag_picker::scores::MakeProfileScoreBlosum62 , protocols::frag_picker::scores::MakeProfileScoreDistWeight , protocols::frag_picker::scores::MakeProfileScoreL1 , protocols::frag_picker::scores::MakeProfileScoreStructL1 , protocols::frag_picker::scores::MakeProfileScoreSubMatrix , protocols::frag_picker::scores::MakeProlinePhiScore , protocols::frag_picker::scores::MakePsi , protocols::frag_picker::scores::MakeRamaScore , protocols::frag_picker::scores::MakeRDCScore , protocols::frag_picker::scores::MakeScoreEValuator , protocols::frag_picker::scores::MakeSecondaryIdentity , protocols::frag_picker::scores::MakeSecondarySimilarity , protocols::frag_picker::scores::MakeSequenceIdentity , protocols::frag_picker::scores::MakeSolventAccessibility , protocols::frag_picker::scores::MakeABEGO_SS_Score , protocols::frag_picker::scores::MakeTalosSSSimilarity , protocols::frag_picker::scores::MakeTorsionBinSimilarity , protocols::frag_picker::scores::MakeAmbigCSScore , protocols::frag_picker::scores::MakeAtomPairConstraintsScore , protocols::frag_picker::scores::MakeBFactor , protocols::frag_picker::scores::MakeConstScore , protocols::frag_picker::scores::MakeCSScore , protocols::frag_picker::scores::MakeDihedralConstraintsScore , protocols::frag_picker::scores::MakeDisulfideDistance , protocols::frag_picker::scores::MakeDisulfideIdentity , protocols::frag_picker::scores::MakeFragmentAllAtomCrmsd , protocols::frag_picker::scores::MakeFragmentCrmsd , protocols::frag_picker::scores::MakeFragmentCrmsdResDepth , protocols::frag_picker::scores::MakeFragmentDME , protocols::frag_picker::scores::MakeFragmentScoringMethod , protocols::frag_picker::scores::MakeGunnCostScore , protocols::frag_picker::scores::MakeHydrophobicityProfileSimilarity , protocols::frag_picker::scores::MakeHydrophobicitySimilarity , protocols::frag_picker::scores::MakeInterbondAngleScore , protocols::frag_picker::scores::MakeJCoupling , protocols::frag_picker::scores::MakeLAMBEGO_Similarity , protocols::frag_picker::scores::MakeMidPhiOut , protocols::frag_picker::scores::MakeMidPsiOut
• make_assymetric_movemap() : core::optimization::symmetry::SymAtomTreeMinimizer
• make_calculator() : protocols::toolbox::task_operations::RestrictToInterfaceOperation , protocols::toolbox::task_operations::RestrictToNeighborhoodOperation
• make_chi_move() : protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover , protocols::simple_moves::sidechain_moves::PerturbChiSidechainMover , protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• make_complete_chunks() : protocols::hybridization::HybridizeFoldtreeDynamic
• make_constraint_covalent() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• make_constraint_covalent_helper() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• make_disjointed_foldtree() : protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover
• make_disulfide() : protocols::forge::remodel::RemodelDesignMover
• make_dna_sequence_combinations() : protocols::dna::DnaInterfacePacker
• make_dockmcm_mover() : protocols::ligand_docking::LigandDockProtocol , protocols::symmetric_docking::SymDockProtocol
• make_edge_vector_current() : core::graph::UEVertex< V, E >
• make_fibril() : protocols::topology_broker::FibrilModelingClaimer
• make_fragment_moves() : protocols::rna::RNA_Relaxer
• make_full_pose() : protocols::swa::StepWisePoseSetup
• make_inner_cycle_from_string_name() : protocols::loops::loop_mover::refine::LoopRefineInnerCycleFactory
• make_interface_set() : protocols::analysis::InterfaceAnalyzerMover
• make_jump() : core::kinematics::Jump , core::kinematics::RT
• make_local_bb_change() : protocols::loophash::LocalInserter , protocols::loophash::LocalInserter_SimpleMin
• make_local_bb_change_close_gaps() : protocols::loophash::LocalInserter , protocols::loophash::LocalInserter_SimpleMin
• make_local_bb_change_include_cut() : protocols::loophash::LocalInserter , protocols::loophash::LocalInserter_SimpleMin
• make_motif_filename() : protocols::motifs::IRCollection
• make_move() : protocols::simple_moves::BackboneMover , protocols::simple_moves::SmallMover , protocols::simple_moves::ShearMover , protocols::simple_moves::BBConRotMover , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• make_movemap() : protocols::ligand_docking::LigandBaseProtocol
• make_multichain_interface_set() : protocols::analysis::InterfaceAnalyzerMover
• make_multifunc() : core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::SCMinMinimizerMap
• make_mutant_structure() : protocols::pmut_scan::PointMutScanDriver
• make_mutants() : protocols::pmut_scan::PointMutScanDriver
• make_name() : protocols::toolbox::task_operations::RestrictToInterfaceOperation , protocols::toolbox::task_operations::RestrictToNeighborhoodOperation
• make_new_grid() : protocols::qsar::scoring_grid::GridManager
• make_orbital_element_name() : core::chemical::orbitals::AssignOrbitals
• make_orbital_type_name() : core::chemical::orbitals::AssignOrbitals
• make_packer_task() : protocols::ligand_docking::HighResDocker , protocols::ligand_docking::LigandBaseProtocol
• make_packer_task_from_vector() : protocols::ligand_docking::HighResDocker
• make_packer_task_ligand_only() : protocols::ligand_docking::LigandBaseProtocol
• make_pairenergy_table() : core::scoring::etable::Etable , core::scoring::etable::MembEtable
• make_pose() : protocols::swa::rna::StepWiseRNA_PoseSetup , protocols::swa::StepWisePoseSetup
• make_pymol_script() : protocols::flxbb::LayerDesignOperation
• make_rasmol_format_file() : protocols::toolbox::SelectResiduesByLayer , protocols::toolbox::task_operations::LayerOperations
• make_rotwell_jump() : protocols::simple_moves::sidechain_moves::SidechainMover
• make_sec() : protocols::hybridization::TMalign
• make_semisymmetric_movemap() : core::optimization::symmetry::SymAtomTreeMinimizer
• make_separated_pose() : protocols::analysis::InterfaceAnalyzerMover
• make_sequence_shift() : protocols::loops::Loops
• make_simple_ssd_from_pdb() : protocols::optimize_weights::IterativeOptEDriver
• make_specific_mutant() : protocols::pmut_scan::PointMutScanDriver
• make_strand_neighbor_two() : protocols::fldsgn::topology::StrandPairingSet
• make_symmetric_task() : protocols::simple_moves::symmetry::SymPackRotamersMover , protocols::simple_moves::symmetry::SymRotamerTrialsMover , protocols::simple_moves::symmetry::SymEnergyCutRotamerTrialsMover
• make_tail() : protocols::simple_moves::TailsScoreMover
• make_tweaked_scorefxn() : protocols::ligand_docking::LigandBaseProtocol
• MakeABEGO_SS_Score() : protocols::frag_picker::scores::MakeABEGO_SS_Score
• MakeAmbigCSScore() : protocols::frag_picker::scores::MakeAmbigCSScore
• MakeAtomPairConstraintsScore() : protocols::frag_picker::scores::MakeAtomPairConstraintsScore
• MakeBFactor() : protocols::frag_picker::scores::MakeBFactor
• makebinary() : protocols::sic_dock::XfoxmScore
• MakeConstScore() : protocols::frag_picker::scores::MakeConstScore
• MakeCSScore() : protocols::frag_picker::scores::MakeCSScore
• MakeDihedralConstraintsScore() : protocols::frag_picker::scores::MakeDihedralConstraintsScore
• MakeDisulfideDistance() : protocols::frag_picker::scores::MakeDisulfideDistance
• MakeDisulfideIdentity() : protocols::frag_picker::scores::MakeDisulfideIdentity
• makeDnaRigid() : protocols::relax::FastRelax
• MakeFragmentAllAtomCrmsd() : protocols::frag_picker::scores::MakeFragmentAllAtomCrmsd
• MakeFragmentCrmsd() : protocols::frag_picker::scores::MakeFragmentCrmsd
• MakeFragmentCrmsdResDepth() : protocols::frag_picker::scores::MakeFragmentCrmsdResDepth
• MakeFragmentDME() : protocols::frag_picker::scores::MakeFragmentDME
• MakeFragmentScoringMethod() : protocols::frag_picker::scores::MakeFragmentScoringMethod
• MakeGunnCostScore() : protocols::frag_picker::scores::MakeGunnCostScore
• MakeHydrophobicityProfileSimilarity() : protocols::frag_picker::scores::MakeHydrophobicityProfileSimilarity
• MakeHydrophobicitySimilarity() : protocols::frag_picker::scores::MakeHydrophobicitySimilarity
• MakeInterbondAngleScore() : protocols::frag_picker::scores::MakeInterbondAngleScore
• MakeJCoupling() : protocols::frag_picker::scores::MakeJCoupling
• MakeLAMBEGO_Similarity() : protocols::frag_picker::scores::MakeLAMBEGO_Similarity
• MakeMidPhiOut() : protocols::frag_picker::scores::MakeMidPhiOut
• MakeMidPsiOut() : protocols::frag_picker::scores::MakeMidPsiOut
• MakePartialSecondarySimilarity() : protocols::frag_picker::scores::MakePartialSecondarySimilarity
• MakePCS_FragDistance() : protocols::frag_picker::scores::MakePCS_FragDistance
• MakePhi() : protocols::frag_picker::scores::MakePhi
• MakePhiPsiRmsd() : protocols::frag_picker::scores::MakePhiPsiRmsd
• MakePhiPsiSquareWell() : protocols::frag_picker::scores::MakePhiPsiSquareWell
• MakePolyXMover() : protocols::simple_moves::MakePolyXMover
• MakeProfileScore() : protocols::frag_picker::scores::MakeProfileScore
• MakeProfileScoreBlosum62() : protocols::frag_picker::scores::MakeProfileScoreBlosum62
• MakeProfileScoreDistWeight() : protocols::frag_picker::scores::MakeProfileScoreDistWeight
• MakeProfileScoreL1() : protocols::frag_picker::scores::MakeProfileScoreL1
• MakeProfileScoreStructL1() : protocols::frag_picker::scores::MakeProfileScoreStructL1
• MakeProfileScoreSubMatrix() : protocols::frag_picker::scores::MakeProfileScoreSubMatrix
• MakeProlinePhiScore() : protocols::frag_picker::scores::MakeProlinePhiScore
• MakePsi() : protocols::frag_picker::scores::MakePsi
• MakeRamaScore() : protocols::frag_picker::scores::MakeRamaScore
• MakeRDCScore() : protocols::frag_picker::scores::MakeRDCScore
• MakeScoreEValuator() : protocols::frag_picker::scores::MakeScoreEValuator
• MakeSecondaryIdentity() : protocols::frag_picker::scores::MakeSecondaryIdentity
• MakeSecondarySimilarity() : protocols::frag_picker::scores::MakeSecondarySimilarity
• MakeSequenceIdentity() : protocols::frag_picker::scores::MakeSequenceIdentity
• MakeSolventAccessibility() : protocols::frag_picker::scores::MakeSolventAccessibility
• MakeTalosSSSimilarity() : protocols::frag_picker::scores::MakeTalosSSSimilarity
• MakeTorsionBinSimilarity() : protocols::frag_picker::scores::MakeTorsionBinSimilarity
• malloc() : boost::unordered_object_pool< T, UserAllocator >
• manager() : protocols::forge::components::VarLengthBuild , protocols::jd2::archive::AbstractArchiveBase
• manager_ptr() : protocols::jd2::archive::AbstractArchiveBase
• manager_type() : protocols::jd2::JD2ResourceManagerCreator
• manipulate_cut_bias() : protocols::topology_broker::CutBiasClaimer , protocols::topology_broker::RigidChunkClaimer , protocols::topology_broker::TopologyClaimer
• manual_call() : protocols::loophash::LoopHashRelaxProtocol
• manualPackerTaskGen() : protocols::forge::remodel::WorkingRemodelSet
• map() : core::id::CacheableAtomID_MapVector
• map2keyvector() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• map2target() : protocols::abinitio::Template
• map2template() : protocols::abinitio::Template
• map_atom_to_bead() : core::coarse::Translator
• map_orbital_name_to_enum() : core::chemical::orbitals::OrbitalTypeMapper
• map_pairing() : protocols::abinitio::Template
• map_pairings2target() : protocols::abinitio::Template
• map_pairings2template() : protocols::abinitio::Template
• map_pdb_info_number() : protocols::hybridization::FoldTreeHybridize
• map_ss_segments() : protocols::fldsgn::MatchResidues
• map_symmetric_res_pairs() : core::conformation::symmetry::SymmetryInfo
• map_to_CEN() : core::scoring::constraints::AmbiguousNMRDistanceConstraint
• MapHotspot() : protocols::protein_interface_design::movers::MapHotspot
• mapping() : core::id::SequenceMapping
• mapStringToRecord() : core::io::pdb::PDB_DReader
• mapto() : core::scoring::constraints::Obsolet_NamedAtomPairConstraint
• mark() : protocols::pockets::PocketGrid
• mark_as_cancelled() : protocols::jd2::archive::Batch
• mark_as_finished() : protocols::jd2::archive::Batch
• mark_as_invalid() : protocols::jd2::archive::Batch
• mark_current_job_id_for_repetition() : protocols::jd2::MPIWorkPoolJobDistributor , protocols::jd2::ShuffleFileSystemJobDistributor , protocols::jd2::BOINCJobDistributor , protocols::jd2::FileSystemJobDistributor , protocols::jd2::JobDistributor , protocols::jd2::MPIFileBufJobDistributor , protocols::jd2::MPIWorkPartitionJobDistributor
• 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::CentroidDisulfideNeighborIterator , core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingNeighborIterator , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::DisulfResNeighbIterator , core::scoring::disulfides::FullatomDisulfideEnergyContainer , core::scoring::ResidueNeighborIterator , core::scoring::OneToAllNeighborIterator , core::scoring::PeptideBondedNeighborIterator
• mark_energy_uncomputed() : core::scoring::constraints::CstResNeighbIterator , core::scoring::DenseNeighborIterator , core::scoring::disulfides::CentroidDisulfideNeighborIterator , core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingNeighborIterator , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::DisulfResNeighbIterator , core::scoring::disulfides::FullatomDisulfideEnergyContainer , core::scoring::ResidueNeighborIterator , core::scoring::OneToAllNeighborIterator , core::scoring::PeptideBondedNeighborIterator
• mark_entity_as_unimportant() : protocols::pack_daemon::PackDaemon , protocols::pack_daemon::DaemonSet
• mark_incomplete() : core::chemical::ResConnID
• mark_job_as_bad() : protocols::jd2::archive::MPIArchiveJobDistributor , protocols::jd2::JobDistributor , protocols::jd2::MPIFileBufJobDistributor
• mark_job_as_completed() : protocols::jd2::archive::MPIArchiveJobDistributor , protocols::jd2::JobDistributor , protocols::jd2::MPIFileBufJobDistributor
• mark_last_entity_as_important() : protocols::pack_daemon::PackDaemon , protocols::pack_daemon::DaemonSet
• mark_loop_moveable() : protocols::forge::remodel::RemodelLoopMover
• mark_loops_moveable() : protocols::forge::remodel::RemodelLoopMover
• mark_residue_moved() : core::kinematics::ResidueCoordinateChangeList
• mark_revision_id_expired() : core::scoring::constraints::ConstraintSet
• mark_rotwell_exists() : core::pack::dunbrack::SingleResidueDunbrackLibrary
• mark_structure_as_sampled() : protocols::features::StructureFeatures
• mark_tags() : protocols::toolbox::KClusterData
• markDepth() : protocols::pockets::PocketGrid
• markEdgeDepth() : protocols::pockets::PocketGrid
• markNativeInterface() : protocols::flexpep_docking::FlexPepDockingProtocol
• markOneEdgeDepth() : protocols::pockets::PocketGrid
• markPocketDepth() : protocols::pockets::PocketGrid
• mask() : protocols::electron_density::SetupForDensityScoringMover
• mask_from_offsets() : protocols::match::Bool3DGrid
• maskResidues() : core::scoring::electron_density::ElectronDensity
• mass() : core::chemical::Element
• master() : core::conformation::ResidueKinWriter , core::conformation::ConformationKinWriter , protocols::match::output::ResidueKinemageWriter , protocols::wum2::WorkUnit
• master_add_unfolded_energy_data() : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor
• master_gather_new_coords() : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD
• master_get_new_job_id() : protocols::jd2::MPIFileBufJobDistributor , protocols::jd2::MPIWorkPoolJobDistributor
• master_go() : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD , protocols::jd2::MPIFileBufJobDistributor , protocols::jd2::MPIWorkPoolJobDistributor , protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor
• master_job_succeeded() : protocols::jd2::MPIFileBufJobDistributor , protocols::jd2::MPIWorkPoolJobDistributor
• master_mark_current_job_id_for_repetition() : protocols::jd2::MPIFileBufJobDistributor , protocols::jd2::MPIWorkPoolJobDistributor
• master_rank() : protocols::jd2::MPIFileBufJobDistributor , protocols::loophash::MPI_LoopHashRefine_Master , protocols::wum::DatabaseQueryWorkUnitManager< T >
• master_remove_bad_inputs_from_job_list() : protocols::jd2::MPIFileBufJobDistributor , protocols::jd2::MPIWorkPoolJobDistributor
• master_set_energy_terms() : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor
• master_to_archive() : protocols::jd2::archive::MPIArchiveJobDistributor
• master_weight() : protocols::toolbox::pose_metric_calculators::EnergiesData
• master_weight_vector() : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• Mat3VecMult() : protocols::sparta::PDB
• match() : protocols::noesy_assign::Resonance
• match_dspos1() : protocols::match::match_dspos1
• match_end_variants() : protocols::swa::protein::StepWiseProteinPoseSetup
• match_groups_dshits() : protocols::match::output::CloudPDBWriter
• match_groups_ushits() : protocols::match::output::CloudPDBWriter
• match_has_been_output() : protocols::match::MatchOutputTracker
• match_possible_for_hit_geometry() : protocols::match::OccupiedSpaceHash
• match_processing_successful() : protocols::match::output::MatchProcessor
• match_score() : core::sequence::SimpleScoringScheme
• match_specific_variants() : protocols::swa::protein::StepWiseProteinPoseSetup
• match_variants() : core::chemical::ResidueSelector
• matchCentroidPose() : core::scoring::electron_density::ElectronDensity
• MatchCollisionFilter() : protocols::match::output::MatchCollisionFilter
• MatchConsolidator() : protocols::match::output::MatchConsolidator
• MatchConstraintFileInfo() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• MatchConstraintFileInfoList() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList
• MatchCounter() : protocols::match::MatchCounter
• matched_tags() : core::io::silent::SilentFileData
• Matcher() : protocols::match::Matcher
• MatcherMover() : protocols::match::MatcherMover
• MatcherOutputStats() : protocols::match::MatcherOutputStats
• MatcherTask() : protocols::match::MatcherTask
• matches() : core::scoring::constraints::CstEnergyContainer , protocols::topology_broker::ClaimerMessage
• MatchFilter() : protocols::match::output::MatchFilter
• MatchGrouper() : protocols::match::output::MatchGrouper
• MatchOutputter() : protocols::match::output::MatchOutputter
• MatchOutputTracker() : protocols::match::MatchOutputTracker
• matchPose() : core::scoring::electron_density::ElectronDensity
• matchPoseToPatterson() : core::scoring::electron_density::ElectronDensity
• MatchPositionModifier() : protocols::match::MatchPositionModifier
• MatchProcessor() : protocols::match::output::MatchProcessor
• matchRes() : core::scoring::electron_density::ElectronDensity
• matchResFast() : core::scoring::electron_density::ElectronDensity
• MatchResidues() : protocols::fldsgn::MatchResidues
• MatchResiduesMover() : protocols::fldsgn::MatchResiduesMover
• matrix() : protocols::frag_picker::LAMBEGO_IO , protocols::frag_picker::TorsionBinIO
• MatrixScoringScheme() : core::sequence::MatrixScoringScheme
• max() : core::id::DOF_ID_Range , core::id::TorsionID_Range
• 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_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_atoms() : protocols::backrub::BackrubMover
• max_bbrms() : protocols::loophash::LoopHashMoverWrapper
• max_branch_depth() : core::scoring::trie::RotamerTrie< AT, CPDATA >
• max_cache_size() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel , protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• max_cb_cb_dist() : protocols::protein_interface_design::movers::PlacementAuctionMover
• 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_degree() : protocols::sasa_scores::PPoly
• max_dis() : core::scoring::carbon_hbonds::CarbonHBondPotential , core::scoring::custom_pair_distance::DistanceFunc , core::scoring::etable::Etable , core::scoring::etable::MembEtable
• max_dist() : core::kinematics::ShortestPathInFoldTree , core::scoring::mm::MMLJEnergyTable
• max_frag_len() : protocols::frag_picker::FragmentPicker
• max_frag_length() : core::fragment::FragSet
• max_gap_percentage() : core::sequence::SequenceAlignment
• max_generations() : protocols::genetic_algorithm::GeneticAlgorithm
• 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_inner_cycles() : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• max_inter_ss_bbrms() : protocols::loophash::LoopHashDiversifier
• max_intra_ss_bbrms() : protocols::loophash::LoopHashDiversifier
• max_iter() : core::optimization::MinimizerOptions
• max_length() : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• max_level_index() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• max_lib_size() : protocols::loophash::MPI_LoopHashRefine
• max_linear_chainbreak() : protocols::fldsgn::BluePrintBDR , protocols::forge::components::BDR , protocols::forge::components::VarLengthBuild , protocols::forge::remodel::RemodelLoopMover , protocols::forge::remodel::RemodelMover
• max_loop_length() : protocols::features::LoopAnchorFeatures
• max_noe_distance() : protocols::noesy_assign::CrossPeakInfo
• max_non_hydrogen_lj_radius() : core::scoring::etable::Etable , core::scoring::etable::MembEtable
• max_nstruct() : protocols::loophash::LoopHashMoverWrapper
• max_outgoing_wu_mem() : protocols::wum2::EndPoint
• max_pools() : protocols::frag_picker::QuotaDebug
• max_pos() : core::fragment::FragSet
• max_residue_count() : protocols::simple_filters::ResidueCountFilter
• max_rms() : protocols::loophash::FastGapMover , protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashMoverWrapper
• max_rotbump_energy() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• max_sample_iterations() : protocols::loops::loop_closure::kinematic_closure::KinematicPerturber
• max_separation_dist_to_target_atom() : protocols::match::downstream::AtomDistanceSecMatchRPE , protocols::match::downstream::GeometrySecMatchRPE , protocols::match::downstream::SecMatchResiduePairEvaluator
• max_seq_sep() : protocols::constraints_additional::MaxSeqSepConstraintSet
• max_seq_sep_fudge() : protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints
• max_tries() : protocols::moves::FilterMover
• max_volume_contribution() : protocols::noesy_assign::CrossPeak
• maxcycles() : protocols::moves::IteratedConvergenceMover
• MaxSeqSepConstraintSet() : protocols::constraints_additional::MaxSeqSepConstraintSet
• Mbhbond() : core::scoring::hbonds::HBondOptions
• mc() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio , protocols::loops::loop_closure::ccd::LoopClosure , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::moves::TrialMover , protocols::simple_moves::EnergyCutRotamerTrialsMover , protocols::simple_moves::symmetry::SymEnergyCutRotamerTrialsMover
• mc_accepted() : protocols::moves::MonteCarlo
• mc_accpeted() : protocols::simple_moves::GenericMonteCarloMover
• mc_ptr() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• MCAligner() : core::sequence::MCAligner
• mcfi() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList
• mcfi_list() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• mcfi_lists_size() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• mcfis_for_upstream_restype() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList
• MCShowMover() : protocols::moves::MCShowMover
• mean() : core::scoring::dna::DNA_BasePotential
• measure_bp_specificities() : protocols::dna::DnaInterfacePacker
• measure_chi4() : core::scoring::methods::ProClosureEnergy
• measure_rotamer_recovery() : protocols::optimize_weights::IterativeOptEDriver , protocols::rotamer_recovery::RRComparer , protocols::rotamer_recovery::RRComparerRotBins , protocols::rotamer_recovery::RRComparerChiDiff , protocols::rotamer_recovery::RRComparerAutomorphicRMSD , protocols::rotamer_recovery::RRProtocol
• measure_sequence_recovery() : protocols::optimize_weights::IterativeOptEDriver , protocols::toolbox::pose_metric_calculators::SequenceComparison
• measure_sp3acc_BAH_from_hvy() : core::scoring::hbonds::HBondOptions
• measure_specificities() : protocols::dna::DnaInterfacePacker
• measure_specificity() : protocols::dna::DnaInterfacePacker
• MedalExchangeMover() : protocols::medal::MedalExchangeMover
• MedalMover() : protocols::medal::MedalMover
• median() : protocols::filters::ReplicateFilter
• mem_foot_print() : protocols::loophash::LoopHashLibrary , protocols::loophash::LoopHashMap , protocols::wum::WorkUnitQueue , protocols::wum::WorkUnitManager
• mem_footprint() : core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::SilentStruct , protocols::relax::SRelaxPose , protocols::wum::SilentStructStore , protocols::wum::WorkUnitBase
• mem_stats() : protocols::wum::WorkUnitQueue
• 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_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
• MembraneAbinitio() : protocols::abinitio::MembraneAbinitio
• MembraneCbetaEnergy() : core::scoring::methods::MembraneCbetaEnergy
• MembraneCenPairEnergy() : core::scoring::methods::MembraneCenPairEnergy
• MembraneCenterPerturbationMover() : protocols::rigid::MembraneCenterPerturbationMover
• MembraneEmbed() : core::scoring::MembraneEmbed
• MembraneEmbed_from_pose() : core::scoring::methods::Fa_MbenvEnergy , protocols::abinitio::MembraneAbinitio
• MembraneEnvEnergy() : core::scoring::methods::MembraneEnvEnergy
• MembraneEnvPenalties() : core::scoring::methods::MembraneEnvPenalties
• MembraneEnvSmoothEnergy() : core::scoring::methods::MembraneEnvSmoothEnergy
• MembraneJump() : protocols::jumping::MembraneJump
• MembraneLipo() : core::scoring::methods::MembraneLipo
• MembraneNormalPerturbationMover() : protocols::rigid::MembraneNormalPerturbationMover
• MembranePotential() : core::scoring::MembranePotential
• MembraneTopology() : core::scoring::MembraneTopology , protocols::simple_moves::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 , protocols::abinitio::MembraneAbinitio
• MembraneTopologyClaimer() : protocols::topology_broker::MembraneTopologyClaimer
• 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
• memory_use() : protocols::optimize_weights::DDGBindOptEData , protocols::optimize_weights::DGBindOptEData , protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData , protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData , protocols::optimize_weights::OptEPositionData , protocols::optimize_weights::PNatAAOptEPositionData , protocols::optimize_weights::PSSMOptEPositionData , protocols::optimize_weights::PNatRotOptEPositionData , protocols::optimize_weights::PNatStructureOptEData , protocols::optimize_weights::DDGMutationOptEData , protocols::optimize_weights::ConstraintedOptimizationWeightFunc
• Menv_penalties() : core::scoring::MembranePotential
• merge() : core::fragment::Frame , core::scoring::dssp::StrandPairing , core::scoring::dssp::StrandPairingSet , core::scoring::ScoreFunction , protocols::comparative_modeling::AlignmentCluster , protocols::loophash::LoopHashLibrary , protocols::wum::WorkUnitList
• merge_bbdb() : protocols::loophash::LoopHashLibrary
• mergeable() : core::scoring::dssp::StrandPairing
• MetalloClaimer() : protocols::topology_broker::MetalloClaimer
• MetalloPlacementEnergy() : core::scoring::methods::MetalloPlacementEnergy
• MetaPoseEvaluator() : protocols::evaluation::MetaPoseEvaluator
• 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
• MethylNameLibrary() : protocols::noesy_assign::MethylNameLibrary
• MethylNames() : protocols::noesy_assign::MethylNames
• metric() : core::pose::Pose
• metric_value() : protocols::multistate_design::SingleStateEntityData
• metric_value_getters() : protocols::multistate_design::MultiStateFitnessFunction
• metric_value_map() : protocols::multistate_design::SingleStateEntityData
• metric_value_template() : protocols::toolbox::pose_metric_calculators::MetricValueGetter
• MetricCalculatorFitnessFunction() : protocols::multistate_design::MetricCalculatorFitnessFunction
• MetricRecorder() : protocols::canonical_sampling::MetricRecorder
• MetricValueGetter() : protocols::toolbox::pose_metric_calculators::MetricValueGetter
• metropolis_hastings_mover() : protocols::canonical_sampling::ThermodynamicMover , protocols::simple_moves::sidechain_moves::SidechainMCMover
• MetropolisHastingsMover() : protocols::canonical_sampling::MetropolisHastingsMover
• mg_calculation_annotated_sequence() : core::scoring::rna::RNA_ScoringInfo
• mid_pos() : protocols::fldsgn::topology::SS_Base
• middle_res() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• MidPhiOut() : protocols::frag_picker::scores::MidPhiOut
• midpoint() : protocols::loops::Loop
• MidPsiOut() : protocols::frag_picker::scores::MidPsiOut
• min() : core::id::DOF_ID_Range , core::id::TorsionID_Range
• min_atoms() : protocols::backrub::BackrubMover
• min_bb() : protocols::protein_interface_design::movers::PrepackMover , protocols::simple_moves::DesignRepackMover
• min_bb_set() : protocols::simple_moves::DesignRepackMover
• min_bbrms() : protocols::loophash::LoopHashMoverWrapper
• min_client_rank() : protocols::jd2::MPIFileBufJobDistributor
• min_dis() : core::scoring::custom_pair_distance::DistanceFunc
• min_dist() : core::scoring::mm::MMLJScore , protocols::noesy_assign::FragsToAtomDist::DistanceRecord
• min_heap() : protocols::cluster::Exemplar
• min_inter_ss_bbrms() : protocols::loophash::LoopHashDiversifier
• min_intra_ss_bbrms() : protocols::loophash::LoopHashDiversifier
• min_length() : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• min_loop_length() : protocols::features::LoopAnchorFeatures
• min_loop_size() : protocols::comparative_modeling::MultiThreadingMover , protocols::comparative_modeling::ThreadingMover
• min_map() : core::optimization::AtomTreeMultifunc , core::optimization::CartesianMultifunc
• min_move() : protocols::abinitio::FoldConstraints
• min_options() : protocols::simple_moves::MinMover , protocols::simple_moves::SaneMinMover
• min_pos() : core::fragment::FragSet
• min_rb() : protocols::simple_moves::DesignRepackMover
• min_rb_set() : protocols::simple_moves::DesignRepackMover
• min_residue_count() : protocols::simple_filters::ResidueCountFilter
• min_rms() : protocols::loophash::FastGapMover , protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashMoverWrapper
• min_sc() : protocols::simple_moves::DesignRepackMover
• min_sc_set() : protocols::simple_moves::DesignRepackMover
• min_seq_separation_residue_assignment() : protocols::noesy_assign::CrossPeak
• min_trial() : protocols::abinitio::FoldConstraints
• min_type() : protocols::simple_moves::MinMover , core::optimization::MinimizerOptions , protocols::simple_moves::MinMover
• min_VC_to_write() : protocols::noesy_assign::PeakFileFormat_Base
• mindata_from_pose() : core::scoring::methods::RG_Energy_Fast
• MinDebug() : core::optimization::symmetry::MinDebug
• mine() : core::graph::ArrayPool< T > , core::pack::interaction_graph::InteractionGraphBase
• mini_pose() : protocols::rna::ChunkSet
• MinimalistFlexbbEdge() : protocols::flexpack::interaction_graph::MinimalistFlexbbEdge
• MinimalistFlexbbInteractionGraph() : protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph
• MinimalistFlexbbNode() : protocols::flexpack::interaction_graph::MinimalistFlexbbNode
• MinimalRotamer() : protocols::simple_moves::MinimalRotamer
• minimization_graph() : core::scoring::Energies
• minimization_score_function() : protocols::ddg::ddGMover
• MinimizationEdge() : core::scoring::MinimizationEdge
• MinimizationGraph() : core::scoring::MinimizationGraph
• MinimizationNode() : core::scoring::MinimizationNode
• minimize() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• minimize_() : protocols::simple_moves::PeptideStapleMover
• minimize_all() : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• minimize_backbone() : protocols::ligand_docking::MoveMapBuilder
• minimize_base_step() : protocols::rna::RNA_HelixAssembler
• 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_conformation() : protocols::vip::VIP_Mover
• minimize_flexible_region() : protocols::enzdes::EnzdesFlexBBProtocol
• minimize_in_stages() : protocols::enzdes::EnzRepackMinimize
• minimize_in_whole_structure_context() : core::scoring::methods::SequenceDependentRefEnergy , core::scoring::hackelec::RNAHackElecEnergy , core::scoring::constraints::ConstraintsEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy , core::pack::dunbrack::DunbrackEnergy , core::scoring::carbon_hbonds::CarbonHBondEnergy , core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy , core::scoring::disulfides::FullatomDisulfideEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::hackelec::HackElecEnergy , core::scoring::hackelec::HackElecEnergyAroAll , core::scoring::hackelec::HackElecEnergyAroAro , core::scoring::hbonds::HBondEnergy , core::scoring::methods::CartesianBondedEnergy , core::scoring::methods::EnergyMethod , core::scoring::methods::NMerPSSMEnergy , core::scoring::methods::NMerRefEnergy , core::scoring::methods::OmegaTetherEnergy , core::scoring::methods::P_AA_pp_Energy , core::scoring::methods::PairEnergy , core::scoring::methods::ProClosureEnergy , core::scoring::methods::RamachandranEnergy , core::scoring::methods::ReferenceEnergy , core::scoring::methods::YHHPlanarityEnergy , core::scoring::orbitals::OrbitalsScore
• minimize_no_bb() : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• minimize_only() : protocols::flexpep_docking::FlexPepDockingProtocol
• minimize_region() : protocols::enzdes::EnzdesFlexibleRegion
• minimize_tensors_fix_from_PCS_data() : protocols::scoring::methods::pcs2::PcsEnergy
• minimize_tensors_from_PCS_data() : protocols::scoring::methods::pcs::PCS_Energy , protocols::scoring::methods::pcs2::PcsEnergy
• minimize_tensors_from_PCS_data_with_svd() : protocols::scoring::methods::pcs2::PcsEnergy
• minimize_tolerance() : core::optimization::MinimizerOptions
• minimize_toward_stub() : protocols::protein_interface_design::movers::PlaceOnLoop
• minimize_with_constraints() : protocols::simple_moves::symmetry::SymShakeStructureMover , protocols::ddg::ddGMover , protocols::simple_moves::ShakeStructureMover
• MinimizeBackbone() : protocols::ligand_docking::MinimizeBackbone
• MinimizeHotspots() : protocols::protein_interface_design::movers::MapHotspot
• MinimizeLigand() : protocols::ligand_docking::MinimizeLigand
• Minimizer() : core::optimization::Minimizer
• minimizer() : protocols::loops::loop_mover::refine::ShearMinCCDTrial , protocols::loops::loop_mover::refine::SmallMinCCDTrial
• minimizer_options() : protocols::loops::loop_mover::refine::SmallMinCCDTrial
• MinimizerMap() : core::optimization::MinimizerMap
• MinimizerMapBase() : core::kinematics::MinimizerMapBase
• MinimizerOptions() : core::optimization::MinimizerOptions
• MinimizeStoredRBConfs() : protocols::enzdes::MinimizeStoredRBConfs
• MiniPose() : core::pose::MiniPose
• MiniRelax() : protocols::relax::MiniRelax
• MinMover() : protocols::simple_moves::MinMover
• MinMultiHarmonicFunc() : core::scoring::constraints::MinMultiHarmonicFunc
• MinPackMover() : protocols::simple_moves::MinPackMover
• MinScoreScoreFunction() : core::scoring::MinScoreScoreFunction
• MinValueEvaluator() : protocols::simple_filters::MinValueEvaluator< T >
• mismatch_score() : core::sequence::SimpleScoringScheme
• missing_in_pose() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters , protocols::toolbox::match_enzdes_util::EnzdesCstParamCache
• MissingDensityToJumpMover() : protocols::simple_moves::MissingDensityToJumpMover
• MixtureFunc() : core::scoring::constraints::MixtureFunc
• mkdir_pred() : protocols::sparta::Sparta::SpartaLib
• mm() : protocols::protein_interface_design::movers::PrepackMover
• 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
• 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
• mode() : protocols::rosetta_scripts::ParsedProtocol
• mode1_packertask() : protocols::forge::remodel::RemodelDesignMover
• mode2_packertask() : protocols::forge::remodel::RemodelDesignMover
• mode3_packertask() : protocols::forge::remodel::RemodelDesignMover
• mode4_packertask() : protocols::forge::remodel::RemodelDesignMover
• mode5_packertask() : protocols::forge::remodel::RemodelDesignMover
• mode6_packertask() : protocols::forge::remodel::RemodelDesignMover
• model_count() : protocols::canonical_sampling::TrajectoryRecorder
• model_h3() : protocols::antibody::CDRH3Modeler
• model_loop() : protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD , protocols::loop_build::LoopMover_SlidingWindow , protocols::loops::loop_mover::IndependentLoopMover , protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC , protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD , protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves
• ModelCDRH3() : protocols::antibody2::ModelCDRH3
• models() : protocols::abinitio::PairingStatEntry
• modeltag() : core::pose::PDBInfo
• modifiable() : protocols::moves::ResId
• modified2original_interval_endpoints() : protocols::forge::build::BuildManager
• modified2original_intervals() : protocols::forge::build::BuildManager
• modified_i2p_defined() : protocols::forge::build::BuildManager
• modified_i2p_new() : protocols::forge::build::BuildManager
• modified_i2p_preexisting() : protocols::forge::build::BuildManager
• modified_i2p_undefined() : protocols::forge::build::BuildManager
• modified_interval2movemap() : protocols::forge::build::BuildManager
• modified_match_positions() : protocols::match::MatchPositionModifier , protocols::match::SecondaryStructureMPM , protocols::match::NumNeighborsMPM , protocols::match::BfactorMPM , protocols::match::RemoveNorCTermMPM , protocols::match::TaskOperationMPM , protocols::match::AddAllPositionsMPM
• modified_task() : protocols::enzdes::EnzdesFlexBBProtocol
• modify() : protocols::forge::build::BuildManager , protocols::forge::build::BuildInstruction
• modify_after_jump() : protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• modify_before_jump() : protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• modify_impl() : protocols::forge::build::Bridge , protocols::forge::build::BuildInstruction , protocols::forge::build::ConnectRight , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::forge::build::RelativeConnectRight , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap , protocols::forge::build::SegmentInsert
• modify_pdb_segments_with_current_segment() : protocols::protein_interface_design::movers::Splice
• modify_pose_build_resids_from_endes_input() : protocols::match::MatcherTask
• modify_pot() : core::scoring::etable::MembEtable
• modify_pot_one_pair() : core::scoring::etable::Etable
• modify_relative_filters_pdb_names() : protocols::simple_filters::Operator
• modify_task() : core::pack::task::TaskFactory
• modify_volume() : core::scoring::FACTSResidueInfo
• modify_was_successful() : protocols::forge::build::BuildInstruction
• ModifyAnnealer() : protocols::toolbox::task_operations::ModifyAnnealer
• ModifyStoredRBConfs() : protocols::enzdes::ModifyStoredRBConfs
• ModifyVariantTypeMover() : protocols::simple_moves::ModifyVariantTypeMover
• molar_mass() : core::chemical::ResidueType
• MolarMassFilter() : protocols::ligand_docking::MolarMassFilter
• MolData() : core::chemical::sdf::MolData
• molecular_mass() : core::chemical::ResidueType
• MolecularDynamics() : protocols::cartesian::MolecularDynamics
• MolecularMassFilter() : protocols::ligand_docking::MolecularMassFilter
• MolecularSurfaceCalculator() : core::scoring::sc::MolecularSurfaceCalculator
• MolFileParser() : core::chemical::sdf::MolFileParser
• moltenres_2_resid() : protocols::flexpack::rotamer_set::FlexbbRotamerSets , core::pack::rotamer_set::RotamerSetsBase , core::pack::rotamer_set::RotamerSubsets , core::pack::rotamer_set::RotamerSets
• moltenres_2_resid_vector() : core::pack::rotamer_set::FixbbRotamerSets , core::pack::rotamer_set::RotamerSubsets , core::pack::rotamer_set::RotamerSets
• moltenres_atomtree_collection() : core::pack::scmin::AtomTreeCollection
• moltenres_for_rotamer() : core::pack::rotamer_set::RotamerSubsets , protocols::flexpack::rotamer_set::FlexbbRotamerSets , core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSetsBase
• moltenres_for_sample_rot() : core::pack::rotamer_set::ContinuousRotamerSets
• moltenres_part_of_flexsegment() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• moltenres_rotid_2_rotid() : core::pack::rotamer_set::RotamerSetsBase , protocols::flexpack::rotamer_set::FlexbbRotamerSets , core::pack::rotamer_set::RotamerSets , 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::hackelec::HackElecEnergy
• monoub_apply() : protocols::ub_e2c::ubi_e2c_modeler
• monoub_assign_CSPs() : protocols::ub_e2c::ubi_e2c_modeler
• monoub_calc_interaction_energy() : protocols::ub_e2c::ubi_e2c_modeler
• monoub_calc_Lrmsd() : protocols::ub_e2c::ubi_e2c_modeler
• monoub_centroid_filter() : protocols::ub_e2c::ubi_e2c_modeler
• monoub_centroid_mode_perturbation() : protocols::ub_e2c::ubi_e2c_modeler
• monoub_CSP_fraction() : protocols::ub_e2c::ubi_e2c_modeler
• monoub_first_perturbation() : protocols::ub_e2c::ubi_e2c_modeler
• monoub_fold_tree() : protocols::ub_e2c::ubi_e2c_modeler
• monoub_fullatom_filter() : protocols::ub_e2c::ubi_e2c_modeler
• monoub_fullatom_mode_perturbation() : protocols::ub_e2c::ubi_e2c_modeler
• monoub_initial_cter_perturbation() : protocols::ub_e2c::ubi_e2c_modeler
• monoub_initial_perturbation() : protocols::ub_e2c::ubi_e2c_modeler
• monoub_setup_key_residues() : protocols::ub_e2c::ubi_e2c_modeler
• monoub_setup_move_maps() : protocols::ub_e2c::ubi_e2c_modeler
• monte_carlo() : protocols::canonical_sampling::MetropolisHastingsMover , protocols::canonical_sampling::TemperatureController
• MonteCarlo() : protocols::moves::MonteCarlo
• MonteCarloLoader() : protocols::jd2::parser::MonteCarloLoader
• MonteCarloRecover() : protocols::simple_moves::MonteCarloRecover
• MonteCarloTest() : protocols::simple_moves::MonteCarloTest
• MonteCarloUtil() : protocols::moves::MonteCarloUtil
• more_precise_base_pair_classification() : core::scoring::rna::RNA_LowResolutionPotential
• most_probable_bin() : protocols::frag_picker::quota::ABEGO_SS_Config
• Motif() : protocols::motifs::Motif
• motif_library() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• motifcop() : protocols::motifs::MotifHit
• MotifDnaPacker() : protocols::motifs::MotifDnaPacker
• MotifHit() : protocols::motifs::MotifHit
• MotifLibrary() : protocols::motifs::MotifLibrary
• MotifSearch() : protocols::motifs::MotifSearch
• movable_jumps() : protocols::docking::DockingProtocol , protocols::docking::TemperedDocking , protocols::toolbox::task_operations::InterfaceTaskOperation , protocols::docking::DockMCMCycle , protocols::docking::DockingProtocol , protocols::docking::RigidBodyInfo , protocols::docking::DockingHighRes
• move_all_inserted() : protocols::abinitio::MembraneAbinitio
• move_atoms_to_collcheck_begin() : protocols::toolbox::match_enzdes_util::LigandConformer
• move_ligand_() : protocols::pockets::PlaidFingerprint
• move_ligand_and_update_rhos_() : protocols::pockets::PlaidFingerprint
• move_ligand_to_desired_centroid() : protocols::ligand_docking::LigandBaseProtocol
• move_map() : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::simple_moves::SaneMinMover
• move_pose_to_standard_orie() : protocols::pockets::PocketGrid
• MoveBeforeFilter() : protocols::filters::MoveBeforeFilter
• moved() : core::scoring::EnergyNode , core::pack::interaction_graph::SimpleNode
• moveFromStubFrame() : protocols::hotspot_hashing::StubGenerator
• moveIntoStubFrame() : protocols::hotspot_hashing::StubGenerator
• movemap() : protocols::abinitio::ClassicAbinitio , protocols::forge::build::BuildInstruction , protocols::forge::build::ConnectRight , protocols::forge::build::GrowRight , protocols::loops::loop_closure::ccd::CcdLoopClosureMover , protocols::loops::loop_closure::ccd::LoopClosure , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::simple_moves::BBGaussianMover , protocols::simple_moves::carbohydrates::RingConformationMover , protocols::simple_moves::MinMover , protocols::simple_moves::BackboneMover
• MoveMap() : core::kinematics::MoveMap
• movemap() : protocols::simple_moves::FragmentMover , protocols::simple_moves::BackboneMover , protocols::simple_moves::MinMover , protocols::simple_moves::BBGaussianMover , protocols::forge::build::BuildManager , protocols::forge::build::SegmentInsert , protocols::simple_moves::carbohydrates::RingConformationMover , protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure , protocols::abinitio::KinematicControl , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap , protocols::forge::build::GrowLeft , protocols::forge::build::Bridge , protocols::abinitio::MembraneAbinitio , protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• movemap_as_OP() : protocols::forge::build::BuildManager
• movemap_cen() : protocols::anchored_design::AnchorMoversData
• movemap_cen_all() : protocols::anchored_design::AnchorMoversData
• movemap_cen_omegafixed() : protocols::anchored_design::AnchorMoversData
• movemap_fa() : protocols::anchored_design::AnchorMoversData
• movemap_fa_all() : protocols::anchored_design::AnchorMoversData
• movemap_fa_omegafixed() : protocols::anchored_design::AnchorMoversData
• movemap_from_blueprint() : protocols::flxbb::FlxbbDesign
• movemap_ptr() : protocols::abinitio::KinematicControl
• movemap_torsion_id_begin() : core::kinematics::MoveMap
• movemap_torsion_id_end() : core::kinematics::MoveMap
• MoveMapBuilder() : protocols::ligand_docking::MoveMapBuilder
• MoveMapBuilderLoader() : protocols::ligand_docking::MoveMapBuilderLoader
• MovePoseToMembraneCenterMover() : protocols::rigid::MovePoseToMembraneCenterMover
• mover() : protocols::moves::TrialMover , protocols::simple_moves::rational_mc::RationalMonteCarlo , protocols::topology_broker::FragmentClaimer
• Mover() : protocols::moves::Mover
• mover() : protocols::topology_broker::TopologyBroker , protocols::abinitio::FragmentSampler , protocols::flxbb::DesignTask
• mover_by_index() : protocols::canonical_sampling::MetropolisHastingsMover
• Mover_LoopHashRefine() : protocols::loophash::Mover_LoopHashRefine
• mover_name() : protocols::backrub::BackrubMoverCreator , protocols::canonical_sampling::PDBTrajectoryRecorderCreator , protocols::simple_moves::PackRotamersMoverCreator , protocols::simple_moves::MutateResidueCreator , protocols::canonical_sampling::MetropolisHastingsMoverCreator , protocols::protein_interface_design::movers::RepackMinimizeCreator , protocols::canonical_sampling::SimulatedTemperingCreator , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMoverCreator , protocols::simple_moves::MonteCarloRecoverCreator , protocols::ligand_docking::RandomConformersCreator , protocols::protein_interface_design::movers::LoopLengthChangeCreator , protocols::simple_moves::RepackSidechainsMoverCreator , protocols::protein_interface_design::movers::DisulfideMoverCreator , protocols::protein_interface_design::movers::PlaceStubMoverCreator , protocols::dna::DnaInterfaceMultiStateDesignCreator , protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMoverCreator , protocols::backrub::BackrubSidechainMoverCreator , protocols::ligand_docking::RotatesCreator , protocols::ligand_docking::RotateCreator , protocols::simple_moves::ScoreMoverCreator , protocols::docking::DockSetupMoverCreator , protocols::protein_interface_design::movers::PlacementAuctionMoverCreator , protocols::forge::remodel::RemodelLoopMoverCreator , protocols::canonical_sampling::TrialCounterObserverCreator , protocols::docking::TemperedDockingCreator , protocols::ligand_docking::StartFromCreator , protocols::enzdes::EnzRepackMinimizeCreator , protocols::simple_moves::sidechain_moves::PerturbChiSidechainMoverCreator , protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMoverCreator , protocols::protein_interface_design::movers::LoopOverCreator , protocols::fldsgn::CircularPermutationCreator , protocols::simple_moves::sidechain_moves::SetChiMoverCreator , protocols::protein_interface_design::movers::FavorNativeResiduePreCycleCreator , protocols::simple_moves::symmetry::SymPackRotamersMoverCreator , protocols::ligand_docking::AddHydrogensCreator , protocols::seeded_abinitio::CoordinateCstCreator , protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMoverCreator , protocols::protein_interface_design::movers::SpliceCreator , protocols::enzdes::BackboneSamplerCreator , protocols::seeded_abinitio::SeedSetupMoverCreator , protocols::protein_interface_design::movers::VLBCreator , protocols::protein_interface_design::movers::HotspotHasherMoverCreator , protocols::simple_moves::PackRotamersMoverLazyCreator , protocols::fldsgn::BluePrintBDRCreator , protocols::canonical_sampling::ParallelTemperingCreator , protocols::design_opt::GreedyOptMutationMoverCreator , protocols::ligand_docking::TransformCreator , protocols::enzdes::PredesignPerturbMoverCreator , protocols::loophash::LoopHashDiversifierCreator , protocols::simple_moves::MinPackMoverCreator , protocols::protein_interface_design::movers::PrepackMoverCreator , protocols::dna::DesignProteinBackboneAroundDNACreator , protocols::design_opt::ParetoOptMutationMoverCreator , protocols::simple_moves::sidechain_moves::SidechainMoverCreator , protocols::ligand_docking::HighResDockerCreator , protocols::docking::ConformerSwitchMoverCreator , protocols::ligand_docking::CompoundTranslateCreator , protocols::protein_interface_design::movers::PeptideStapleDesignMoverCreator , protocols::dna::DnaInterfaceMinMoverCreator , protocols::loops::FoldTreeFromLoopsCreator , protocols::simple_moves::PDBReloadMoverCreator , protocols::nonlocal::SingleFragmentMoverCreator , protocols::simple_moves::RotamerTrialsMoverCreator , protocols::contact_map::ContactMapCreator , protocols::simple_moves::MakePolyXMoverCreator , protocols::abinitio::DomainAssemblyCreator , protocols::simple_moves::FavorSequenceProfileCreator , protocols::canonical_sampling::SilentTrajectoryRecorderCreator , protocols::protein_interface_design::movers::PlaceOnLoopCreator , protocols::protein_interface_design::movers::SetAtomTreeCreator , protocols::simple_moves::SequenceProfileMoverCreator , protocols::protein_interface_design::movers::ShoveResidueMoverCreator , protocols::protein_interface_design::movers::RandomMutationCreator , protocols::simple_moves::GenericMonteCarloMoverCreator , protocols::canonical_sampling::MetricRecorderCreator , protocols::idealize::IdealizeMoverCreator , protocols::simple_moves::ShearMoverCreator , protocols::moves::IteratedConvergenceMoverCreator , protocols::simple_moves::symmetry::DetectSymmetryMoverCreator , protocols::simple_moves::MinMoverCreator , protocols::simple_moves::SwitchChainOrderMoverCreator , protocols::simple_moves::symmetry::SymMinMoverCreator , protocols::fldsgn::SheetCstGeneratorCreator , protocols::qsar::qsarCreator , protocols::simple_moves::RotamerTrialsMinMoverCreator , protocols::protein_interface_design::movers::BestHotspotCstMoverCreator , protocols::ligand_docking::MinimizeBackboneCreator , protocols::protein_interface_design::movers::SpinMoverCreator , protocols::simple_moves::symmetry::SetupForSymmetryMoverCreator , protocols::protein_interface_design::movers::InterfaceRecapitulationMoverCreator , protocols::protein_interface_design::movers::LoopFinderCreator , protocols::protein_interface_design::movers::DockAndRetrieveSidechainsCreator , protocols::simple_moves::DumpPdbCreator , protocols::ligand_docking::SlideTogetherCreator , protocols::flxbb::FlxbbDesignCreator , protocols::simple_moves::ForceDisulfidesMoverCreator , protocols::simple_moves::ConstraintSetMoverCreator , protocols::rigid::RigidBodyPerturbNoCenterMoverCreator , protocols::features::ReportToDBCreator , protocols::simple_moves::SaneMinMoverCreator , protocols::simple_moves::LoadUnboundRotMoverCreator , protocols::ligand_docking::InterfaceScoreCalculatorCreator , protocols::docking::DockingProtocolCreator , protocols::simple_moves::ExtendedPoseMoverCreator , protocols::ligand_docking::LigandDesignCreator , protocols::simple_moves::TaskAwareMinMoverCreator , protocols::simple_moves::CutChainMoverCreator , protocols::simple_moves::ConsensusDesignMoverCreator , protocols::relax::ClassicRelaxCreator , protocols::simple_moves::LoadPDBMoverCreator , protocols::canonical_sampling::SidechainMetropolisHastingsMoverCreator , protocols::seeded_abinitio::SwapSegmentCreator , protocols::rotamer_recovery::RotamerRecoveryMoverCreator , protocols::simple_moves::SuperimposeMoverCreator , protocols::simple_moves::sidechain_moves::SidechainMCMoverCreator , protocols::enzdes::AddOrRemoveMatchCstsCreator , protocols::qsar::scoring_grid::GridInitMoverCreator , protocols::flxbb::InterlockAromaCreator , protocols::forge::remodel::ResidueVicinityCstGeneratorCreator , protocols::simple_moves::AddConstraintsToCurrentConformationMoverCreator , protocols::simple_moves::ClearConstraintsMoverCreator , protocols::forge::remodel::RemodelMoverCreator , protocols::relax::FastRelaxCreator , protocols::seeded_abinitio::CloseFoldCreator , protocols::hybridization::CartesianSamplerCreator , protocols::hotspot_hashing::movers::PlaceSurfaceProbeCreator , protocols::rosetta_scripts::SavePoseMoverCreator , protocols::qsar::RenderGridsToKinemageCreator , protocols::simple_moves::SwitchResidueTypeSetMoverCreator , protocols::simple_moves::SmallMoverCreator , protocols::rosetta_scripts::ParsedProtocolCreator , protocols::seeded_abinitio::SeedFoldTreeCreator , protocols::seeded_abinitio::CAcstGeneratorCreator , protocols::forge::constraints::NtoCCstGeneratorCreator , protocols::seeded_abinitio::GrowPeptidesCreator , protocols::forge::constraints::RemoveCstsCreator , protocols::hybridization::HybridizeProtocolCreator , protocols::rigid::RollMoverCreator , protocols::simple_moves::symmetry::ExtractAsymmetricUnitMoverCreator , protocols::forge::constraints::ConstraintFileCstGeneratorCreator , protocols::fldsgn::potentials::SetSecStructEnergiesCreator , protocols::simple_moves::SetTorsionCreator , protocols::simple_moves::symmetry::ExtractAsymmetricPoseMoverCreator , protocols::forge::constraints::InvrotTreeCstGeneratorCreator , protocols::protein_interface_design::movers::SetupHotspotConstraintsMoverCreator , protocols::protein_interface_design::movers::TryRotamersCreator , protocols::simple_moves::symmetry::SymRotamerTrialsMoverCreator , protocols::protein_interface_design::movers::FavorNonNativeResiduePreCycleCreator , protocols::canonical_sampling::HamiltonianExchangeCreator , protocols::seeded_abinitio::SegmentHybridizerCreator , protocols::simple_moves::ddGCreator , protocols::protein_interface_design::movers::SubroutineMoverCreator , protocols::protein_interface_design::movers::TaskAwareCstsCreator , protocols::seeded_abinitio::DefineMovableLoopsCreator , protocols::simple_moves::MembraneTopologyCreator , protocols::dna::DnaInterfacePackerCreator , protocols::protein_interface_design::movers::SetTemperatureFactorCreator , protocols::simple_moves::MonteCarloTestCreator , protocols::protein_interface_design::movers::SaveAndRetrieveSidechainsCreator , protocols::protein_interface_design::movers::PlaceSimultaneouslyMoverCreator , protocols::dna::SeparateDnaFromNonDnaCreator , protocols::fldsgn::potentials::SetAACompositionPotentialCreator , protocols::comparative_modeling::LoopRelaxMoverCreator , protocols::protein_interface_design::movers::PlacementMinimizationMoverCreator , protocols::protein_interface_design::movers::LoopRemodelCreator , protocols::flexpep_docking::FlexPepDockingProtocolCreator , protocols::docking::DockingInitialPerturbationCreator , protocols::protein_interface_design::movers::MapHotspotCreator , protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMoverCreator , protocols::forge::constraints::InverseRotamersCstGeneratorCreator , protocols::protein_interface_design::movers::LoopMoverFromCommandLineCreator , protocols::loophash::LoopHashMoverWrapperCreator , protocols::ligand_docking::FinalMinimizerCreator , protocols::ligand_docking::GrowLigandCreator , protocols::ligand_docking::TranslateCreator , protocols::electron_density::SetupForDensityScoringMoverCreator , protocols::match::MatcherMoverCreator , protocols::moves::DsspMoverCreator , protocols::protein_interface_design::movers::DesignMinimizeHbondsCreator , protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspotsCreator , protocols::moves::RandomMoverCreator , protocols::protein_interface_design::movers::AddChainBreakCreator , protocols::motifs::MotifDnaPackerCreator , protocols::protein_interface_design::movers::BackrubDDMoverCreator , protocols::moves::RampingMoverCreator , protocols::pb_potential::SetupPoissonBoltzmannPotentialCreator , protocols::moves::IfMoverCreator , protocols::protein_interface_design::movers::BuildAlaPoseCreator , protocols::enzdes::PackRotamersMoverPartGreedyCreator , protocols::analysis::InterfaceAnalyzerMoverCreator , protocols::simple_moves::symmetry::SetupNCSMoverCreator
• mover_tag() : protocols::topology_broker::FragmentClaimer
• mover_weight() : protocols::topology_broker::TopologyClaimer
• MoverContainer() : protocols::moves::MoverContainer
• MoverCreator() : protocols::moves::MoverCreator
• MoverFactory() : protocols::moves::MoverFactory
• MoverList() : protocols::wum::MoverList
• MoverRegistrator() : protocols::moves::MoverRegistrator< T >
• movers() : protocols::moves::MoverContainer
• MoverStatistics() : protocols::moves::MoverStatistics
• moves_residue() : core::fragment::NonContinuousFrame , core::fragment::Frame
• moving_pos() : protocols::swa::StepWiseJobParameters
• moving_res() : protocols::swa::rna::StepWiseRNA_JobParameters
• moving_res_contact_filter() : protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer
• moving_res_list() : protocols::swa::monte_carlo::SubToFullInfo
• moving_residues() : protocols::swa::protein::StepWiseProteinPoseSetup
• moving_suite() : protocols::swa::rna::StepWiseRNA_RotamerGenerator
• mpi_broadcast_eval_dfunc() : protocols::optimize_weights::OptEMultifunc
• mpi_broadcast_eval_func() : protocols::optimize_weights::OptEMultifunc
• mpi_broadcast_receive_vars() : protocols::optimize_weights::OptEMultifunc
• mpi_broadcast_send_vars() : protocols::optimize_weights::OptEMultifunc
• mpi_feedback() : protocols::loophash::MPI_LoopHashRefine
• mpi_finalize() : protocols::jd2::JobDistributor , protocols::jd2::MPIWorkPoolJobDistributor
• MPI_LoopHashRefine() : protocols::loophash::MPI_LoopHashRefine
• MPI_LoopHashRefine_Emperor() : protocols::loophash::MPI_LoopHashRefine_Emperor
• MPI_LoopHashRefine_Master() : protocols::loophash::MPI_LoopHashRefine_Master
• mpi_receive_dfunc() : protocols::optimize_weights::OptEMultifunc
• mpi_receive_func() : protocols::optimize_weights::OptEMultifunc
• MPI_Relax() : protocols::wum::MPI_Relax
• mpi_resume() : protocols::loophash::MPI_LoopHashRefine
• MPI_WorkUnitManager() : protocols::wum::MPI_WorkUnitManager
• MPI_WorkUnitManager_Slave() : protocols::wum::MPI_WorkUnitManager_Slave
• MPIArchiveJobDistributor() : protocols::jd2::archive::MPIArchiveJobDistributor
• MPIBPool_RMSD() : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD
• MpiFileBuffer() : protocols::jd2::MpiFileBuffer
• MPIFileBufJobDistributor() : protocols::jd2::MPIFileBufJobDistributor
• MPIHPool_RMSD() : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• MPIMultiCommJobDistributor() : protocols::jd2::MPIMultiCommJobDistributor
• MPIMultistateFitnessFunction() : protocols::pack_daemon::MPIMultistateFitnessFunction
• MPIPool_RMSD() : protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD
• MPIWorkPartitionJobDistributor() : protocols::jd2::MPIWorkPartitionJobDistributor
• MPIWorkPoolJobDistributor() : protocols::jd2::MPIWorkPoolJobDistributor
• msa() : core::scoring::packstat::PackingScoreResData
• mu() : core::scoring::methods::BBDepCartBondedParameters , core::scoring::methods::CartBondedParameters , core::scoring::methods::BBIndepCartBondedParameters
• multi_cool_annealer() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• multi_cool_annealer_history_size() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• multi_fast_relax() : protocols::abinitio::AbrelaxApplication
• multi_relative() : protocols::simple_filters::Operator
• multi_threading_inner_job() : protocols::jd2::MultiThreadingJob
• multicomp() : protocols::simple_filters::ShapeComplementarityFilter
• MultiConstraint() : core::scoring::constraints::MultiConstraint
• MultiConstraintCreator() : core::scoring::constraints::MultiConstraintCreator
• MultiCoolAnnealer() : core::pack::annealer::MultiCoolAnnealer
• Multifunc() : core::optimization::Multifunc
• MultipleDomainMover() : protocols::rna::MultipleDomainMover
• MultiplicitiveFactor() : core::scoring::FACTSPotential
• multiplicity() : core::scoring::constraints::AmbiguousNMRDistanceConstraint
• MultiProbePerSphereAccumulator() : core::scoring::packstat::MultiProbePerSphereAccumulator
• MultiProbePoseAccumulator() : core::scoring::packstat::MultiProbePoseAccumulator
• MultistateAggregateFunction() : protocols::pack_daemon::MultistateAggregateFunction
• MultiStateAggregateFunction() : protocols::multistate_design::MultiStateAggregateFunction
• MultiStateEntity() : protocols::multistate_design::MultiStateEntity< T >
• MultiStateFitnessFunction() : protocols::multistate_design::MultiStateFitnessFunction
• MultistateFitnessFunction() : protocols::pack_daemon::MultistateFitnessFunction
• MultiStatePacker() : protocols::multistate_design::MultiStatePacker
• MultiTemperatureTrialCounter() : protocols::canonical_sampling::MultiTemperatureTrialCounter
• MultiThreadingJob() : protocols::jd2::MultiThreadingJob
• MultiThreadingMover() : protocols::comparative_modeling::MultiThreadingMover
• mut_residue() : protocols::pmut_scan::MutationData
• mut_to_gly() : protocols::analysis::InterfaceAnalyzerMover
• Mutant() : protocols::pmut_scan::Mutant
• mutant_score_components() : protocols::ddg::ddGMover
• mutants_begin() : protocols::pmut_scan::PointMutScanDriver
• mutants_end() : protocols::pmut_scan::PointMutScanDriver
• mutate() : protocols::genetic_algorithm::DiscreteRandomizer , protocols::genetic_algorithm::EntityRandomizer , core::optimization::GA_Minimizer , protocols::genetic_algorithm::PositionSpecificRandomizer
• mutate_and_relax() : protocols::design_opt::PointMutationCalculator
• MutateResidue() : protocols::simple_moves::MutateResidue
• mutation_ddGs() : core::io::PositionDdGInfo::PositionDdGInfo
• mutation_label() : protocols::ddg::ddGMover
• mutation_rate() : protocols::genetic_algorithm::EntityRandomizer
• mutation_string() : protocols::pmut_scan::MutationData
• mutation_string_PDB_numbering() : protocols::pmut_scan::MutationData
• mutation_threshold() : protocols::protein_interface_design::filters::SequenceRecoveryFilter
• MutationData() : protocols::pmut_scan::MutationData
• mutations() : protocols::protein_interface_design::filters::SequenceRecoveryFilter
• mutations_begin() : protocols::pmut_scan::Mutant
• mutations_end() : protocols::pmut_scan::Mutant
• mvmul() : protocols::frag_picker::scores::RDCScore
• my_emperor() : protocols::wum::DatabaseQueryWorkUnitManager< T > , protocols::loophash::MPI_LoopHashRefine_Master
• my_residue_pair_energy() : core::scoring::methods::DirectReadoutEnergy
• MyAtom() : protocols::fldsgn::MyAtom