- 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_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() : protocols::abinitio::abscript::StructPerturberCM
• magnitude_rotation() : protocols::rigid::RigidBodyMotionMover
• magnitude_translation() : protocols::rigid::RigidBodyMotionMover
• main_atom() : protocols::noesy_assign::CrossPeakInfo
• main_chain_torsion_set() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer
• main_chain_torsion_set_lists() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger , protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• main_chain_torsion_set_lists_real() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• main_chain_torsion_set_save() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer
• main_chain_torsion_sets() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_MultiPoseCloser
• 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
• MainChainTorsionSet() : protocols::stepwise::modeler::protein::MainChainTorsionSet
• make() : protocols::frag_picker::scores::MakeABEGO_SS_Score , 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::MakeFragmentChunkCrms , 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 , 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::MakeTalosSSSimilarity , protocols::frag_picker::scores::MakeTorsionBinSimilarity
• make_asymmetric_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_claim() : protocols::environment::claims::EnvClaim
• make_compatible_with_ROCS_custom_ForceField() : protocols::pockets::GenPharmacophore
• 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::denovo_design::DisulfidizeMover , protocols::forge::remodel::RemodelDesignMover
• make_disulfide_fast() : protocols::forge::remodel::RemodelDesignMover
• make_disulfides() : protocols::denovo_design::DisulfidizeMover
• 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_extended_pose() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• make_fibril() : protocols::topology_broker::FibrilModelingClaimer
• make_filename() : protocols::ncbb::SecStructFinder
• make_fragment_moves() : protocols::farna::movers::RNA_Relaxer
• make_full_pose() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• make_Hessian_ANM() : protocols::normalmode::NormalMode
• make_Hessian_TNM() : protocols::normalmode::NormalMode
• make_inner_cycle_from_string_name() : protocols::loops::loop_mover::refine::LoopRefineInnerCycleFactory
• make_interface_combos() : protocols::features::InterfaceFeatures
• 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::BBConRotMover , protocols::simple_moves::ShearMover , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase , protocols::simple_moves::SmallMover
• make_movemap() : protocols::ligand_docking::LigandBaseProtocol
• make_movie() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• 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_mutations() : protocols::membrane::MPMutateRelaxMover
• 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_partially_soft_etable() : core::scoring::ScoringManager
• make_pose() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• make_pymol_script() : protocols::flxbb::LayerDesignOperation
• make_rasmol_format_file() : core::select::util::SelectResiduesByLayer
• 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_claim() : protocols::topology_broker::SequenceClaimer
• make_sequence_shift() : protocols::loops::Loops
• make_sequence_symmetric() : protocols::topology_broker::TopologyBroker
• 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::SymEnergyCutRotamerTrialsMover , protocols::simple_moves::symmetry::SymPackRotamersMover , protocols::simple_moves::symmetry::SymRotamerTrialsMover
• make_tail() : protocols::simple_moves::TailsScoreMover
• make_three_fold_symmetry_90_210_330() : protocols::make_rot_lib::MakeRotLibMover
• make_tweaked_scorefxn() : protocols::ligand_docking::LigandBaseProtocol
• make_two_fold_symmetry_0_180() : protocols::make_rot_lib::MakeRotLibMover
• make_two_fold_symmetry_135_315() : protocols::make_rot_lib::MakeRotLibMover
• make_vrt() : protocols::cryst::MakeLatticeMover , protocols::cryst::MakeLayerMover , protocols::simple_moves::PeriodicBoxMover
• 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
• MakeBundle() : protocols::helical_bundle::MakeBundle
• MakeBundleHelix() : protocols::helical_bundle::MakeBundleHelix
• MakeCanonicalHelix() : protocols::membrane::benchmark::MakeCanonicalHelix
• 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
• MakeFragmentAllAtomCrmsd() : protocols::frag_picker::scores::MakeFragmentAllAtomCrmsd
• MakeFragmentChunkCrms() : protocols::frag_picker::scores::MakeFragmentChunkCrms
• 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
• MakeLatticeMover() : protocols::cryst::MakeLatticeMover
• MakeLayerMover() : protocols::cryst::MakeLayerMover
• 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
• MakeRotLibJob() : protocols::make_rot_lib::MakeRotLibJob
• MakeRotLibJobInputter() : protocols::make_rot_lib::MakeRotLibJobInputter
• MakeRotLibMover() : protocols::make_rot_lib::MakeRotLibMover
• MakeRotLibOptionsData() : protocols::make_rot_lib::MakeRotLibOptionsData
• 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
• MakeStarTopologyMover() : protocols::rbsegment_relax::MakeStarTopologyMover
• 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::RemodelWorkingSet
• map() : core::id::CacheableAtomID_MapVector
• map2keyvector() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• map2target() : protocols::abinitio::Template
• map2template() : protocols::abinitio::Template
• map_from_reference() : protocols::toolbox::AtomID_Mapper
• map_from_spectrum() : protocols::electron_density::DockIntoDensityMover
• 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_residues() : protocols::sewing::Assembly
• map_ss_segments() : protocols::fldsgn::MatchResidues
• map_symmetric_res_pairs() : core::conformation::symmetry::SymmetryInfo
• map_to_CEN() : core::scoring::constraints::AmbiguousNMRDistanceConstraint
• map_to_reference() : protocols::toolbox::AtomID_Mapper
• mapfile_activated() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• MapHotspot() : protocols::protein_interface_design::movers::MapHotspot
• mapping() : core::id::SequenceMapping
• mapSphericalSamples() : core::scoring::electron_density::ElectronDensity
• mapto() : core::scoring::constraints::Obsolet_NamedAtomPairConstraint
• mark() : protocols::pockets::ComparisonGrid , protocols::pockets::PocketGrid
• mark_as_cancelled() : protocols::jd2::archive::Batch
• mark_as_default() : protocols::kinematic_closure::perturbers::PerturberSet , protocols::loop_modeling::LoopProtocol , protocols::loop_modeling::utilities::LoopMoverGroup
• mark_as_finished() : protocols::jd2::archive::Batch
• mark_as_invalid() : protocols::jd2::archive::Batch
• mark_as_test_run() : protocols::loop_modeling::LoopProtocol
• mark_atom_espGrid_points() : protocols::pockets::ElectrostaticpotentialGrid
• mark_buried_solvent_points() : protocols::pockets::ElectrostaticpotentialGrid
• mark_connected() : protocols::denovo_design::components::StructureData
• mark_current_job_id_for_repetition() : protocols::jd2::BOINCJobDistributor , protocols::jd2::FileSystemJobDistributor , protocols::jd2::JobDistributor , protocols::jd2::MPIFileBufJobDistributor , protocols::jd2::MPIWorkPartitionJobDistributor , protocols::jd2::MPIWorkPoolJobDistributor , protocols::jd2::MSDJobDistributor , protocols::jd2::ShuffleFileSystemJobDistributor
• mark_designable() : protocols::toolbox::task_operations::DatabaseThread
• mark_disconnected() : protocols::denovo_design::components::StructureData
• 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::PolymerBondedNeighborIterator , 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::PolymerBondedNeighborIterator , core::scoring::ResidueNeighborIterator
• mark_entity_as_unimportant() : protocols::pack_daemon::DaemonSet , protocols::pack_daemon::PackDaemon
• 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_job_as_having_begun() : protocols::jd3::JobQueen
• mark_job_as_having_started() : protocols::jd3::pose_outputters::PDBPoseOutputter , protocols::jd3::PoseOutputter
• mark_last_entity_as_important() : protocols::pack_daemon::DaemonSet , protocols::pack_daemon::PackDaemon
• mark_leave_as_is() : protocols::toolbox::task_operations::DatabaseThread
• mark_loop_moveable() : protocols::forge::remodel::RemodelLoopMover
• mark_loops_moveable() : protocols::forge::remodel::RemodelLoopMover
• mark_protein_espGrid_points() : protocols::pockets::ElectrostaticpotentialGrid
• mark_residue_moved() : core::kinematics::ResidueCoordinateChangeList
• mark_revision_id_expired() : core::scoring::constraints::ConstraintSet
• mark_rotwell_exists() : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::rotamers::SingleResiduePeptoidLibrary
• mark_similar_jobs_which_have_bad_inputs_in_job_list() : protocols::jd3::JobDistributor
• 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::ResidueType
• master() : core::conformation::ConformationKinWriter , core::conformation::ResidueKinWriter , protocols::match::output::ResidueKinemageWriter
• 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_mark_job_as_completed() : protocols::jd2::MPIWorkPoolJobDistributor
• master_mark_job_as_failed() : protocols::jd2::MPIWorkPoolJobDistributor
• master_mover() : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• master_rank() : protocols::jd2::MPIFileBufJobDistributor , protocols::loophash::MPI_LoopHashRefine_Master , protocols::mpi_refinement::MPI_Refine_Master
• 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
• match2D() : protocols::noesy_assign::FloatingResonance , protocols::noesy_assign::LabelResonance , protocols::noesy_assign::ProtonResonance , protocols::noesy_assign::Resonance
• match_aa1() : core::scoring::motif::ResPairMotifQuery
• match_aa2() : core::scoring::motif::ResPairMotifQuery
• match_chi_rmsd() : core::scoring::motif::ResPairMotifQuery
• match_dspos1() : protocols::match::match_dspos1
• 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_radius() : core::scoring::motif::ResPairMotifQuery
• match_score() : core::sequence::SimpleScoringScheme
• match_ss1() : core::scoring::motif::ResPairMotifQuery
• match_ss2() : core::scoring::motif::ResPairMotifQuery
• match_variants() : core::chemical::ResidueTypeSelector , protocols::environment::ProtectedConformation
• 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
• matches_any_atom_name() : core::chemical::ResidueTypeFinder
• matches_any_patch_name() : core::chemical::ResidueTypeFinder
• matches_residue_type() : core::scoring::lkball::LKB_ResidueInfo
• MatchFilter() : protocols::match::output::MatchFilter
• MatchGrafter() : protocols::metal_interface::MatchGrafter
• MatchGrouper() : protocols::match::output::MatchGrouper
• MatchOutputter() : protocols::match::output::MatchOutputter
• MatchOutputTracker() : protocols::match::MatchOutputTracker
• matchPointFast() : core::scoring::electron_density::ElectronDensity
• matchPose() : 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
• MatchScoreWriter() : protocols::match::output::MatchScoreWriter
• MatDesGreedyOptMutationMover() : protocols::matdes::MatDesGreedyOptMutationMover
• MatDesPointMutationCalculator() : protocols::matdes::MatDesPointMutationCalculator
• matrix() : protocols::frag_picker::LAMBEGO_IO , protocols::frag_picker::TorsionBinIO
• matrix3f_to_xyzMatrix() : protocols::forge::remodel::RemodelGlobalFrame , protocols::simple_filters::RepeatParameterFilter
• matrix_finalized() : core::scoring::bin_transitions::BinTransitionData
• matrix_initialized() : core::scoring::bin_transitions::BinTransitionData
• MatrixScoringScheme() : core::sequence::MatrixScoringScheme
• mature_larval_job() : protocols::jd3::JobQueen
• max() : core::id::DOF_ID_Range , core::id::TorsionID_Range
• max_angle() : protocols::simple_filters::AngleToVector
• 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_ca_dis2() : core::scoring::motif::ResPairMotifQuery
• 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_cycles() : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• max_degree() : protocols::sasa_scores::PPoly
• max_dis() : core::scoring::carbon_hbonds::CarbonHBondPotential , core::scoring::custom_pair_distance::DistanceFunc , core::scoring::etable::coulomb::Coulomb , core::scoring::etable::Etable , core::scoring::methods::GoapEnergy
• max_dis2() : core::scoring::carbon_hbonds::CarbonHBondEnergy , core::scoring::etable::coulomb::Coulomb , core::scoring::etable::Etable
• max_dist() : core::kinematics::ShortestPathInFoldTree , core::scoring::mm::MMLJEnergyTable
• max_dist_squared() : protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker
• max_distance() : protocols::simple_moves::AddConstraintsToCurrentConformationMover , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• max_frag_len() : protocols::frag_picker::FragmentPicker
• max_frag_length() : core::fragment::FragSet
• max_gap_percentage() : core::sequence::SequenceAlignment
• max_generations() : protocols::genetic_algorithm::GeneticAlgorithmBase
• 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 , protocols::relax::RelaxProtocolBase , protocols::simple_moves::MinMover
• max_length() : protocols::antibody::CDRSetOptions , protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• max_level_index() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• max_lib_size() : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• max_linear_chainbreak() : protocols::fldsgn::BluePrintBDR , protocols::forge::components::BDR , protocols::forge::components::VarLengthBuild , protocols::forge::remodel::RemodelLoopMover , protocols::forge::remodel::RemodelMover
• max_loop_length() : protocols::features::LoopAnchorFeatures
• max_missing_weight() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• max_noe_distance() : protocols::noesy_assign::CrossPeakInfo
• max_non_hydrogen_lj_radius() : core::scoring::etable::Etable , core::scoring::etable::MembEtable
• max_nstruct() : protocols::jd2::archive::ArchiveBase , protocols::loophash::LoopHashMoverWrapper
• max_ntries() : protocols::stepwise::StepWiseSampleAndScreen
• max_path_length() : protocols::simple_filters::AveragePathLengthFilter
• max_per_move_torsion_delta_per_residue() : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• max_pools() : protocols::frag_picker::QuotaDebug
• max_population_size() : protocols::genetic_algorithm::GeneticAlgorithmBase
• max_pos() : core::fragment::FragSet
• max_rama_score_increase() : protocols::loops::loop_closure::ccd::RamaCheckBase
• max_ref_lib_size() : protocols::mpi_refinement::MPI_Refinement
• 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_samples() : protocols::helical_bundle::BackboneGridSampler , protocols::helical_bundle::BundleGridSampler
• max_score() : core::scoring::motif::XformScore
• max_segments() : protocols::sewing::sampling::requirements::RequirementSet
• 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_struct() : protocols::simple_moves::CombinePoseMover
• max_struct_try() : protocols::simple_moves::CombinePoseMover
• max_total_torsion_delta_per_residue() : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• max_tries() : protocols::moves::FilterMover
• max_tries_multiplier_for_ccd() : protocols::stepwise::options::StepWiseBasicOptions
• max_valence_electrons_sp() : core::chemical::ElectronConfiguration
• max_value() : protocols::simple_moves::PSSM2BfactorMover
• max_volume_contribution() : protocols::noesy_assign::CrossPeak
• maxcycles() : protocols::moves::IteratedConvergenceMover
• maxNominalRes() : core::scoring::electron_density::ElectronDensity
• MaxSeqSepConstraintSet() : protocols::constraints_additional::MaxSeqSepConstraintSet
• maxtrials() : protocols::simple_moves::GenericMonteCarloMover
• may_change_aa() : core::chemical::ChiralFlipNaming , core::chemical::PatchCase , core::chemical::PatchOperation
• 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
• MC() : protocols::moves::DualMonteCarlo
• mc() : protocols::moves::TrialMover , protocols::simple_moves::EnergyCutRotamerTrialsMover , protocols::simple_moves::symmetry::SymEnergyCutRotamerTrialsMover
• mc_accepted() : protocols::moves::MonteCarlo
• mc_accepted_string() : protocols::moves::MonteCarlo
• mc_accpeted() : protocols::simple_moves::GenericMonteCarloMover
• MC_Comb() : protocols::stepwise::sampler::MC_Comb
• MC_OneTorsion() : protocols::stepwise::sampler::MC_OneTorsion
• mc_ptr() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• MC_StepWiseSampler() : protocols::stepwise::sampler::MC_StepWiseSampler
• 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
• MDBase() : protocols::md::MDBase
• mean() : core::scoring::dna::DNA_BasePotential
• Mean() : protocols::pack_daemon::Mean
• 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::RRComparerAutomorphicRMSD , protocols::rotamer_recovery::RRComparerChiDiff , protocols::rotamer_recovery::RRComparerElecDensDiff , protocols::rotamer_recovery::RRComparerRotBins , 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
• meets_requirements() : core::chemical::Metapatch
• mem_cbeta_2TM_den12() : core::scoring::membrane::MembraneData
• mem_cbeta_2TM_den6() : core::scoring::membrane::MembraneData
• mem_cbeta_4TM_den12() : core::scoring::membrane::MembraneData
• mem_cbeta_4TM_den6() : core::scoring::membrane::MembraneData
• mem_cbeta_den12() : core::scoring::membrane::MembraneData
• mem_cbeta_den6() : core::scoring::membrane::MembraneData
• mem_env_log10() : core::scoring::membrane::MembraneData
• mem_env_log6() : core::scoring::membrane::MembraneData
• mem_foot_print() : protocols::loophash::LoopHashLibrary , protocols::loophash::LoopHashMap , protocols::wum::WorkUnitManager , protocols::wum::WorkUnitQueue
• mem_footprint() : core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::SilentStruct , protocols::relax::SRelaxPose , protocols::wum::SilentStructStore , protocols::wum::WorkUnitBase
• mem_pair_log() : core::scoring::membrane::MembraneData
• mem_stats() : protocols::wum::WorkUnitQueue
• memb_dsolv1() : core::scoring::etable::MembEtable
• memb_dsolv2() : core::scoring::etable::MembEtable
• memb_etable() : core::scoring::ScoringManager
• 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::import_pose::ImportPoseOptions
• 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_from_topology() : protocols::membrane::MPQuickRelaxMover
• membrane_info() : core::conformation::Conformation
• membrane_jump() : core::conformation::membrane::MembraneInfo
• membrane_normal() : core::conformation::membrane::MembraneInfo
• membrane_rsd_num() : core::conformation::membrane::MembraneInfo
• membrane_steepness() : core::conformation::membrane::MembraneInfo
• membrane_thickness() : core::conformation::membrane::MembraneInfo
• MembraneAbinitio() : protocols::abinitio::MembraneAbinitio
• MembraneCbetaEnergy() : core::scoring::methods::MembraneCbetaEnergy
• MembraneCenPairEnergy() : core::scoring::methods::MembraneCenPairEnergy
• MembraneCenterPerturbationMover() : protocols::rigid::MembraneCenterPerturbationMover
• MembraneData() : core::scoring::membrane::MembraneData
• 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
• MembraneInfo() : core::conformation::membrane::MembraneInfo
• MembraneJump() : protocols::jumping::MembraneJump
• MembraneLipo() : core::scoring::methods::MembraneLipo
• MembraneNormalPerturbationMover() : protocols::rigid::MembraneNormalPerturbationMover
• MembranePositionFromTopologyMover() : protocols::membrane::MembranePositionFromTopologyMover
• 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
• Memento() : protocols::kinematic_closure::ClosureProblem::Memento
• memory_usage_dynamic() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::rotamers::RotamericSingleResiduePeptoidLibrary< T, N > , core::pack::rotamers::SingleResiduePeptoidLibrary
• memory_usage_in_bytes() : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::rotamers::SingleResiduePeptoidLibrary
• memory_usage_static() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::rotamers::RotamericSingleResiduePeptoidLibrary< T, N > , core::pack::rotamers::SingleResiduePeptoidLibrary
• memory_use() : protocols::optimize_weights::ConstraintedOptimizationWeightFunc , protocols::optimize_weights::DDGBindOptEData , protocols::optimize_weights::DDGMutationOptEData , protocols::optimize_weights::DGBindOptEData , protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData , protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData , protocols::optimize_weights::OptEPositionData , protocols::optimize_weights::PNatAAOptEPositionData , protocols::optimize_weights::PNatRotOptEPositionData , protocols::optimize_weights::PNatStructureOptEData , protocols::optimize_weights::PSSMOptEPositionData
• 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::denovo_design::components::StructureData , protocols::loophash::LoopHashLibrary , protocols::wum::WorkUnitList
• merge_bbdb() : protocols::loophash::LoopHashLibrary
• merge_before() : protocols::denovo_design::components::StructureData
• merge_behavior_for_name3() : core::chemical::MergeBehaviorManager
• merge_behavior_manager() : core::chemical::ResidueTypeSet
• merge_protein_surface_poses() : protocols::surface_docking::SurfaceDockingProtocol
• merge_segments() : protocols::denovo_design::components::StructureData
• mergeable() : core::scoring::dssp::StrandPairing
• MergeBehaviorManager() : core::chemical::MergeBehaviorManager
• MergeFragSetMover() : protocols::frag_picker::frag_movers::MergeFragSetMover
• MergePDBMover() : protocols::simple_moves::MergePDBMover
• message() : protocols::denovo_design::components::EXCN_Apply , protocols::denovo_design::connection::EXCN_ConnectionFailed
• metal_bond_angle_constraint_multiplier() : core::import_pose::ImportPoseOptions
• metal_bond_dist_constraint_multiplier() : core::import_pose::ImportPoseOptions
• metal_bond_LJ_multiplier() : core::import_pose::ImportPoseOptions
• metal_set() : core::io::NomenclatureManager
• metalbinding_constraint_energy() : core::scoring::constraints::ConstraintEdge
• MetalloClaimer() : protocols::topology_broker::MetalloClaimer
• MetalSiteResidue() : protocols::metal_interface::MetalSiteResidue
• Metapatch() : core::chemical::Metapatch
• metapatch() : core::chemical::ResidueTypeSet
• MetapatchEnumeration() : protocols::residue_optimization::MetapatchEnumeration
• metapatches() : core::chemical::ResidueTypeSet
• 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
• methodname() : protocols::mpi_refinement::Scheduler
• methods_picked() : protocols::mpi_refinement::Scheduler
• 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
• mg_coord_cst_dist() : protocols::magnesium::MgMinimizer
• mg_res() : protocols::magnesium::MgMinimizer
• MgEnergy() : core::scoring::magnesium::MgEnergy
• MgHydrater() : protocols::magnesium::MgHydrater
• MgKnowledgeBasedPotential() : core::scoring::magnesium::MgKnowledgeBasedPotential
• MgMinimizer() : protocols::magnesium::MgMinimizer
• MgMonteCarlo() : protocols::magnesium::MgMonteCarlo
• MgOrbitalFrameFinder() : protocols::magnesium::MgOrbitalFrameFinder
• MgScanner() : protocols::magnesium::MgScanner
• MgWaterHydrogenPacker() : protocols::magnesium::MgWaterHydrogenPacker
• 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_angle() : protocols::simple_filters::AngleToVector
• 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 , core::scoring::etable::coulomb::Coulomb , core::scoring::etable::Etable
• min_dis2() : core::scoring::etable::coulomb::Coulomb , core::scoring::etable::Etable
• 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_lattice() : protocols::cryst::DockLatticeMover
• min_len_helix() : protocols::frags::TorsionFragmentMover
• min_len_strand() : protocols::frags::TorsionFragmentMover
• min_length() : protocols::antibody::CDRSetOptions , 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 , protocols::normalmode::NormalModeMultifunc
• min_move() : protocols::abinitio::FoldConstraints
• min_neighbor_sc() : protocols::antibody::design::CDRGraftDesignOptions
• min_options() : protocols::simple_moves::MinMover , protocols::simple_moves::SaneMinMover
• min_pair_data_type() : core::scoring::etable::BaseEtableEnergy< Derived >
• min_pos() : core::fragment::FragSet
• min_rb() : protocols::antibody::design::CDRGraftDesignOptions , 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::antibody::design::CDRGraftDesignOptions , protocols::simple_moves::DesignRepackMover
• min_sc_set() : protocols::simple_moves::DesignRepackMover
• min_segments() : protocols::sewing::sampling::requirements::RequirementSet
• min_seq_sep() : protocols::simple_moves::AddConstraintsToCurrentConformationMover
• min_seq_separation_residue_assignment() : protocols::noesy_assign::CrossPeak
• min_single_data_type() : core::scoring::etable::BaseEtableEnergy< Derived >
• min_solution_count() : protocols::generalized_kinematic_closure::GeneralizedKIC
• min_tolerance() : protocols::stepwise::options::StepWiseBasicOptions
• min_trial() : protocols::abinitio::FoldConstraints
• min_type() : core::optimization::MinimizerOptions , protocols::relax::RelaxProtocolBase , protocols::simple_moves::MinMover , protocols::stepwise::options::StepWiseBasicOptions
• min_type_enum_to_string() : protocols::antibody::design::AntibodyDesignEnumManager
• min_type_is_present() : protocols::antibody::design::AntibodyDesignEnumManager
• min_type_string_to_enum() : protocols::antibody::design::AntibodyDesignEnumManager
• min_value() : protocols::simple_moves::PSSM2BfactorMover
• min_VC_to_write() : protocols::noesy_assign::PeakFileFormat_Base
• 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
• mini_pose() : protocols::farna::libraries::ChunkSet
• mini_pose_list() : protocols::farna::libraries::BasePairStepLibrary
• MinimalFragSet() : core::fragment::MinimalFragSet
• MinimalFragSetIterator_() : core::fragment::MinimalFragSetIterator_
• 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
• MinimizationRefiner() : protocols::loop_modeling::refiners::MinimizationRefiner
• minimize() : protocols::analysis::PeptideDeriverFilter , protocols::forge::remodel::RemodelLigandHandler , protocols::magnesium::MgScanner , protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• minimize_() : protocols::simple_moves::PeptideStapleMover
• minimize_after_delete() : protocols::stepwise::monte_carlo::mover::DeleteMover , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• minimize_all() : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• minimize_all_rotamers() : protocols::make_rot_lib::MakeRotLibMover
• minimize_and_score_native_pose() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• minimize_and_score_sugar() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• minimize_append_res() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• minimize_backbone() : protocols::ligand_docking::MoveMapBuilder
• minimize_base_step() : protocols::stepwise::modeler::rna::helix::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_bps() : protocols::farna::options::RNA_MinimizerOptions
• minimize_cdrs() : protocols::antibody::design::GeneralAntibodyModeler
• minimize_conformation() : protocols::vip::VIP_Mover
• minimize_during_scoring() : protocols::magnesium::MgScanner
• minimize_flexible_region() : protocols::enzdes::EnzdesFlexBBProtocol
• minimize_in_stages() : protocols::enzdes::EnzRepackMinimize
• 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::FA_GrpElecEnergy , core::scoring::elec::RNA_FA_ElecEnergy , core::scoring::electron_density::FastDensEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::geometric_solvation::ContextDependentGeometricSolEnergy , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy , core::scoring::hbonds::HBondEnergy , core::scoring::lkball::LK_BallEnergy , core::scoring::methods::carbohydrates::SugarBackboneEnergy , core::scoring::methods::CartesianBondedEnergy , core::scoring::methods::DNA_ReferenceEnergy , core::scoring::methods::EnergyMethod , core::scoring::methods::GoapEnergy , core::scoring::methods::MMLJEnergyIntra , core::scoring::methods::MMTorsionEnergy , 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::RamachandranEnergy , core::scoring::methods::RamaPreProEnergy , core::scoring::methods::ReferenceEnergy , core::scoring::methods::RingClosureEnergy , core::scoring::methods::SequenceDependentRefEnergy , core::scoring::methods::SplitUnfoldedTwoBodyEnergy , core::scoring::methods::UnfoldedStateEnergy , core::scoring::methods::YHHPlanarityEnergy , core::scoring::orbitals::OrbitalsScore , core::scoring::rna::RNA_SuiteEnergy , core::scoring::rna::StackElecEnergy
• minimize_interface() : protocols::antibody::design::GeneralAntibodyModeler
• minimize_loop() : protocols::pose_length_moves::PossibleLoop
• minimize_mg_coord_constraint_distance() : protocols::magnesium::MgScanner
• minimize_no_bb() : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• minimize_only() : protocols::flexpep_docking::FlexPepDockingProtocol
• minimize_prepend_res() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• minimize_rebuild() : protocols::simple_moves::CyclizationMover
• minimize_region() : protocols::enzdes::EnzdesFlexibleRegion
• minimize_rotamer() : protocols::make_rot_lib::MakeRotLibMover
• minimize_rounds() : protocols::farna::options::RNA_MinimizerOptions
• minimize_scorefxn() : protocols::magnesium::MgMinimizer
• minimize_single_res() : protocols::stepwise::monte_carlo::mover::ResampleMover
• minimize_single_res_frequency() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• minimize_structure() : protocols::farna::options::RNA_FragmentMonteCarloOptions
• minimize_sugar() : protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler
• minimize_sugar_sets_legacy() : protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator
• minimize_tensors_fix_from_PCS_data() : protocols::scoring::methods::pcs2::PcsEnergy
• minimize_tensors_from_PCS_data() : protocols::scoring::methods::pcs2::PcsEnergy , protocols::scoring::methods::pcs::PCS_Energy , protocols::scoring::methods::pcsTs1::PCS_Energy_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_Ts4
• 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::ddg::ddGMover , protocols::simple_moves::ShakeStructureMover , protocols::simple_moves::symmetry::SymShakeStructureMover
• MinimizeBackbone() : protocols::ligand_docking::MinimizeBackbone
• minimized_pose_list() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer
• 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
• minimizer_rename_tag() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• minimizer_use_coordinate_constraints() : protocols::farna::options::RNA_MinimizerOptions
• MinimizerMap() : core::optimization::MinimizerMap
• MinimizerMapBase() : core::kinematics::MinimizerMapBase
• MinimizerOptions() : core::optimization::MinimizerOptions
• MinimizeStoredRBConfs() : protocols::enzdes::MinimizeStoredRBConfs
• minimum_peak_intensity() : protocols::noesy_assign::PeakFileFormat_Base
• minimum_sampling_probability() : core::scoring::Ramachandran2B , core::scoring::Ramachandran
• MiniPose() : core::pose::MiniPose
• MiniRelax() : protocols::relax::MiniRelax
• MinMover() : protocols::simple_moves::MinMover
• minmult() : protocols::cryst::Spacegroup , protocols::cryst::WallpaperGroup
• MinMultiHarmonicFunc() : core::scoring::func::MinMultiHarmonicFunc
• MinPackMover() : protocols::simple_moves::MinPackMover
• MinScoreScoreFunction() : core::scoring::MinScoreScoreFunction
• mintolerance() : protocols::cyclic_peptide::TryDisulfPermutations
• mintype() : protocols::antibody::design::CDRGraftDesignOptions , protocols::cyclic_peptide::TryDisulfPermutations , protocols::grafting::AnchoredGraftMover
• mirror_z() : core::conformation::symmetry::SymmetryTransform
• MirrorSymmetricConformation() : core::conformation::symmetry::MirrorSymmetricConformation
• mismatch_score() : core::sequence::SimpleScoringScheme
• missing_atoms() : core::io::pose_from_sfr::PoseFromSFRBuilder
• missing_dens_as_jump() : core::io::StructFileRepOptions
• missing_in_pose() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters , protocols::toolbox::match_enzdes_util::EnzdesCstParamCache
• missing_residues() : core::scoring::loop_graph::LoopGraph
• MissingDensityToJumpMover() : protocols::simple_moves::MissingDensityToJumpMover
• MissingEnergy() : core::scoring::methods::MissingEnergy
• mixed_disulfide() : protocols::denovo_design::DisulfidizeMover
• MixtureFunc() : core::scoring::func::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 , core::chemical::ResidueTypeSet
• mm_atom_type_set_tag() : core::chemical::ResidueLoaderOptions
• mm_atom_types_ptr() : core::chemical::ResidueType
• 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
• mmCIFParser() : core::chemical::mmCIF::mmCIFParser
• 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::matdes::SymUnsatHbondFilter , protocols::normalmode::NormalMode , protocols::rosetta_scripts::ParsedProtocol , protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::toolbox::task_operations::StoreCompoundTaskMover
• mode1_1_packertask() : protocols::forge::remodel::RemodelDesignMover
• 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() : protocols::sewing::Model
• model() : protocols::sewing::ModelNode
• model_begin() : protocols::sewing::Model
• model_count() : protocols::canonical_sampling::TrajectoryRecorder
• model_end() : protocols::sewing::Model
• model_h3() : protocols::antibody_legacy::CDRH3Modeler
• model_id() : protocols::sewing::sampling::requirements::ResidueRetentionRequirement
• model_ids() : protocols::sewing::Assembly
• model_loop() : protocols::loop_build::LoopMover_SlidingWindow , protocols::loops::loop_mover::IndependentLoopMover , protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD , 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
• model_post_design() : protocols::antibody::design::AntibodyDesignProtocol
• model_resnum() : protocols::sewing::HashEdge
• model_tag() : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• ModelCDRH3() : protocols::antibody::ModelCDRH3
• ModelConstIterator() : protocols::sewing::ModelConstIterator< T >
• modeler_sugar() : protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator
• modeler_sugar_at_chain_break() : protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator
• ModelFeatures() : protocols::features::ModelFeatures
• ModelFeaturesCreator() : protocols::features::ModelFeaturesCreator
• ModelIterator() : protocols::sewing::ModelIterator< T >
• ModelNode() : protocols::sewing::ModelNode
• models() : protocols::abinitio::PairingStatEntry
• modeltag() : core::io::StructFileRep , 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::AddAllPositionsMPM , protocols::match::BfactorMPM , protocols::match::MatchPositionModifier , protocols::match::NumNeighborsMPM , protocols::match::RemoveNorCTermMPM , protocols::match::SecondaryStructureMPM , protocols::match::TaskOperationMPM
• modified_task() : protocols::enzdes::EnzdesFlexBBProtocol
• modify() : protocols::forge::build::BuildInstruction , protocols::forge::build::BuildManager
• 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::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap
• modify_lattice() : protocols::cryst::DockLatticeMover
• 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_unselected_residues() : protocols::toolbox::task_operations::SelectResiduesWithinChainOperation
• modify_was_successful() : protocols::forge::build::BuildInstruction
• ModifyAnnealer() : protocols::toolbox::task_operations::ModifyAnnealer
• ModifyStoredRBConfs() : protocols::enzdes::ModifyStoredRBConfs
• ModifyVariantTypeMover() : protocols::simple_moves::ModifyVariantTypeMover
• modres_map() : core::io::StructFileRep
• MolarMassFilter() : protocols::ligand_docking::MolarMassFilter
• MolecularDynamics() : protocols::cartesian::MolecularDynamics
• MolecularMassFilter() : protocols::ligand_docking::MolecularMassFilter
• MolecularSurfaceCalculator() : core::scoring::sc::MolecularSurfaceCalculator
• MolecularWeightNormalization() : protocols::qsar::scoring_grid::MolecularWeightNormalization
• MolFileIOAtom() : core::chemical::sdf::MolFileIOAtom
• MolFileIOBond() : core::chemical::sdf::MolFileIOBond
• MolFileIOMolecule() : core::chemical::sdf::MolFileIOMolecule
• MolFileIOReader() : core::chemical::sdf::MolFileIOReader
• moltenres_2_resid() : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSetsBase , core::pack::rotamer_set::RotamerSubsets , protocols::flexpack::rotamer_set::FlexbbRotamerSets
• 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 , protocols::flexpack::rotamer_set::FlexbbRotamerSets
• 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::RotamerSets , core::pack::rotamer_set::RotamerSetsBase , core::pack::rotamer_set::RotamerSubsets , protocols::flexpack::rotamer_set::FlexbbRotamerSets
• 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 , core::scoring::elec::FA_GrpElecEnergy
• monopole() : core::scoring::MultipoleElecResidueInfo , core::scoring::MultipoleParameter
• 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
• monte_carlo_cycles() : protocols::farna::options::RNA_FragmentMonteCarloOptions
• MonteCarlo() : protocols::moves::MonteCarlo
• MonteCarloAssemblyMover() : protocols::sewing::MonteCarloAssemblyMover
• MonteCarloLoader() : protocols::jd2::parser::MonteCarloLoader
• MonteCarloRecover() : protocols::simple_moves::MonteCarloRecover
• MonteCarloReset() : protocols::simple_moves::MonteCarloReset
• MonteCarloTest() : protocols::simple_moves::MonteCarloTest
• MonteCarloUtil() : protocols::moves::MonteCarloUtil
• more_jobs_in_current_round() : protocols::jd3::JobDistributor
• more_jobs_remain() : protocols::jd3::JobQueen
• more_precise_base_pair_classification() : core::scoring::rna::RNA_LowResolutionPotential
• morpheme_from_ring_size() : core::chemical::carbohydrates::CarbohydrateInfoManager
• most_probable_bin() : protocols::frag_picker::quota::ABEGO_SS_Config
• Motif() : protocols::denovo_design::connection::Connection::Motif , protocols::motifs::Motif
• motif_bin_hash() : core::scoring::motif::ResPairMotifMetaBinner
• motif_bin_label() : core::scoring::motif::ResPairMotifMetaBinner
• motif_expansion_inner_loop() : protocols::motifs::MotifDnaPacker
• motif_hash() : protocols::sic_dock::scores::MotifHashRigidScore
• motif_library() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• motif_set_names() : core::scoring::motif::MotifHashManager
• motifcop() : protocols::motifs::MotifHit
• MotifDnaPacker() : protocols::motifs::MotifDnaPacker
• MotifGraftMover() : protocols::motif_grafting::movers::MotifGraftMover
• MotifHash() : core::scoring::motif::MotifHash
• MotifHashManager() : core::scoring::motif::MotifHashManager
• MotifHashRigidScore() : protocols::sic_dock::scores::MotifHashRigidScore
• MotifHit() : core::scoring::motif::MotifHit , protocols::motifs::MotifHit
• MotifLibrary() : protocols::motifs::MotifLibrary
• MotifMatch() : protocols::motif_grafting::movers::MotifMatch
• motifs() : protocols::denovo_design::connection::Connection
• MotifScoreFilter() : protocols::simple_filters::MotifScoreFilter
• MotifScorer() : protocols::sewing::scoring::MotifScorer
• MotifSearch() : protocols::motifs::MotifSearch
• movable_group() : protocols::denovo_design::components::StructureData
• movable_groups() : protocols::denovo_design::components::StructureData
• movable_jumps() : protocols::docking::DockingHighRes , protocols::docking::DockingProtocol , protocols::docking::DockMCMCycle , protocols::docking::RigidBodyInfo , protocols::docking::TemperedDocking , protocols::toolbox::task_operations::InterfaceTaskOperation
• move() : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• move_all_inserted() : protocols::abinitio::MembraneAbinitio
• move_apart_first() : protocols::docking::SlideIntoContact
• move_atoms_to_collcheck_begin() : protocols::toolbox::match_enzdes_util::LigandConformer
• move_element() : protocols::stepwise::monte_carlo::mover::StepWiseMove
• move_first_rigid_body() : protocols::farna::options::RNA_BasicOptions
• move_forward_to_next_model() : protocols::stepwise::setup::StepWiseMonteCarloJobDistributor
• move_jump_points_away() : protocols::stepwise::monte_carlo::mover::TransientCutpointHandler
• move_jumps_between_chains() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• move_jumps_to_safety() : protocols::denovo_design::components::StructureData
• 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
• move_segment() : protocols::denovo_design::components::StructureData
• move_segment_in_pose() : protocols::denovo_design::components::StructureData
• move_segments() : protocols::denovo_design::connection::Connection
• move_segments_cyclic() : protocols::denovo_design::connection::Connection
• move_side_chain() : protocols::stepwise::modeler::StepWiseMinimizer
• move_spans() : protocols::topology_broker::TMHTopologySamplerClaimer
• move_type() : protocols::stepwise::monte_carlo::mover::StepWiseMove
• move_type_string() : protocols::stepwise::monte_carlo::mover::StepWiseMasterMover
• move_with_rama() : protocols::simple_moves::ShearMover , protocols::simple_moves::SmallMover
• move_with_scorefxn() : protocols::simple_moves::ShearMover , protocols::simple_moves::SmallMover
• MoveBeforeFilter() : protocols::filters::MoveBeforeFilter
• moved() : core::pack::interaction_graph::SimpleNode , core::scoring::EnergyNode
• moveFromStubFrame() : protocols::hotspot_hashing::StubGenerator
• moveIntoStubFrame() : protocols::hotspot_hashing::StubGenerator
• MoveMap() : core::kinematics::MoveMap
• movemap() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::KinematicControl , protocols::abinitio::MembraneAbinitio , protocols::forge::build::Bridge , protocols::forge::build::BuildInstruction , protocols::forge::build::BuildManager , protocols::forge::build::ConnectRight , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap , protocols::grafting::AnchoredGraftMover , protocols::loops::loop_closure::ccd::CCDLoopClosureMover , protocols::loops::loop_closure::ccd::LoopClosure , protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::md::CartesianMD , protocols::md::MDBase , protocols::moves::MoveMapMover , protocols::moves::NullMover , protocols::simple_moves::BackboneMover , protocols::simple_moves::BBGaussianMover , protocols::simple_moves::FragmentMover , protocols::simple_moves::MinMover , protocols::simple_moves::RingConformationMover
• 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
• MoveMapMover() : protocols::moves::MoveMapMover
• MovePoseToMembraneCenterMover() : protocols::rigid::MovePoseToMembraneCenterMover
• mover() : core::environment::DofPassport , protocols::abinitio::abscript::FragmentCM , protocols::abinitio::FragmentSampler , protocols::flxbb::DesignTask , protocols::jd3::MoverAndPoseJob
• Mover() : protocols::moves::Mover
• mover() : protocols::moves::MoverApplyingMover , protocols::moves::TrialMover , protocols::simple_moves::ChangeAndResetFoldTreeMover , protocols::simple_moves::ContingentAcceptMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::rational_mc::RationalMonteCarlo , protocols::topology_broker::FragmentClaimer , protocols::topology_broker::TopologyBroker
• mover_by_index() : protocols::canonical_sampling::MetropolisHastingsMover
• Mover_LoopHashRefine() : protocols::loophash::Mover_LoopHashRefine
• mover_name() : protocols::aa_composition::AddCompositionConstraintMoverCreator , protocols::aa_composition::ClearCompositionConstraintsMoverCreator , protocols::abinitio::abscript::AbscriptLoopCloserCMCreator , protocols::abinitio::abscript::AbscriptMoverCreator , protocols::abinitio::abscript::ConstraintPreparerCreator , protocols::abinitio::abscript::FragmentCMCreator , protocols::abinitio::abscript::FragmentJumpCMCreator , protocols::abinitio::abscript::RigidChunkCMCreator , protocols::abinitio::abscript::StructPerturberCMCreator , protocols::abinitio::DomainAssemblyCreator , protocols::analysis::InterfaceAnalyzerMoverCreator , protocols::antibody::AntibodyCDRGrafterCreator , protocols::antibody::constraints::CDRDihedralConstraintMoverCreator , protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMoverCreator , protocols::antibody::constraints::ParatopeSiteConstraintMoverCreator , protocols::antibody::design::AntibodyDesignMoverCreator , protocols::antibody::design::AntibodyDesignProtocolCreator , protocols::antibody::design::MutateFrameworkForClusterCreator , protocols::backrub::BackrubMoverCreator , protocols::backrub::BackrubProtocolCreator , protocols::backrub::BackrubSidechainMoverCreator , protocols::canonical_sampling::DbTrajectoryRecorderCreator , protocols::canonical_sampling::HamiltonianExchangeCreator , protocols::canonical_sampling::MetricRecorderCreator , protocols::canonical_sampling::MetropolisHastingsMoverCreator , protocols::canonical_sampling::ParallelTemperingCreator , protocols::canonical_sampling::PDBTrajectoryRecorderCreator , protocols::canonical_sampling::ProgressBarObserverCreator , protocols::canonical_sampling::SidechainMetropolisHastingsMoverCreator , protocols::canonical_sampling::SilentTrajectoryRecorderCreator , protocols::canonical_sampling::SimulatedTemperingCreator , protocols::canonical_sampling::TrialCounterObserverCreator , protocols::carbohydrates::GlycanRelaxMoverCreator , protocols::carbohydrates::LinkageConformerMoverCreator , protocols::carbohydrates::SimpleGlycosylateMoverCreator , protocols::comparative_modeling::LoopRelaxMoverCreator , protocols::contact_map::ContactMapCreator , protocols::cryst::DockLatticeMoverCreator , protocols::cryst::FitBfactorsMoverCreator , protocols::cryst::LoadDensityMapMoverCreator , protocols::cryst::MakeLatticeMoverCreator , protocols::cryst::MakeLayerMoverCreator , protocols::cryst::RecomputeDensityMapMoverCreator , protocols::cryst::ReportGradientsMoverCreator , protocols::cryst::SetCrystWeightMoverCreator , protocols::cryst::SetRefinementOptionsMoverCreator , protocols::cryst::TagPoseWithRefinementStatsMoverCreator , protocols::cryst::UpdateCrystInfoCreator , protocols::cryst::UpdateSolventMoverCreator , protocols::cyclic_peptide::CreateAngleConstraintCreator , protocols::cyclic_peptide::CreateDistanceConstraintCreator , protocols::cyclic_peptide::CreateTorsionConstraintCreator , protocols::cyclic_peptide::DeclareBondCreator , protocols::cyclic_peptide::PeptideStubMoverCreator , protocols::cyclic_peptide::TryDisulfPermutationsCreator , protocols::denovo_design::connection::BridgeChainsCreator , protocols::denovo_design::connection::BridgeTomponentsCreator , protocols::denovo_design::connection::ConnectTerminiWithDisulfideCreator , protocols::denovo_design::connection::ExtendChainCreator , protocols::denovo_design::connection::StapleChainsCreator , protocols::denovo_design::constraints::CoordinateConstraintGeneratorCreator , protocols::denovo_design::constraints::FileConstraintGeneratorCreator , protocols::denovo_design::DisulfidizeMoverCreator , protocols::design_opt::GreedyOptMutationMoverCreator , protocols::dna::DesignProteinBackboneAroundDNACreator , protocols::dna::DnaInterfaceMinMoverCreator , protocols::dna::DnaInterfaceMultiStateDesignCreator , protocols::dna::DnaInterfacePackerCreator , protocols::dna::SeparateDnaFromNonDnaCreator , protocols::docking::ConformerSwitchMoverCreator , protocols::docking::DockingInitialPerturbationCreator , protocols::docking::DockingProtocolCreator , protocols::docking::DockSetupMoverCreator , protocols::docking::membrane::MPDockingMoverCreator , protocols::docking::membrane::MPDockingSetupMoverCreator , protocols::docking::membrane::MPFindInterfaceMoverCreator , protocols::docking::membrane::QuickRelaxPartnersSeparatelyCreator , protocols::docking::TemperedDockingCreator , protocols::electron_density::BfactorFittingMoverCreator , protocols::electron_density::ReportFSCCreator , protocols::electron_density::ScaleMapIntensitiesCreator , protocols::electron_density::SetupForDensityScoringMoverCreator , protocols::electron_density::VoxelSpacingRefinementMoverCreator , protocols::environment::CoMTrackerCMCreator , protocols::environment::EnvMoverCreator , protocols::environment::ScriptCMCreator , protocols::enzdes::AddOrRemoveMatchCstsCreator , protocols::enzdes::BackboneSamplerCreator , protocols::enzdes::EnzRepackMinimizeCreator , protocols::enzdes::PackRotamersMoverPartGreedyCreator , protocols::enzdes::PredesignPerturbMoverCreator , protocols::enzdes::UpdateEnzdesHeaderMoverCreator , protocols::features::ReportToDBCreator , protocols::features::TrajectoryReportToDBCreator , protocols::fldsgn::BluePrintBDRCreator , protocols::fldsgn::CircularPermutationCreator , protocols::fldsgn::potentials::SetAACompositionPotentialCreator , protocols::fldsgn::potentials::SetSecStructEnergiesCreator , protocols::fldsgn::SheetConstraintGeneratorCreator , protocols::flexpep_docking::FlexPepDockingProtocolCreator , protocols::flxbb::FlxbbDesignCreator , protocols::flxbb::InterlockAromaCreator , protocols::forge::constraints::InverseRotamersCstGeneratorCreator , protocols::forge::constraints::InvrotTreeCstGeneratorCreator , protocols::forge::constraints::NtoCConstraintGeneratorCreator , protocols::forge::constraints::RemoveConstraintsCreator , protocols::forge::remodel::RemodelMoverCreator , protocols::forge::remodel::ResidueVicinityCstGeneratorCreator , protocols::frag_picker::frag_movers::FragSetFromH5MoverCreator , protocols::frag_picker::frag_movers::MergeFragSetMoverCreator , protocols::frag_picker::frag_movers::ReduceFragLengthMoverCreator , protocols::generalized_kinematic_closure::GeneralizedKICCreator , protocols::grafting::AnchoredGraftMoverCreator , protocols::grafting::CCDEndsGraftMoverCreator , protocols::grafting::simple_movers::DeleteRegionMoverCreator , protocols::grafting::simple_movers::InsertPoseIntoPoseMoverCreator , protocols::grafting::simple_movers::KeepRegionMoverCreator , protocols::grafting::simple_movers::ReplaceRegionMoverCreator , protocols::helical_bundle::BackboneGridSamplerCreator , protocols::helical_bundle::BundleGridSamplerCreator , protocols::helical_bundle::FitSimpleHelixCreator , protocols::helical_bundle::MakeBundleCreator , protocols::helical_bundle::MakeBundleHelixCreator , protocols::helical_bundle::PerturbBundleCreator , protocols::helical_bundle::PerturbBundleHelixCreator , protocols::hotspot_hashing::movers::PlaceSurfaceProbeCreator , protocols::hybridization::BackboneTorsionPerturbationCreator , protocols::hybridization::BackboneTorsionSamplerCreator , protocols::hybridization::CartesianSamplerCreator , protocols::hybridization::HybridizeProtocolCreator , protocols::idealize::IdealizeMoverCreator , protocols::ligand_docking::AddHydrogensCreator , protocols::ligand_docking::CompoundTranslateCreator , protocols::ligand_docking::ComputeLigandRDFCreator , protocols::ligand_docking::FinalMinimizerCreator , protocols::ligand_docking::GrowLigandCreator , protocols::ligand_docking::HighResDockerCreator , protocols::ligand_docking::InterfaceScoreCalculatorCreator , protocols::ligand_docking::LigandDesignCreator , protocols::ligand_docking::MinimizeBackboneCreator , protocols::ligand_docking::RandomConformersCreator , protocols::ligand_docking::RotateCreator , protocols::ligand_docking::RotatesCreator , protocols::ligand_docking::SlideTogetherCreator , protocols::ligand_docking::StartFromCreator , protocols::ligand_docking::TransformCreator , protocols::ligand_docking::TranslateCreator , protocols::ligand_docking::WriteLigandMolFileCreator , protocols::loophash::LoopHashDiversifierCreator , protocols::loophash::LoopHashMoverWrapperCreator , protocols::loops::FoldTreeFromLoopsCreator , protocols::loops::loop_closure::ccd::CCDLoopClosureMoverCreator , protocols::loops::loop_mover::LoopCMCreator , protocols::match::MatcherMoverCreator , protocols::matdes::ExtractSubposeMoverCreator , protocols::matdes::MatDesGreedyOptMutationMoverCreator , protocols::matdes::SchemePlaceMotifsMoverCreator , protocols::matdes::SymDofMoverCreator , protocols::md::CartesianMDCreator , protocols::membrane::AddMembraneMoverCreator , protocols::membrane::AddMPLigandMoverCreator , protocols::membrane::benchmark::MakeCanonicalHelixCreator , protocols::membrane::benchmark::SampleTiltAnglesCreator , protocols::membrane::FlipMoverCreator , protocols::membrane::MembranePositionFromTopologyMoverCreator , protocols::membrane::MPMutateRelaxMoverCreator , protocols::membrane::MPQuickRelaxMoverCreator , protocols::membrane::OptimizeMembranePositionMoverCreator , protocols::membrane::OptimizeProteinEmbeddingMoverCreator , protocols::membrane::RotationMoverCreator , protocols::membrane::SetMembraneCenterMoverCreator , protocols::membrane::SetMembraneNormalMoverCreator , protocols::membrane::SetMembranePositionMoverCreator , protocols::membrane::SpinAroundPartnerMoverCreator , protocols::membrane::symmetry::SymmetricAddMembraneMoverCreator , protocols::membrane::TiltMoverCreator , protocols::membrane::TransformIntoMembraneMoverCreator , protocols::membrane::TranslationMoverCreator , protocols::membrane::TranslationRotationMoverCreator , protocols::membrane::visualize::VisualizeEmbeddingMoverCreator , protocols::membrane::visualize::VisualizeMembraneMoverCreator , protocols::motif_grafting::movers::MotifGraftCreator , protocols::motifs::MotifDnaPackerCreator , protocols::moves::DsspMoverCreator , protocols::moves::IfMoverCreator , protocols::moves::IteratedConvergenceMoverCreator , protocols::moves::PyMolMoverCreator , protocols::moves::RampingMoverCreator , protocols::moves::RandomMoverCreator , protocols::ncbb::NcbbDockDesignProtocolCreator , protocols::ncbb::oop::OopCreatorMoverCreator , protocols::ncbb::oop::OopDockDesignProtocolCreator , protocols::ncbb::SecStructFinderCreator , protocols::ncbb::SecStructMinimizeMoverCreator , protocols::nonlocal::SingleFragmentMoverCreator , protocols::normalmode::NormalModeMinimizerCreator , protocols::pb_potential::SetupPoissonBoltzmannPotentialCreator , protocols::pose_length_moves::FixAllLoopsMoverCreator , protocols::pose_length_moves::InsertResMoverCreator , protocols::pose_length_moves::NearNativeLoopCloserCreator , protocols::protein_interface_design::movers::AddChainBreakCreator , protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspotsCreator , protocols::protein_interface_design::movers::BackrubDDMoverCreator , protocols::protein_interface_design::movers::BestHotspotCstMoverCreator , protocols::protein_interface_design::movers::BuildAlaPoseCreator , protocols::protein_interface_design::movers::DesignMinimizeHbondsCreator , protocols::protein_interface_design::movers::DisulfideMoverCreator , protocols::protein_interface_design::movers::DockAndRetrieveSidechainsCreator , protocols::protein_interface_design::movers::DockWithHotspotMoverCreator , protocols::protein_interface_design::movers::FavorNativeResiduePreCycleCreator , protocols::protein_interface_design::movers::FavorNonNativeResiduePreCycleCreator , protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMoverCreator , protocols::protein_interface_design::movers::HotspotHasherMoverCreator , protocols::protein_interface_design::movers::InterfaceRecapitulationMoverCreator , protocols::protein_interface_design::movers::LoopFinderCreator , protocols::protein_interface_design::movers::LoopLengthChangeCreator , protocols::protein_interface_design::movers::LoopMoverFromCommandLineCreator , protocols::protein_interface_design::movers::LoopOverCreator , protocols::protein_interface_design::movers::LoopRemodelCreator , protocols::protein_interface_design::movers::MapHotspotCreator , protocols::protein_interface_design::movers::PatchdockTransformCreator , protocols::protein_interface_design::movers::PeptideStapleDesignMoverCreator , protocols::protein_interface_design::movers::PlacementAuctionMoverCreator , protocols::protein_interface_design::movers::PlacementMinimizationMoverCreator , protocols::protein_interface_design::movers::PlaceOnLoopCreator , protocols::protein_interface_design::movers::PlaceSimultaneouslyMoverCreator , protocols::protein_interface_design::movers::PlaceStubMoverCreator , protocols::protein_interface_design::movers::PrepackMoverCreator , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMoverCreator , protocols::protein_interface_design::movers::RandomMutationCreator , protocols::protein_interface_design::movers::RepackMinimizeCreator , protocols::protein_interface_design::movers::SaveAndRetrieveSidechainsCreator , protocols::protein_interface_design::movers::SetAtomTreeCreator , protocols::protein_interface_design::movers::SetTemperatureFactorCreator , protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMoverCreator , protocols::protein_interface_design::movers::SetupHotspotConstraintsMoverCreator , protocols::protein_interface_design::movers::ShoveResidueMoverCreator , protocols::protein_interface_design::movers::SpinMoverCreator , protocols::protein_interface_design::movers::SubroutineMoverCreator , protocols::protein_interface_design::movers::TaskAwareCstsCreator , protocols::protein_interface_design::movers::TopologyBrokerMoverCreator , protocols::protein_interface_design::movers::TryRotamersCreator , protocols::protein_interface_design::movers::VLBCreator , protocols::qsar::qsarCreator , protocols::qsar::RenderGridsToKinemageCreator , protocols::qsar::scoring_grid::GridInitMoverCreator , protocols::rbsegment_relax::IdealizeHelicesMoverCreator , protocols::rbsegment_relax::MakeStarTopologyMoverCreator , protocols::rbsegment_relax::OptimizeThreadingMoverCreator , protocols::relax::AtomCoordinateCstMoverCreator , protocols::relax::ClassicRelaxCreator , protocols::relax::FastRelaxCreator , protocols::relax::LocalRelaxCreator , protocols::relax::membrane::MPFastRelaxMoverCreator , protocols::rigid::RigidBodyPerturbNoCenterMoverCreator , protocols::rigid::RigidBodyTiltMoverCreator , protocols::rigid::RigidBodyTransMoverCreator , protocols::rigid::RollMoverCreator , protocols::rigid::UniformRigidBodyCMCreator , protocols::rigid::UniformRigidBodyMoverCreator , protocols::rosetta_scripts::AdditionalOutputWrapperCreator , protocols::rosetta_scripts::MultipleOutputWrapperCreator , protocols::rosetta_scripts::MultiplePoseMoverCreator , protocols::rosetta_scripts::ParsedProtocolCreator , protocols::rosetta_scripts::SavePoseMoverCreator , protocols::rotamer_recovery::RotamerRecoveryMoverCreator , protocols::seeded_abinitio::CAcstGeneratorCreator , protocols::seeded_abinitio::CloseFoldCreator , protocols::seeded_abinitio::CoordinateCstCreator , protocols::seeded_abinitio::DefineMovableLoopsCreator , protocols::seeded_abinitio::GrowPeptidesCreator , protocols::seeded_abinitio::SeedFoldTreeCreator , protocols::seeded_abinitio::SeedSetupMoverCreator , protocols::seeded_abinitio::SegmentHybridizerCreator , protocols::seeded_abinitio::SwapSegmentCreator , protocols::sewing::AddStartnodeFragmentsCreator , protocols::sewing::AppendAssemblyMoverCreator , protocols::sewing::AssemblyConstraintsMoverCreator , protocols::sewing::AssemblyMoverCreator , protocols::sewing::EnumerateAssemblyMoverCreator , protocols::sewing::GivenPathAssemblyMoverCreator , protocols::sewing::GreedyAssemblyMoverCreator , protocols::sewing::LoophashAssemblyMoverCreator , protocols::sewing::MonteCarloAssemblyMoverCreator , protocols::sewing::NodeConstraintAssemblyMoverCreator , protocols::sewing::RehashAssemblyMoverCreator , protocols::sewing::RepeatAssemblyMoverCreator , protocols::simple_moves::AddChainMoverCreator , protocols::simple_moves::AddConstraintsToCurrentConformationMoverCreator , protocols::simple_moves::AddJobPairDataCreator , protocols::simple_moves::AlignChainMoverCreator , protocols::simple_moves::BBDihedralSamplerMoverCreator , protocols::simple_moves::BBGaussianMoverCreator , protocols::simple_moves::bin_transitions::InitializeByBinsCreator , protocols::simple_moves::bin_transitions::PerturbByBinsCreator , protocols::simple_moves::BoltzmannRotamerMoverCreator , protocols::simple_moves::ChangeAndResetFoldTreeMoverCreator , protocols::simple_moves::ClearConstraintsMoverCreator , protocols::simple_moves::ConsensusDesignMoverCreator , protocols::simple_moves::ConstraintSetMoverCreator , protocols::simple_moves::ContingentAcceptMoverCreator , protocols::simple_moves::CoupledMoverCreator , protocols::simple_moves::CutChainMoverCreator , protocols::simple_moves::ddGCreator , protocols::simple_moves::DeleteChainMoverCreator , protocols::simple_moves::DeleteChainsMoverCreator , protocols::simple_moves::DumpPdbCreator , protocols::simple_moves::ExtendedPoseMoverCreator , protocols::simple_moves::FavorSequenceProfileCreator , protocols::simple_moves::FavorSymmetricSequenceCreator , protocols::simple_moves::FindConsensusSequenceCreator , protocols::simple_moves::ForceDisulfidesMoverCreator , protocols::simple_moves::GenericMonteCarloMoverCreator , protocols::simple_moves::LoadPDBMoverCreator , protocols::simple_moves::LoadUnboundRotMoverCreator , protocols::simple_moves::MakePolyXMoverCreator , protocols::simple_moves::MembraneTopologyCreator , protocols::simple_moves::MergePDBMoverCreator , protocols::simple_moves::MinMoverCreator , protocols::simple_moves::MinPackMoverCreator , protocols::simple_moves::MonteCarloRecoverCreator , protocols::simple_moves::MonteCarloResetCreator , protocols::simple_moves::MonteCarloTestCreator , protocols::simple_moves::MSDMoverCreator , protocols::simple_moves::MutateResidueCreator , protocols::simple_moves::PackRotamersMoverCreator , protocols::simple_moves::PackRotamersMoverLazyCreator , protocols::simple_moves::PDBReloadMoverCreator , protocols::simple_moves::PeriodicBoxMoverCreator , protocols::simple_moves::PSSM2BfactorMoverCreator , protocols::simple_moves::RandomOmegaFlipMoverCreator , protocols::simple_moves::RandomTorsionMoverCreator , protocols::simple_moves::RepackSidechainsMoverCreator , protocols::simple_moves::RepeatPropagationMoverCreator , protocols::simple_moves::ReportEffectivePKACreator , protocols::simple_moves::ResetBaselineMoverCreator , protocols::simple_moves::ResidueTypeConstraintMoverCreator , protocols::simple_moves::RingConformationMoverCreator , protocols::simple_moves::RotamerTrialsMinMoverCreator , protocols::simple_moves::RotamerTrialsMoverCreator , protocols::simple_moves::SaneMinMoverCreator , protocols::simple_moves::ScoreMoverCreator , protocols::simple_moves::SequenceProfileMoverCreator , protocols::simple_moves::SetTorsionCreator , protocols::simple_moves::ShearMoverCreator , protocols::simple_moves::ShortBackrubMoverCreator , protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMoverCreator , protocols::simple_moves::sidechain_moves::PerturbChiSidechainMoverCreator , protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMoverCreator , protocols::simple_moves::sidechain_moves::SetChiMoverCreator , protocols::simple_moves::sidechain_moves::SidechainMCMoverCreator , protocols::simple_moves::sidechain_moves::SidechainMoverCreator , protocols::simple_moves::SimpleThreadingMoverCreator , protocols::simple_moves::SmallMoverCreator , protocols::simple_moves::StorePoseSnapshotCreator , protocols::simple_moves::StructProfileMoverCreator , protocols::simple_moves::SuperimposeMoverCreator , protocols::simple_moves::SwitchChainOrderMoverCreator , protocols::simple_moves::SwitchResidueTypeSetMoverCreator , protocols::simple_moves::symmetry::DetectSymmetryMoverCreator , protocols::simple_moves::symmetry::ExtractAsymmetricPoseMoverCreator , protocols::simple_moves::symmetry::ExtractAsymmetricUnitMoverCreator , protocols::simple_moves::symmetry::SetupForSymmetryMoverCreator , protocols::simple_moves::symmetry::SetupNCSMoverCreator , protocols::simple_moves::symmetry::SymMinMoverCreator , protocols::simple_moves::symmetry::SymPackRotamersMoverCreator , protocols::simple_moves::symmetry::SymRotamerTrialsMoverCreator , protocols::simple_moves::symmetry::TaskAwareSymMinMoverCreator , protocols::simple_moves::TaskAwareMinMoverCreator , protocols::simple_moves::TumbleCreator , protocols::simple_moves::VirtualRootMoverCreator , protocols::symmetric_docking::membrane::MPSymDockMoverCreator , protocols::symmetric_docking::SymDockProtocolCreator , protocols::symmetric_docking::SymFoldandDockMoveRbJumpMoverCreator , protocols::symmetric_docking::SymFoldandDockRbTrialMoverCreator , protocols::symmetric_docking::SymFoldandDockSlideTrialMoverCreator , protocols::toolbox::task_operations::StoreCombinedStoredTasksMoverCreator , protocols::toolbox::task_operations::StoreCompoundTaskMoverCreator , protocols::toolbox::task_operations::StoreTaskMoverCreator
• mover_stopping_condition() : protocols::simple_moves::GenericMonteCarloMover
• mover_tag() : protocols::topology_broker::FragmentClaimer
• mover_weight() : protocols::topology_broker::TopologyClaimer
• MoverAndPoseJob() : protocols::jd3::MoverAndPoseJob
• MoverApplyingMover() : protocols::moves::MoverApplyingMover
• MoverContainer() : protocols::moves::MoverContainer
• MoverCreator() : protocols::moves::MoverCreator
• MoverFactory() : protocols::moves::MoverFactory
• MoverFilterPair() : protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair
• MoverForPoseList() : protocols::moves::MoverForPoseList
• moverkey() : protocols::abinitio::abscript::FragmentJumpCM , protocols::abinitio::abscript::JumpSampleData
• MoverList() : protocols::wum::MoverList
• MoverRegistrator() : protocols::moves::MoverRegistrator< T >
• movers() : protocols::moves::MoverContainer
• MoverStatistics() : protocols::moves::MoverStatistics
• moves_residue() : core::fragment::Frame , core::fragment::NonContinuousFrame
• moving_partition_res() : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler
• moving_res() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters , protocols::stepwise::monte_carlo::mover::StepWiseMove , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler
• moving_res_contact_filter() : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• moving_residue_at_origin() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler
• mp_param() : core::scoring::MultipoleElecResidueInfo
• MPCbetaEnergy() : core::scoring::membrane::MPCbetaEnergy
• MPDockingMover() : protocols::docking::membrane::MPDockingMover
• MPDockingSetupMover() : protocols::docking::membrane::MPDockingSetupMover
• MPEnvEnergy() : core::scoring::membrane::MPEnvEnergy
• MPFastRelaxMover() : protocols::relax::membrane::MPFastRelaxMover
• MPFindInterfaceMover() : protocols::docking::membrane::MPFindInterfaceMover
• mphbond() : core::scoring::hbonds::HBondOptions
• 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 , protocols::mpi_refinement::MPI_Refinement
• 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_Refine_Emperor() : protocols::mpi_refinement::MPI_Refine_Emperor
• MPI_Refine_Master() : protocols::mpi_refinement::MPI_Refine_Master
• MPI_Refinement() : protocols::mpi_refinement::MPI_Refinement
• mpi_resume() : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• 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
• MPLipoEnergy() : core::scoring::membrane::MPLipoEnergy
• MPMutateRelaxMover() : protocols::membrane::MPMutateRelaxMover
• MPNonHelixPenalty() : core::scoring::membrane::MPNonHelixPenalty
• mpose() : core::scoring::motif::MotifHit
• mposeptr() : core::scoring::motif::MotifHit
• MPPairEnergy() : core::scoring::membrane::MPPairEnergy
• MPQuickRelaxMover() : protocols::membrane::MPQuickRelaxMover
• MPRangeRelaxMover() : protocols::relax::membrane::MPRangeRelaxMover
• MPSymDockMover() : protocols::symmetric_docking::membrane::MPSymDockMover
• MPTerminiPenalty() : core::scoring::membrane::MPTerminiPenalty
• MPTMProjPenalty() : core::scoring::membrane::MPTMProjPenalty
• MRMover() : protocols::hybridization::MRMover
• msa() : core::scoring::packstat::PackingScoreResData
• MSDMover() : protocols::simple_moves::MSDMover
• 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_
• multi_fast_relax() : protocols::abinitio::AbrelaxApplication
• multi_origin_list() : protocols::pockets::FingerprintBase
• multi_relative() : protocols::simple_filters::Operator
• multi_threading_inner_job() : protocols::jd2::MultiThreadingJob
• multi_use() : protocols::protein_interface_design::movers::SaveAndRetrieveSidechains
• MultiChainStructureData() : protocols::denovo_design::components::MultiChainStructureData
• multicomp() : protocols::matdes::InterfacePackingFilter , protocols::matdes::OligomericAverageDegreeFilter , protocols::simple_filters::ShapeComplementarityFilter
• MultiConstraint() : core::scoring::constraints::MultiConstraint
• MultiConstraintCreator() : core::scoring::constraints::MultiConstraintCreator
• MultiCoolAnnealer() : core::pack::annealer::MultiCoolAnnealer
• Multifunc() : core::optimization::Multifunc
• MultiObjective() : protocols::mpi_refinement::MultiObjective
• MultiPhosphateSampler() : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• MultipleDomainMover() : protocols::farna::MultipleDomainMover
• MultipleOutputWrapper() : protocols::rosetta_scripts::MultipleOutputWrapper
• MultiplePoseMover() : protocols::rosetta_scripts::MultiplePoseMover
• MultipleSigmoids() : protocols::simple_filters::MultipleSigmoids
• MultiplexedAnnealableGraph() : core::pack::interaction_graph::MultiplexedAnnealableGraph
• MultiplicitiveFactor() : core::scoring::FACTSPotential
• multiplicity() : core::scoring::constraints::AmbiguousNMRDistanceConstraint
• MultipoleElecEnergy() : core::scoring::methods::MultipoleElecEnergy
• MultipoleElecPoseInfo() : core::scoring::MultipoleElecPoseInfo
• MultipoleElecPotential() : core::scoring::MultipoleElecPotential
• MultipoleElecResidueInfo() : core::scoring::MultipoleElecResidueInfo
• MultipoleElecResPairMinData() : core::scoring::methods::MultipoleElecResPairMinData
• MultipoleElecRotamerSetInfo() : core::scoring::MultipoleElecRotamerSetInfo
• MultipoleParameter() : core::scoring::MultipoleParameter
• MultiProbePerSphereAccumulator() : core::scoring::packstat::MultiProbePerSphereAccumulator
• MultiProbePoseAccumulator() : core::scoring::packstat::MultiProbePoseAccumulator
• MultiStateAggregateFunction() : protocols::multistate_design::MultiStateAggregateFunction
• MultistateAggregateFunction() : protocols::pack_daemon::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
• multivec2poseBfacts() : protocols::electron_density::BfactorMultifunc
• must_switch_bins() : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber , protocols::simple_moves::bin_transitions::PerturbByBins
• 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() : core::optimization::GA_Minimizer , protocols::genetic_algorithm::DiscreteRandomizer , protocols::genetic_algorithm::EntityRandomizer , protocols::genetic_algorithm::Mutate1Randomizer , protocols::genetic_algorithm::PositionSpecificRandomizer
• mutate_and_relax() : protocols::design_opt::PointMutationCalculator , protocols::matdes::MatDesPointMutationCalculator
• mutate_disulfides_to_ala() : protocols::denovo_design::DisulfidizeMover
• MutateFrameworkForCluster() : protocols::antibody::design::MutateFrameworkForCluster
• 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 , protocols::simple_filters::MutationsFilter
• MutationData() : protocols::pmut_scan::MutationData
• mutations() : protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::simple_filters::MutationsFilter
• mutations_begin() : protocols::pmut_scan::Mutant
• mutations_end() : protocols::pmut_scan::Mutant
• MutationSetDesignOperation() : protocols::toolbox::task_operations::MutationSetDesignOperation
• MutationsFilter() : protocols::simple_filters::MutationsFilter
• my_emperor() : protocols::loophash::MPI_LoopHashRefine_Master , protocols::mpi_refinement::MPI_Refine_Master
• my_group() : core::scoring::MultipoleElecResidueInfo
• my_group_members() : core::scoring::MultipoleParameter
• my_local_coord_frame() : core::scoring::MultipoleElecResidueInfo
• my_residue_pair_energy() : core::scoring::methods::DirectReadoutEnergy
• MyAtom() : protocols::fldsgn::MyAtom