Here is a list of all class members with links to the classes they belong to:

- m -

• M : core::kinematics::Stub , protocols::sic_dock::Rose
• m1_ : protocols::hybridization::TMalign
• m1_b1_Ktheta() : protocols::branch_angle::BranchParam1
• m1_b1_Ktheta_ : protocols::branch_angle::BranchParam1
• m1_b1_theta0() : protocols::branch_angle::BranchParam1
• m1_b1_theta0_ : protocols::branch_angle::BranchParam1
• m1_b2_Ktheta() : protocols::branch_angle::BranchParam2
• m1_b2_Ktheta_ : protocols::branch_angle::BranchParam2
• m1_b2_theta0() : protocols::branch_angle::BranchParam2
• m1_b2_theta0_ : protocols::branch_angle::BranchParam2
• m1_m2_Ktheta() : protocols::branch_angle::BranchParam1
• m1_m2_Ktheta_ : protocols::branch_angle::BranchParam1
• m1_m2_theta0() : protocols::branch_angle::BranchParam1
• m1_m2_theta0_ : protocols::branch_angle::BranchParam1
• m2_ : protocols::hybridization::TMalign
• m2_b1_Ktheta() : protocols::branch_angle::BranchParam1
• m2_b1_Ktheta_ : protocols::branch_angle::BranchParam1
• m2_b1_theta0() : protocols::branch_angle::BranchParam1
• m2_b1_theta0_ : protocols::branch_angle::BranchParam1
• m2_b2_Ktheta() : protocols::branch_angle::BranchParam2
• m2_b2_Ktheta_ : protocols::branch_angle::BranchParam2
• m2_b2_theta0() : protocols::branch_angle::BranchParam2
• m2_b2_theta0_ : protocols::branch_angle::BranchParam2
• m_ : core::scoring::func::CircularSigmoidalFunc
• m_AtomTypesByDecreasingStability : core::chemical::gasteiger::PossibleAtomTypesForAtom
• m_done_all : protocols::simple_moves::TailsScoreMover
• m_FinalizeFunction : core::chemical::gasteiger::PossibleAtomTypesForAtom
• m_hill_size_ : protocols::simple_moves::TailsScoreMover
• m_number_of_hill_points_ : protocols::simple_moves::TailsScoreMover
• m_NumberAtomTypesWithHybridization : core::chemical::gasteiger::PossibleAtomTypesForAtom
• m_NumberConjugatedTypes : core::chemical::gasteiger::PossibleAtomTypesForAtom
• m_Temperature : protocols::relax::ClassicRelax
• m_Temperature_ : protocols::LoopRebuild
• m_term_ : core::scoring::SecondaryStructurePotential
• m_term_initializer() : core::scoring::SecondaryStructurePotential
• machine_letter_ : protocols::wum::MPI_WorkUnitManager
• MACQ_ : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• MACR_ : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• mag_rot_ : protocols::rigid::RigidBodyMotionMover
• mag_trans_ : protocols::rigid::RigidBodyMotionMover
• 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_ : protocols::abinitio::abscript::StructPerturberCM , protocols::kinematic_closure::perturbers::WalkingBondAnglePerturber , protocols::kinematic_closure::perturbers::WalkingPerturber , protocols::rbsegment_relax::SequenceShiftMover , protocols::simple_moves::sidechain_moves::PerturbChiSidechainMover
• magnitude_last_surface_deltaE_ : core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G > , core::pack::interaction_graph::SurfaceEdge< V, E, G >
• 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_ : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer
• main_chain_torsion_set_for_moving_residues_ : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• main_chain_torsion_set_lists() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger , protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• main_chain_torsion_set_lists_ : protocols::stepwise::sampler::protein::ProteinMainChainStepWiseSampler
• 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_set_save_ : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer
• main_chain_torsion_sets() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_MultiPoseCloser
• main_chain_torsion_sets_ : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_MultiPoseCloser
• main_chain_torsion_sets_for_moving_residues_ : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger , protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• main_group_ : core::chemical::Element
• main_mover_ : protocols::simple_moves::ChangeAndResetFoldTreeMover
• main_task_factory_ : protocols::backrub::BackrubProtocol , protocols::coupled_moves::CoupledMovesProtocol , protocols::hydrate::Hydrate
• mainchain_atom() : core::chemical::ResidueType , core::conformation::Residue
• mainchain_atoms() : core::chemical::MutableResidueType , core::chemical::ResidueType , core::conformation::Residue
• mainchain_atoms_ : core::chemical::MutableResidueType
• mainchain_atoms_indices_ : core::chemical::ResidueType
• mainchain_child_ : core::conformation::carbohydrates::GlycanNode
• mainchain_dihedral_values() : protocols::stepwise::modeler::protein::MainChainTorsionSet
• mainchain_dihedral_values_ : protocols::stepwise::modeler::protein::MainChainTorsionSet
• mainchain_glycosidic_bond_acceptor() : core::chemical::carbohydrates::CarbohydrateInfo
• mainchain_glycosidic_bond_acceptor_ : core::chemical::carbohydrates::CarbohydrateInfo
• mainchain_potentials_match() : core::chemical::ResidueTypeBase
• mainchain_torsion() : core::conformation::Residue , core::io::silent::RNA_SilentStruct
• mainchain_torsion_diff_threshold_ : protocols::dna::PDBOutput
• mainchain_torsions() : core::conformation::Residue , core::io::silent::RNA_SilentStruct
• mainchain_torsions_ : core::conformation::Residue , core::io::silent::RNA_SilentStruct
• mainchain_torsions_covered() : protocols::mainchain_potential::GenerateMainchainPotentialOptions
• mainchain_torsions_covered_ : core::chemical::mainchain_potential::MainchainScoreTable , protocols::mainchain_potential::GenerateMainchainPotentialOptions
• mainchain_torsions_differ() : protocols::cyclic_peptide::CycpepSymmetryFilter
• MainchainScoreTable() : core::chemical::mainchain_potential::MainchainScoreTable
• MainChainTorsionSet() : protocols::stepwise::modeler::protein::MainChainTorsionSet
• maintain_cap_ : protocols::simple_moves::RepeatPropagationMover
• maintain_cap_sequence_only_ : protocols::simple_moves::RepeatPropagationMover
• maintain_ligand_ : protocols::simple_moves::RepeatPropagationMover
• maintain_links() : core::io::StructFileRepOptions
• maintain_links_ : core::io::StructFileRepOptions
• make() : core::chemical::ResidueType , 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_aligned_residue() : protocols::sewing::hashing::LigandBindingResPlacer
• make_asymmetric_movemap() : core::optimization::symmetry::SymAtomTreeMinimizer
• make_bundle_ : protocols::helical_bundle::BundleGridSampler
• make_bundle_helix_movers_ : protocols::helical_bundle::MakeBundle
• make_calculator() : protocols::task_operations::RestrictToInterfaceOperation , protocols::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_conditional_packed_rotno_index() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >
• make_constraint_covalent() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• make_constraint_covalent_helper() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• make_context() : protocols::simple_filters::ResidueDepthFilter
• make_context_ref() : protocols::simple_filters::ResidueDepthFilter
• make_cutpoints_coherent_to_foldtree() : protocols::fold_from_loops::movers::NubInitioLoopClosureMover
• 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 , protocols::energy_based_clustering::EnergyBasedClusteringProtocol
• make_dna_sequence_combinations() : protocols::dna::DnaInterfacePacker
• make_dockmcm_mover() : protocols::ligand_docking::LigandDockProtocol , protocols::symmetric_docking::SymDockProtocol
• make_extended_pose() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• make_fibril() : protocols::topology_broker::FibrilModelingClaimer
• make_filename() : protocols::ncbb::SecStructFinder
• make_final_tree() : protocols::fold_from_loops::movers::NubInitioLoopClosureMover
• make_foldtree_coherent_to_cutpoints() : protocols::fold_from_loops::movers::NubInitioLoopClosureMover
• make_fragment_moves() : protocols::rna::denovo::movers::RNA_Relaxer
• make_fragment_picker() : protocols::struct_fragment::StructFragmentMover
• make_full_pose() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• make_Hessian_ANM() : protocols::normalmode::NormalMode
• make_Hessian_TNM() : protocols::normalmode::NormalMode
• make_index_selector() : protocols::chemically_conjugated_docking::UBQ_GTPaseMover
• make_initial_power_diagram() : core::scoring::power_diagram::PowerDiagram
• 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_manager() : protocols::protein_interface_design::movers::VLB
• make_model() : protocols::tcr::TCRmodel
• make_motif_filename() : protocols::motifs::IRCollection
• make_move() : protocols::simple_moves::BackboneMover , protocols::simple_moves::BBConRotMover , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• make_movemap() : protocols::fold_from_loops::utils::Nub , protocols::ligand_docking::LigandBaseProtocol
• make_movie() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• make_movie_ : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• make_multi_pose_grids() : protocols::ligand_docking::Transform , protocols::ligand_docking::TransformEnsemble
• 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_mutation() : protocols::simple_moves::MutateResidue
• make_mutations() : protocols::membrane::MPMutateRelaxMover
• make_name() : protocols::task_operations::RestrictToInterfaceOperation , protocols::task_operations::RestrictToNeighborhoodOperation
• make_new_grid() : protocols::qsar::scoring_grid::GridSet
• make_new_pose() : protocols::ncbb::ResidueReplacementRebuildMover
• make_new_sphere() : core::scoring::power_diagram::PowerDiagram
• make_no_pore_parameters() : core::conformation::membrane::ImplicitLipidInfo
• 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 , protocols::ligand_docking::ProtLigEnsemble
• 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_pose_from_design() : protocols::pose_creation::MakeJunctionsMover
• make_pose_from_fasta_contents() : protocols::helical_bundle_predict::HelicalBundlePredictApplication
• make_pose_from_sequence_file_contents() : protocols::helical_bundle_predict::HelicalBundlePredictApplication
• make_pre_proline_potential() : protocols::mainchain_potential::GenerateMainchainPotentialOptions
• make_pre_proline_potential_ : protocols::mainchain_potential::GenerateMainchainPotentialOptions
• make_pymol_script() : protocols::flxbb::LayerDesignOperation
• make_pymol_script_ : protocols::flxbb::LayerDesignOperation
• make_rasmol_format_file() : core::select::util::SelectResiduesByLayer
• 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_starting_pose_for_virtual_screening() : protocols::ligand_docking::ga_ligand_dock::GALigandDock
• make_strand_neighbor_two() : protocols::fldsgn::topology::StrandPairingSet
• make_symmetric_pose() : protocols::symmetry::SetupForSymmetryMover
• make_tail() : protocols::simple_moves::TailsScoreMover
• make_template_ranges() : protocols::fold_from_loops::NubInitioMover
• 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_unfolded_pose() : protocols::fold_from_loops::NubInitioMover
• 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
• MakeAsymmetricStructureDataMover() : protocols::denovo_design::movers::MakeAsymmetricStructureDataMover
• 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
• MakeDefaultPackerPaletteCOP() : core::pack::task::ResidueLevelTask_
• 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
• makeJunctions_apply() : protocols::pose_creation::MergePDBatOverlapMover
• MakeJunctionsMover() : protocols::pose_creation::MakeJunctionsMover
• 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::pose_creation::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
• MakeTagCOP() : core::pack::task::operation::TaskOperationFactory
• MakeTalosSSSimilarity() : protocols::frag_picker::scores::MakeTalosSSSimilarity
• MakeTorsionBinSimilarity() : protocols::frag_picker::scores::MakeTorsionBinSimilarity
• MALARKEY : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• manage_constraints() : protocols::fold_from_loops::NubInitioMover
• manager() : protocols::forge::components::VarLengthBuild , protocols::forge::remodel::RemodelWorkingSet , protocols::jd2::archive::AbstractArchiveBase
• manager_ : protocols::fldsgn::BluePrintBDR , protocols::forge::components::BDR , protocols::forge::components::VarLengthBuild , protocols::forge::remodel::RemodelMover , protocols::jd2::archive::AbstractArchiveBase
• manager_ptr() : protocols::jd2::archive::AbstractArchiveBase
• manipulate_cut_bias() : protocols::topology_broker::CutBiasClaimer , protocols::topology_broker::RigidChunkClaimer , protocols::topology_broker::TopologyClaimer
• manual_call() : protocols::loophash::LoopHashRelaxProtocol
• manual_jump_pairs_ : protocols::seeded_abinitio::SeedFoldTree
• manualPackerTaskGen() : protocols::forge::remodel::RemodelWorkingSet
• map() : core::id::CacheableAtomID_MapVector
• Map : core::scoring::constraints::ResidueConstraints
• map2keyvector() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• map2target() : protocols::abinitio::Template
• map2template() : protocols::abinitio::Template
• map_ : core::fragment::MapCacheUnit< T > , core::id::CacheableAtomID_MapVector , core::scoring::constraints::ResidueConstraints , core::scoring::EMapVector , core::sequence::Blosum62Map , protocols::comparative_modeling::StealSideChainsMover , protocols::noesy_assign::ResonanceList
• map_BB_to_DOF_ : protocols::ncbb::SecStructMinimizeMultiFunc
• map_cst_from_centroid_to_fa_ : protocols::abinitio::ResolutionSwitcher
• map_DOF_to_BB_ : protocols::ncbb::SecStructMinimizeMultiFunc
• map_DOF_to_NM_ : protocols::normalmode::NormalModeMultifunc
• map_from_reference() : core::pose::toolbox::AtomID_Mapper
• map_from_reference_ : core::pose::toolbox::AtomID_Mapper
• map_from_spectrum() : protocols::electron_density::DockIntoDensityMover
• map_helix_pairings_ : protocols::fldsgn::topology::HelixPairingSet
• map_index() : protocols::ligand_docking::ga_ligand_dock::Pharmacophore
• map_index_ : protocols::ligand_docking::ga_ligand_dock::Pharmacophore
• map_is_clean_ : core::sequence::AnnotatedSequence
• map_name_ : protocols::qsar::qsarMap
• map_NM_to_DOF_ : protocols::normalmode::NormalModeMultifunc
• 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_phores() : protocols::ligand_docking::ga_ligand_dock::ConstraintInfo
• map_residues() : protocols::legacy_sewing::Assembly
• map_reso_ : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• map_ss_segments() : protocols::fldsgn::MatchResidues
• map_strand_pairings_ : protocols::fldsgn::topology::StrandPairingSet
• map_symmetric_res_pairs() : core::conformation::symmetry::SymmetryInfo
• map_to_CEN() : core::scoring::constraints::AmbiguousNMRDistanceConstraint
• map_to_cen_atom_ : protocols::noesy_assign::PeakAssignmentParameters
• map_to_reference() : core::pose::toolbox::AtomID_Mapper
• map_to_reference_ : core::pose::toolbox::AtomID_Mapper
• map_type_ : core::scoring::cryst::PhenixInterface , protocols::cryst::SetRefinementOptionsMover
• map_var_to_DOF_ : protocols::normalmode::NormalModeMultifunc
• map_var_to_modeno_ : protocols::normalmode::NormalModeMultifunc
• mapfile_ : protocols::cryst::LoadDensityMapMover
• mapfile_activated() : protocols::stepwise::options::StepWiseBasicOptions
• mapfile_activated_ : protocols::stepwise::options::StepWiseBasicOptions
• MapHotspot() : protocols::protein_interface_design::movers::MapHotspot
• mapout_ : protocols::electron_density::VoxelSpacingRefinementMover
• mapped_coords_ : core::scoring::epr_deer::EPRSpinLabel
• MappedAtom() : protocols::constraint_generator::AtomPairConstraintGenerator::MappedAtom
• MappedAtoms : protocols::constraint_generator::AtomPairConstraintGenerator
• mapping() : core::id::SequenceMapping
• mapping_ : core::id::SequenceMapping , core::io::pose_from_sfr::GeometricRenameIsomorphismCallback , core::scoring::constraints::SequenceProfileConstraint , protocols::abinitio::Template , protocols::symmetry::NCSResMapping
• MappingType : protocols::qsar::scoring_grid::GridSet
• maps_ : protocols::frag_picker::scores::ABEGO_SS_Score
• maps_up_to_date() : core::chemical::ResidueTypeSetCache
• 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_connect_incomplete() : core::conformation::Residue
• 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::ShuffleFileSystemJobDistributor , protocols::jd2::VectorPoseJobDistributor
• mark_designable() : protocols::task_operations::DatabaseThread
• mark_disconnected() : protocols::denovo_design::components::StructureData
• mark_edge_for_deletion() : core::pack::interaction_graph::EdgeBase
• 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_last_entity_as_important() : protocols::pack_daemon::DaemonSet , protocols::pack_daemon::PackDaemon
• mark_leave_as_is() : protocols::task_operations::DatabaseThread
• mark_loop_moveable() : protocols::forge::remodel::RemodelLoopMover
• mark_loops_moveable() : protocols::forge::remodel::RemodelLoopMover
• mark_move_accepted() : protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator , protocols::helical_bundle_predict::HBP_MoveGenerator
• mark_move_rejected() : protocols::helical_bundle_predict::HBP_MoveGenerator
• mark_node_as_complete() : protocols::jd3::job_distributors::JobExtractor
• 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
• mark_structure_as_sampled() : protocols::features::StructureFeatures
• mark_tags() : protocols::toolbox::KClusterData
• markDepth() : protocols::pockets::PocketGrid
• marked_for_deletion() : core::pack::interaction_graph::EdgeBase
• marked_for_deletion_ : core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G > , core::pack::interaction_graph::EdgeBase
• markEdgeDepth() : protocols::pockets::PocketGrid
• markInterfaceBySideChainContacts() : protocols::flexpep_docking::FlexPepDockingProtocol
• markNativeInterface() : protocols::flexpep_docking::FlexPepDockingProtocol
• markOneEdgeDepth() : protocols::pockets::PocketGrid
• markPocketDepth() : protocols::pockets::PocketGrid
• markpsp_ : protocols::pockets::PocketGrid
• marksps_ : protocols::pockets::PocketGrid
• mask : protocols::constel::ResidueMask , protocols::electron_density::SetupForDensityScoringMover
• mask_ : protocols::electron_density::ReportFSC , protocols::electron_density::ScaleMapIntensities
• mask_asu() : protocols::electron_density::DensitySymmInfo
• mask_from_offsets() : protocols::match::Bool3DGrid
• mask_output_ : protocols::electron_density::ScaleMapIntensities
• mask_reses_ : protocols::electron_density::SetupForDensityScoringMover
• maskbits_ : core::scoring::sasa::LeGrandSasa
• maskResidues() : core::scoring::electron_density::ElectronDensity
• masks_ : core::scoring::sasa::LeGrandSasa
• Mass : core::chemical::Element
• mass() : core::chemical::ResidueType , protocols::cartesian::CartesianAtom , protocols::md::MDBase
• mass_ : core::chemical::ResidueType , protocols::md::MDBase
• mass_limit_ : protocols::ligand_docking::MolarMassFilter , protocols::ligand_docking::MolecularMassFilter
• master() : core::conformation::ConformationKinWriter , core::conformation::ResidueKinWriter , protocols::match::output::ResidueKinemageWriter
• master_ : core::conformation::ConformationKinWriter , core::conformation::ResidueKinWriter , protocols::match::Bool3DGridKinemageWriter , protocols::match::output::ResidueKinemageWriter , protocols::match::output::SingleDownstreamResidueWriter , protocols::match::output::WriteUpstreamHitKinemage , protocols::recon_design::FindConsensusSequence
• master_add_unfolded_energy_data() : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor
• master_beam_cutoff_ : protocols::loop_grower::FragmentExtension , protocols::loop_grower::LoopGrower , protocols::loop_grower::LoopPartialSolutionStore
• master_beam_width_ : protocols::loop_grower::FragmentExtension , protocols::loop_grower::LoopGrower , protocols::loop_grower::LoopPartialSolutionStore
• master_get_new_job_id() : protocols::jd2::MPIFileBufJobDistributor , protocols::jd2::MPIWorkPoolJobDistributor
• master_go() : 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_mover_ : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• master_packer_ : protocols::stepwise::modeler::StepWiseConnectionSampler , protocols::stepwise::modeler::StepWiseModeler
• master_rank() : protocols::jd2::MPIFileBufJobDistributor , protocols::loophash::MPI_LoopHashRefine_Master , protocols::mpi_refinement::MPI_Refine_Master
• master_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::pose_metric_calculators::EnergiesData
• master_weight_ : protocols::pose_metric_calculators::EnergiesData
• master_weight_vector() : protocols::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• masters_done_ : protocols::mpi_refinement::MPI_Refine_Emperor
• Mat : protocols::sic_dock::RigidScore
• Mat3VecMult() : protocols::sparta::PDB
• match() : protocols::ligand_docking::ga_ligand_dock::AtomProperties , protocols::ligand_docking::ga_ligand_dock::Pharmacophore , protocols::noesy_assign::Resonance
• match2D() : protocols::noesy_assign::FloatingResonance , protocols::noesy_assign::LabelResonance , protocols::noesy_assign::ProtonResonance , protocols::noesy_assign::Resonance
• match_ : protocols::simple_filters::SimpleMetricFilter
• match_aa1() : core::scoring::motif::ResPairMotifQuery
• match_aa1_ : core::scoring::motif::ResPairMotifQuery
• match_aa2() : core::scoring::motif::ResPairMotifQuery
• match_aa2_ : core::scoring::motif::ResPairMotifQuery
• match_algorithm_ : protocols::match::output::WriteUpstreamCoordinateKinemage
• match_chi_rmsd() : core::scoring::motif::ResPairMotifQuery
• match_chi_rmsd_ : core::scoring::motif::ResPairMotifQuery
• match_dspos1() : protocols::match::match_dspos1
• match_groups_ : protocols::match::output::MatchConsolidator
• match_groups_dshits() : protocols::match::output::CloudPDBWriter
• match_groups_dshits_ : protocols::match::output::CloudPDBWriter
• match_groups_ushits() : protocols::match::output::CloudPDBWriter
• match_groups_ushits_ : protocols::match::output::CloudPDBWriter
• match_has_been_output() : protocols::match::MatchOutputTracker
• match_index : protocols::indexed_structure_store::FragmentLookupResult
• match_names_ : protocols::match::output::MatchScoreWriter
• match_params_ : protocols::enzdes::SecondaryMatchProtocol
• match_positions_ : protocols::match::MatcherMover
• match_possible_for_hit_geometry() : protocols::match::OccupiedSpaceHash
• match_processing_successful() : protocols::match::output::MatchProcessor
• match_processing_successful_ : protocols::match::output::MatchProcessor
• match_radius() : core::scoring::motif::ResPairMotifQuery
• match_radius_ : core::scoring::motif::ResPairMotifQuery
• match_res_ : core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric
• match_res_mode() : core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric
• match_rmsd : protocols::indexed_structure_store::FragmentLookupResult
• match_rmsd_threshold : protocols::indexed_structure_store::FragmentLookupResult
• match_rt_limit_ : protocols::denovo_design::DisulfidizeMover
• match_sampling_of_modeler_ : protocols::carbohydrates::GlycanSampler
• match_score() : core::sequence::SimpleScoringScheme , protocols::indexed_structure_store::FragmentLookupResult
• match_score_ : core::sequence::SimpleScoringScheme
• match_score_writer_ : protocols::match::output::MatchProcessor
• match_scores_ : protocols::match::output::MatchScoreWriter
• match_segments : protocols::sewing::hashing::AlignmentFGMSettings
• match_segments_ : protocols::legacy_sewing::LegacyAppendAssemblyMover , protocols::sewing::hashing::AlignmentSettings
• match_ss1() : core::scoring::motif::ResPairMotifQuery
• match_ss1_ : core::scoring::motif::ResPairMotifQuery
• match_ss2() : core::scoring::motif::ResPairMotifQuery
• match_ss2_ : core::scoring::motif::ResPairMotifQuery
• match_ss_to_abego_ : protocols::denovo_design::components::IdealAbegoGenerator
• match_variants() : core::chemical::ResidueTypeSelector , protocols::environment::ProtectedConformation
• match_window_one_ : protocols::carbohydrates::GlycanTreeModeler
• matchAtomFast() : core::scoring::electron_density::ElectronDensity , protocols::loop_grower::DensSkeleton
• 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
• matchCount : protocols::sparta::Sparta::SpartaLib
• MatchCounter() : protocols::match::MatchCounter
• matched_residues_ : protocols::legacy_sewing::SewResidue
• matched_tags() : core::io::silent::SilentFileData
• Matcher() : protocols::match::Matcher
• matcher_ : protocols::match::output::UpstreamHitCacher
• 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_output_count_ : protocols::match::output::WriteUpstreamHitKinemage
• matches_residue_type() : core::scoring::lkball::LKB_ResidueInfo
• MatchFilter() : protocols::match::output::MatchFilter
• MatchGrafter() : protocols::metal_interface::MatchGrafter
• MatchGrouper() : protocols::match::output::MatchGrouper
• MatchHash : protocols::match::MatchOutputTracker
• matching_database_ : core::scoring::disulfides::DisulfideMatchingPotential
• matchingFrags_ : protocols::forge::remodel::RemodelMover::instruction_flags
• MatchList : protocols::canonical_sampling::AsyncMPITemperingBase
• 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
• MatchSet : protocols::match::HitHasher
• MatDesGreedyOptMutationMover() : protocols::matdes::MatDesGreedyOptMutationMover
• MatDesPointMutationCalculator() : protocols::matdes::MatDesPointMutationCalculator
• Matrix : core::conformation::symmetry::SymmData , core::kinematics::Jump , core::kinematics::RT , core::kinematics::Stub , core::kinematics::tree::Atom , core::scoring::dna::DNA_BasePotential , core::scoring::MultipoleElecResidueInfo , core::scoring::MultipoleParameter , core::scoring::rna::RNA_StubCoordinateEnergy , core::scoring::symmetry::SymmetricEnergies , core::scoring::VdWTinkerResidueInfo , core::sequence::DP_Matrix
• matrix : protocols::evaluation::PCA , protocols::frag_picker::LAMBEGO_IO , protocols::frag_picker::TorsionBinIO
• Matrix : protocols::hotspot_hashing::StubGenerator , protocols::nmr::pcs::PCSLigandTransformMover , protocols::simple_moves::BBGaussianMover
• matrix3f_to_xyzMatrix() : protocols::forge::remodel::RemodelGlobalFrame , protocols::simple_filters::RepeatParameterFilter
• matrix_ : core::chemical::VDDistanceMatrix , protocols::simple_moves::FavorSequenceProfile
• matrix_A : protocols::simple_moves::BBGaussianMover
• matrix_A_ : core::scoring::nmr::pcs::PCSSingleSet , core::scoring::nmr::rdc::RDCMultiSet
• matrix_dRdPhi : protocols::simple_moves::BBGaussianMover
• matrix_finalized() : core::scoring::bin_transitions::BinTransitionData
• matrix_finalized_ : core::scoring::bin_transitions::BinTransitionData
• matrix_G : protocols::simple_moves::BBGaussianMover
• matrix_initialized() : core::scoring::bin_transitions::BinTransitionData
• matrix_initialized_ : core::scoring::bin_transitions::BinTransitionData
• MatrixScoringScheme() : core::sequence::MatrixScoringScheme
• mature_larval_job() : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::JobQueen , protocols::jd3::standard::StandardJobQueen
• max() : core::id::DOF_ID_Range , core::id::TorsionID_Range
• max0_ : core::scoring::hbonds::FadeInterval
• max_ : core::id::DOF_ID_Range , core::id::TorsionID_Range , core::scoring::func::EtableFunc , protocols::recces::Histogram , protocols::simple_filters::RepeatParameterFilter
• max_aa_ : core::scoring::rna::RNP_LowResPairDistPotential , core::scoring::rna::RNP_LowResPotential , core::scoring::rna::RNP_LowResStackData
• max_abs_inter_strand_dihedral_to_not_be_same_direction_strands_ : protocols::features::strand_assembly::SandwichFeatures
• max_accepted_hbond_count() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup
• max_accepted_hbond_count_ : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup
• max_accepted_trials() : protocols::monte_carlo::GenericMonteCarloMover
• max_accepted_trials_ : protocols::monte_carlo::GenericMonteCarloMover
• max_allowed_conserved_pos_mutations_ : protocols::calc_taskop_filters::ConservedPosMutationFilter
• max_allowed_hbonds() : protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter
• max_allowed_oversaturated() : protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter
• max_allowed_oversaturated_ : protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter
• max_amplitude_ : protocols::backbone_moves::local_backbone_mover::free_peptide_movers::TranslationFreePeptideMover
• max_angle() : protocols::simple_filters::AngleToVector
• max_angle_ : protocols::rigid::RollMover , protocols::simple_filters::AngleToVector , protocols::simple_moves::RandomTorsionMover
• max_angle_dev_ : protocols::membrane::FlipMover
• max_angle_disp() : protocols::backrub::BackrubSegment
• max_angle_disp_ : protocols::backrub::BackrubSegment
• max_angle_disp_4() : protocols::backrub::BackrubMover
• max_angle_disp_4_ : protocols::backrub::BackrubMover
• max_angle_disp_7() : protocols::backrub::BackrubMover
• max_angle_disp_7_ : protocols::backrub::BackrubMover
• max_angle_disp_slope() : protocols::backrub::BackrubMover
• max_angle_disp_slope_ : protocols::backrub::BackrubMover
• max_atom_depth() : core::scoring::trie::RotamerTrie< AT, CPDATA >
• max_atom_depth_ : core::scoring::trie::RotamerTrie< AT, CPDATA >
• max_atom_radius() : core::pack::interaction_graph::RotamerDots
• MAX_ATOM_SASA : protocols::constel::FilterBySASA
• max_atom_types() : core::scoring::packing::HolesParams
• max_atom_types_ : core::scoring::packing::HolesParams
• max_atomic_interaction_cutoff() : core::scoring::ScoreFunction
• max_atomic_interaction_distance() : core::scoring::ScoreFunctionInfo
• max_atomic_interaction_distance_ : core::scoring::ScoreFunctionInfo
• max_atoms() : protocols::backrub::BackrubMover
• max_atoms_ : protocols::backrub::BackrubMover , protocols::backrub::BackrubProtocol
• max_atoms_per_rotamer_ : core::scoring::trie::RotamerTrie< AT, CPDATA >
• max_attempts_ : protocols::loop_modeling::LoopBuilder , protocols::rosetta_scripts::MultipleOutputWrapper
• max_base_ : core::scoring::rna::RNP_LowResPairDistPotential , core::scoring::rna::RNP_LowResPotential , core::scoring::rna::RNP_LowResStackData
• max_bbrms() : protocols::loophash::LoopHashMoverWrapper
• max_bbrms_ : protocols::loophash::LoopHashMoverWrapper , protocols::loophash::LoopHashSampler
• max_bfactor_ : protocols::match::BfactorMPM
• max_bin_ : core::scoring::PairEPotential , protocols::scoring::methods::saxs::PDDFEnergy
• max_bond_length() : core::io::StructFileRepOptions
• max_bond_length_ : core::io::StructFileRepOptions
• max_branch_depth() : core::scoring::trie::RotamerTrie< AT, CPDATA >
• max_branch_depth_ : core::scoring::trie::RotamerTrie< AT, CPDATA >
• max_buried_sasa_ : protocols::task_operations::CrystalContactsOperation
• MAX_C_SIZE_LIMIT : core::chemical::carbohydrates::CarbohydrateInfo
• max_CA_CA_dis_ : protocols::features::strand_assembly::SandwichFeatures
• max_ca_dis2() : core::scoring::motif::ResPairMotifQuery
• max_ca_dis2_ : core::scoring::motif::ResPairMotifQuery
• max_cache_size() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• max_cache_size_ : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• max_calpha_distance() : protocols::loop_grower::LoopPartialSolution
• max_capacity_ : protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering >
• max_cav_ : protocols::simple_moves::AddCavitiesMover
• max_cb_cb_dist() : protocols::protein_interface_design::movers::PlacementAuctionMover
• max_cb_cb_dist_ : protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::protein_interface_design::movers::PlaceSimultaneouslyMover , protocols::protein_interface_design::movers::PlaceStubMover
• max_ccd_cycles_ : protocols::antibody::H3PerturbCCD
• max_center_x_ : core::conformation::membrane::AqueousPoreParameters
• max_center_y_ : core::conformation::membrane::AqueousPoreParameters
• max_chainbreak_ : protocols::analysis::LoopAnalyzerMover
• max_chi() : core::io::silent::ProteinSilentStruct_Template< T >
• max_chi_ : core::io::silent::ProteinSilentStruct_Template< T >
• max_chi_considered_ : protocols::rotamer_recovery::RRComparerChiDiff
• max_chunk_size_ : protocols::frag_picker::scores::GunnCostScore
• max_clash_score : protocols::sewing::hashing::HasherSettings
• MAX_CLASS : protocols::noesy_assign::CrossPeak
• max_cluster_size_ : protocols::pose_selectors::ClusterPoseSelector
• max_clusters_ : protocols::pose_selectors::ClusterPoseSelector
• max_com_vector_ang_cos_ : protocols::match::NumNeighborsMPM
• max_connpoints_for_residue() : core::scoring::trie::CPDataCorrespondence
• max_connpoints_for_residue_ : core::scoring::trie::CPDataCorrespondence
• max_contacts : protocols::sewing::hashing::IdealContact
• max_context_neighbor_cutoff() : core::scoring::Energies , core::scoring::ScoreFunctionInfo
• max_context_neighbor_cutoff_ : core::scoring::Energies , core::scoring::ScoreFunctionInfo
• max_contig_insertion_ : protocols::hybridization::CartesianHybridize , protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol
• max_coord_ : protocols::canonical_sampling::HamiltonianExchange
• max_count_ : protocols::denovo_design::components::RandomVectorSelector< T >
• max_cst_seq_sep_ : core::scoring::methods::CustomAtomPairEnergy
• max_ct_dist2_ : protocols::constel::FilterByProxTerm
• max_cycle_close_trial_ : protocols::antibody::H3RefineCCD
• max_cycles() : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• max_cycles_ : protocols::loops::loop_closure::ccd::CCDLoopClosureMover , protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover , protocols::sewing::movers::AssemblyMover
• max_ddg_score_ : protocols::frag_picker::nonlocal::NonlocalFrags
• max_decoys_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::modeler::align::StepWiseClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased , protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• max_degree() : protocols::sasa_scores::PPoly
• max_del_grid : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• max_dis() : core::scoring::carbon_hbonds::CarbonHBondPotential , core::scoring::custom_pair_distance::DistanceFunc , core::scoring::etable::coulomb::Coulomb , core::scoring::etable::Etable , core::scoring::etable::EtableOptions , core::scoring::methods::GoapEnergy
• max_dis2() : core::scoring::carbon_hbonds::CarbonHBondEnergy , core::scoring::etable::coulomb::Coulomb , core::scoring::etable::Etable
• max_dis2_ : core::scoring::carbon_hbonds::CarbonHBondEnergy , core::scoring::etable::coulomb::Coulomb , core::scoring::etable::Etable
• max_dis_ : core::scoring::carbon_hbonds::CarbonHBondEnergy , core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy , core::scoring::etable::coulomb::Coulomb , core::scoring::etable::Etable , core::scoring::methods::FACTSEnergy , core::scoring::methods::GoapEnergy , core::scoring::methods::LK_PolarNonPolarEnergy
• max_dist() : core::kinematics::ShortestPathInFoldTree , core::scoring::mm::MMLJEnergyTable
• max_dist_ : core::kinematics::ShortestPathInFoldTree , core::scoring::carbon_hbonds::CarbonHBondPotential , core::scoring::mm::MMLJEnergyTable , core::scoring::saxs::DistanceHistogram , protocols::features::AtomAtomPairFeatures , protocols::simple_filters::ContactMapEvaluator
• max_dist_from_dot_to_intersection : core::pack::interaction_graph::InvRotamerDots
• max_dist_multiplier_ : protocols::simple_moves::DisulfideInsertionMover
• max_dist_ndx_ : protocols::toolbox::KClusterElement
• max_dist_sq_ : protocols::denovo_design::DisulfidizeMover
• max_dist_squared() : protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker
• max_dist_squared_ : core::scoring::orbitals::OrbitalsScore , protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker
• max_dist_to_center() : core::conformation::UltraLightResidue
• max_distance() : protocols::constraint_generator::TerminiConstraintGenerator , protocols::constraint_movers::AddConstraintsToCurrentConformationMover , protocols::fold_from_loops::constraint_generator::ConstraintConditions , protocols::fold_from_loops::movers::SplitAndMixPoseMover , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• max_distance_ : protocols::constraint_generator::AtomPairConstraintGenerator , protocols::constraint_generator::TerminiConstraintGenerator , protocols::constraint_movers::AddConstraintsToCurrentConformationMover , protocols::fold_from_loops::movers::SplitAndMixPoseMover , protocols::hotspot_hashing::LSMSearchPattern , protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange , protocols::toolbox::KClusterElement
• max_distance_squared_ : protocols::stepwise::modeler::StepWiseConnectionSampler , protocols::stepwise::screener::CentroidDistanceScreener , protocols::stepwise::screener::StubDistanceScreener
• max_disulf_score_ : protocols::denovo_design::DisulfidizeMover
• max_disulfides_ : protocols::denovo_design::DisulfidizeMover
• max_donated_hbond_count() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup
• max_dslf_energy_ : protocols::simple_moves::DisulfideInsertionMover
• max_dslf_pot_ : protocols::simple_moves::DisulfideInsertionMover
• max_e_contribution_to_pi_system_ : core::chemical::gasteiger::GasteigerAtomTypeData
• max_E_in_extracted_sw_loop_ : protocols::features::strand_assembly::SandwichFeatures
• max_edges_per_node_ : protocols::legacy_sewing::LegacyGreedyAssemblyMover
• max_emperor_lib_round_ : protocols::loophash::MPI_LoopHashRefine_Emperor , protocols::mpi_refinement::MPI_Refine_Emperor
• max_ending_loop_size_ : protocols::features::strand_assembly::SandwichFeatures
• max_ensemble_size_ : core::scoring::nmr::NMRSpinlabel
• max_env_enrichment_ : core::scoring::dna::DNA_EnvPairPotential
• max_frag_len() : protocols::frag_picker::FragmentPicker
• max_frag_length() : core::fragment::FragSet
• max_frag_length_ : core::fragment::FragSet
• max_frag_size_ : protocols::frag_picker::FragmentPicker , protocols::rna::denovo::movers::RNA_Relaxer
• max_gap_percentage() : core::sequence::SequenceAlignment
• max_gaplength_to_model_ : protocols::hybridization::MRMover
• max_generations() : protocols::genetic_algorithm::GeneticAlgorithmBase
• max_generations_ : protocols::genetic_algorithm::GeneticAlgorithmBase
• max_H_in_extracted_sw_loop_ : protocols::features::strand_assembly::SandwichFeatures
• max_hb_energy() : core::scoring::hbonds::HBondOptions
• max_hb_energy_ : core::scoring::hbonds::HBondOptions , protocols::simple_pose_metric_calculators::NumberHBondsCalculator
• max_hbond_energy_ : protocols::simple_filters::BuriedUnsatHbondFilter , protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator
• max_heavy_heavy_cutoff() : core::scoring::etable::Etable
• max_heavy_hydrogen_cutoff() : core::scoring::etable::Etable
• max_heavy_hydrogen_cutoff_ : core::scoring::etable::Etable
• max_heavyatom_depth() : core::scoring::trie::RotamerTrie< AT, CPDATA >
• max_heavyatom_depth_ : core::scoring::trie::RotamerTrie< AT, CPDATA >
• max_helix_fraction_ : protocols::simple_filters::AbinitioBaseFilter
• max_helix_length_ : protocols::fldsgn::filters::SecondaryStructureCountFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter , protocols::simple_filters::AbinitioBaseFilter
• MAX_HPATCH_AREA : core::pack::interaction_graph::SurfacePotential
• MAX_HPATCH_SCORE : core::pack::interaction_graph::SurfacePotential
• max_hphobe_atoms_any_restype() : core::pack::interaction_graph::HPatchNode< V, E, G >
• max_hphobes_ : core::pack::interaction_graph::HPatchNode< V, E, G >
• max_hydrogen_hydrogen_cutoff() : core::scoring::etable::Etable
• max_hydrogen_hydrogen_cutoff_ : core::scoring::etable::Etable
• max_hydrogen_lj_radius() : core::scoring::etable::Etable , core::scoring::etable::MembEtable
• max_hydrogen_lj_radius_ : core::scoring::etable::Etable , core::scoring::etable::MembEtable
• max_inner_cycles() : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• max_inner_cycles_ : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• max_input_poses_ : protocols::rosetta_scripts::MultiplePoseMover
• max_insertion_length : protocols::indexed_structure_store::DirectSegmentLookupConfig
• max_inter_sheet_dis_CA_CA_ : protocols::features::strand_assembly::SandwichFeatures
• max_inter_ss_bbrms() : protocols::loophash::LoopHashDiversifier
• max_inter_ss_bbrms_ : protocols::loophash::LoopHashDiversifier
• max_inter_strand_angle_to_not_be_same_direction_strands_ : protocols::features::strand_assembly::SandwichFeatures
• max_intra_ss_bbrms() : protocols::loophash::LoopHashDiversifier
• max_intra_ss_bbrms_ : protocols::loophash::LoopHashDiversifier
• max_iter() : core::import_pose::options::RNA_MinimizerOptions , core::optimization::MinimizerOptions , protocols::minimization_packing::MinMover , protocols::relax::RelaxProtocolBase
• max_iter_ : core::import_pose::options::RNA_MinimizerOptions , core::optimization::MinimizerOptions , protocols::electron_density::BfactorFittingMover , protocols::electron_density::VoxelSpacingRefinementMover , protocols::relax::LocalRelax , protocols::relax::RelaxProtocolBase
• max_iterations_ : protocols::protein_interface_design::movers::LoopOver
• max_k48_cter_dist_ : protocols::ub_e2c::ubi_e2c_modeler
• max_kic_build_attempts_ : protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC
• max_length() : protocols::antibody::CDRSetOptions , protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• max_length_ : protocols::antibody::CDRSetOptions , protocols::frag_picker::scores::PCS_FragDistance , protocols::legacy_sewing::sampling::requirements::LegacyGlobalLengthRequirement , protocols::legacy_sewing::sampling::requirements::LegacySegmentLengthRequirement , protocols::ncbb::SecStructFinder , protocols::pose_creation::SliceToMiniProteinMover , protocols::protein_interface_design::movers::LoopFinder , protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• max_level_index() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• max_levels_ : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• max_lib_size() : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• max_lib_size_ : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• max_lig_unsat_ : protocols::hbnet::HBNet
• max_linear_chainbreak() : protocols::fldsgn::BluePrintBDR , protocols::forge::components::BDR , protocols::forge::components::VarLengthBuild , protocols::forge::remodel::RemodelLoopMover , protocols::forge::remodel::RemodelMover
• 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_loop_length_ : protocols::features::LoopAnchorFeatures , protocols::fldsgn::filters::SecondaryStructureCountFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter
• max_loop_rebuild : protocols::comparative_modeling::LoopRelaxThreadingMover
• max_loop_size_ : protocols::loophash::FastGapMover , protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• max_loophash_per_structure_ : protocols::loophash::MPI_LoopHashRefine_Master
• max_major_radius_ : core::conformation::membrane::AqueousPoreParameters
• max_mc_nets_ : protocols::hbnet::HBNet
• max_memory_pose_num_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• max_minor_radius_ : core::conformation::membrane::AqueousPoreParameters
• max_missing_weight() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• max_missing_weight_ : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions , protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• max_natoms_ : core::pack::interaction_graph::NPDHBondNode< V, E, G >
• max_nbrs_ : core::scoring::dna::DNA_EnvPairPotential
• max_neighbors_ : protocols::match::NumNeighborsMPM
• max_network_size() : core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy
• max_network_size_ : core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy , protocols::hbnet::HBNet
• max_networks_per_pose_ : protocols::hbnet::HBNetStapleInterface
• max_noe_distance() : protocols::noesy_assign::CrossPeakInfo
• max_noe_distance_ : protocols::noesy_assign::CrossPeakInfo
• max_non_hydrogen_lj_radius() : core::scoring::etable::Etable , core::scoring::etable::MembEtable
• max_non_hydrogen_lj_radius_ : core::scoring::etable::Etable , core::scoring::etable::MembEtable
• max_nstr : protocols::simple_filters::SheetFilter
• max_nstruct() : protocols::jd2::archive::ArchiveBase , protocols::loophash::LoopHashMoverWrapper
• max_nstruct_ : protocols::jd2::archive::ArchiveBase , protocols::loophash::LoopHashMoverWrapper , protocols::loophash::LoopHashSampler
• max_nstruct_list_ : protocols::abinitio::IterativeBase
• max_ntries() : protocols::stepwise::StepWiseSampleAndScreen
• max_ntries_ : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_MultiPoseCloser , protocols::stepwise::StepWiseSampleAndScreen
• max_num_results() : protocols::multistage_rosetta_scripts::MRSJob
• max_num_results_ : protocols::indexed_structure_store::movers::DirectSegmentLookupMover , protocols::multistage_rosetta_scripts::MRSJob
• max_num_results_to_keep_per_input_struct_for_stage_ : protocols::multistage_rosetta_scripts::MRSJobQueen
• max_num_results_to_keep_per_instance_for_stage_ : protocols::multistage_rosetta_scripts::MRSJobQueen
• max_num_results_with_same_token_per_partition_ : protocols::jd3::dag_node_managers::NodeManager , protocols::jd3::dag_node_managers::NodeManagerStorageMatrix
• max_num_segments_ : protocols::sewing::movers::AssemblyMover
• max_num_strands_to_deal_ : protocols::features::strand_assembly::SandwichFeatures , protocols::features::strand_assembly::StrandBundleFeatures
• max_num_sw_per_pdb_ : protocols::features::strand_assembly::SandwichFeatures
• max_O_N_dis_ : protocols::features::strand_assembly::StrandBundleFeatures
• max_omega_ : protocols::analysis::LoopAnalyzerMover
• max_orbital_dist_squared_ : core::scoring::orbitals::OrbitalsScore
• max_output_poses_ : protocols::rosetta_scripts::MultiplePoseMover
• max_overlap_dis_ : protocols::match::output::UpstreamDownstreamCollisionFilter
• max_overlap_rmsd_ : protocols::pose_creation::MergePDBatOverlapMover
• max_packet_size_ : protocols::moves::UDPSocketClient
• max_pair_enrichment_ : core::scoring::dna::DNA_EnvPairPotential
• MAX_PATCH_SURFACE_AREA : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::interaction_graph::SurfacePotential
• max_path_length() : protocols::simple_filters::AveragePathLengthFilter
• max_path_length_ : protocols::simple_filters::AveragePathLengthFilter
• max_pbond_ : protocols::analysis::LoopAnalyzerMover
• max_penalty_ : protocols::simple_filters::ResidueIEFilter
• max_per_move_torsion_delta_ : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• max_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_population_size_ : protocols::genetic_algorithm::GeneticAlgorithmBase
• max_pos() : core::fragment::FragSet
• max_pos_ : core::fragment::FragSet
• max_pose_data_list_size_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• max_poses_ : protocols::rosetta_scripts::AdditionalOutputWrapper , protocols::rosetta_scripts::MultipleOutputWrapper
• max_possible_chis_ : core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser
• max_possible_rotamers_ : core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser
• max_primary_distance : protocols::indexed_structure_store::search::StructurePairQuery
• MAX_PROBABILITY : protocols::calc_taskop_filters::RotamerBoltzmannWeight2
• max_radius_ : protocols::hotspot_hashing::LSMSearchPattern , protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashMoverWrapper , protocols::loophash::LoopHashSampler
• max_rama_ : protocols::analysis::LoopAnalyzerMover
• max_rama_score_increase() : protocols::loops::loop_closure::ccd::RamaCheckBase
• max_rama_score_increase_ : protocols::loops::loop_closure::ccd::RamaCheckBase
• max_rand_ : protocols::frag_picker::scores::ScoreEValuator
• max_range_ : protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler
• max_ref_lib_size() : protocols::mpi_refinement::MPI_Refinement
• max_ref_lib_size_ : protocols::mpi_refinement::MPI_Refinement
• max_registry_shift_ : protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol
• max_registry_shift_global_ : protocols::hybridization::ChunkTrialMover
• max_rep_ : protocols::hbnet::HBNet
• max_repeats_ : protocols::symmetric_docking::SymDockProtocol , protocols::ub_e2c::ubi_e2c_modeler
• max_replicates_before_branch_ : protocols::hbnet::HBNet
• max_replicates_before_unsat_check_ : protocols::hbnet::HBNet
• max_repulsion_energy_ : protocols::flxbb::InterlockAroma
• max_res_in_strand_ : protocols::features::strand_assembly::StrandBundleFeatures
• max_residue_count() : protocols::simple_filters::ResidueCountFilter
• max_residue_count_ : protocols::simple_filters::ResidueCountFilter
• max_rms() : protocols::loophash::FastGapMover , protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashMoverWrapper
• max_rms_ : protocols::enzdes::ResidueConformerFilter , protocols::loophash::FastGapMover , protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashMoverWrapper , protocols::loophash::LoopHashSampler
• max_rmsd_after_relax_ : protocols::frag_picker::nonlocal::NonlocalFrags
• max_rmsd_in_region() : protocols::indexed_structure_store::SSHashedFragmentStore
• max_rot_bumpenergy_ : core::pack::rotamer_set::BumpSelector
• max_rot_cumulative_prob_ : protocols::ligand_docking::ga_ligand_dock::GALigandDock , protocols::ligand_docking::ga_ligand_dock::GAOptimizer
• MAX_ROT_ENERGY : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary
• max_rot_num : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary
• max_rot_per_trans_ : protocols::electron_density::DockIntoDensityMover
• max_rotation_angle_ : core::conformation::membrane::AqueousPoreParameters
• max_rotbump_energy() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• max_rotbump_energy_ : core::pack::task::PackerTask_
• max_rounds() : protocols::helical_bundle_predict::HBP_MoveGenerator , protocols::helical_bundle_predict::HBP_TemperatureScheduleGenerator
• max_rounds_ : protocols::helical_bundle_predict::HBP_MoveGenerator , protocols::helical_bundle_predict::HBP_TemperatureScheduleGenerator
• max_sample_iterations() : protocols::loops::loop_closure::kinematic_closure::KinematicPerturber
• max_sample_iterations_ : protocols::loops::loop_closure::kinematic_closure::KinematicPerturber
• max_sample_per_structure_ : protocols::mpi_refinement::MPI_Refine_Master
• max_samples() : protocols::helical_bundle::BackboneGridSampler , protocols::helical_bundle::BundleGridSampler
• max_samples_ : protocols::helical_bundle::BackboneGridSampler , protocols::helical_bundle::BundleGridSampler
• max_score() : core::scoring::motif::XformScore
• max_score_diffs() : protocols::evolution::AlignmentGapInserter
• max_score_diffs_ : protocols::evolution::AlignmentGapInserter
• max_seglen_ : protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC , protocols::loops::loop_mover::refine::LoopMover_Refine_KIC
• max_segment_length_ : protocols::sewing::movers::AssemblyMover
• max_segments() : protocols::legacy_sewing::sampling::requirements::LegacyRequirementSet
• max_segments_ : protocols::legacy_sewing::sampling::requirements::LegacyRequirementSet
• 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_ : protocols::constraints_additional::ConstraintEvaluator , protocols::constraints_additional::MaxSeqSepConstraintSet
• max_seq_sep_fudge() : protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints
• max_seq_sep_fudge_ : protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints
• max_sheet_angle_ : protocols::features::strand_assembly::StrandBundleFeatures
• max_sheet_angle_by_four_term_cen_res_ : protocols::features::strand_assembly::SandwichFeatures
• max_sheet_angle_with_cen_res_in_smaller_sheet_and_two_terminal_res_in_larger_sheet_ : protocols::features::strand_assembly::SandwichFeatures
• max_sheet_dis_ : protocols::features::strand_assembly::SandwichFeatures , protocols::features::strand_assembly::StrandBundleFeatures
• max_sheet_length_ : protocols::fldsgn::filters::SecondaryStructureCountFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter
• max_sheet_torsion_ : protocols::features::strand_assembly::StrandBundleFeatures
• max_sheet_torsion_cen_res_ : protocols::features::strand_assembly::SandwichFeatures
• max_shift_ : protocols::rbsegment_relax::OptimizeThreadingMover
• max_sims_per_pt_ : protocols::cluster::APCluster
• max_size_col() : protocols::mean_field::jagged_array< T, A >
• max_small_angle_ : protocols::simple_moves::oop::OopRandomSmallMover , protocols::simple_moves::triazolamer::TriazolamerRandomSmallMover
• max_ss_cluster_size_ : protocols::features::ModelFeatures
• max_starting_loop_size_ : protocols::features::strand_assembly::SandwichFeatures
• max_step_limit_ : core::optimization::ArmijoLineMinimization
• max_strand_dist_cutoff_ : core::scoring::SecondaryStructureWeights
• max_strands() : protocols::splice::AlignEndsMover
• max_strands_ : protocols::splice::AlignEndsMover
• max_struct() : protocols::simple_moves::CombinePoseMover
• max_struct_ : protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashMoverWrapper , protocols::loophash::LoopHashSampler , protocols::simple_moves::CombinePoseMover
• max_struct_per_radius_ : protocols::loophash::LoopHashMoverWrapper , protocols::loophash::LoopHashSampler
• max_struct_try() : protocols::simple_moves::CombinePoseMover
• max_struct_try_ : protocols::simple_moves::CombinePoseMover
• max_structures_ : protocols::pose_selectors::ClusterPoseSelector
• max_surface_deltaE_last_50_commits_ : core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G > , core::pack::interaction_graph::SurfaceEdge< V, E, G >
• max_surface_deltaE_recent_50_commits_ : core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G > , core::pack::interaction_graph::SurfaceEdge< V, E, G >
• MAX_SURFACE_ENERGY : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::interaction_graph::SurfacePotential
• max_swap_buffer_size_ : protocols::wum::WorkUnitQueue_Swapped
• MAX_TARGETS : protocols::pockets::PocketGrid
• max_temperature() : protocols::helical_bundle_predict::HBP_TemperatureScheduleGenerator
• max_temperature_ : protocols::helical_bundle_predict::HBP_TemperatureScheduleGenerator , protocols::legacy_sewing::LegacyMonteCarloAssemblyMover
• max_threads_ : protocols::frag_picker::FragmentPicker
• max_total_torsion_delta_ : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• max_total_torsion_delta_per_residue() : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• max_trans_ : protocols::topology_broker::RigidBodyRandomTMHMover
• max_trial_num_ : protocols::backbone_moves::local_backbone_mover::LocalBackboneMover
• max_trials() : protocols::fold_from_loops::movers::NubInitioLoopClosureMover , protocols::fold_from_loops::NubInitioMover
• max_trials_ : protocols::enzdes::DiversifyStoredRBConfs , protocols::fold_from_loops::movers::NubInitioLoopClosureMover , protocols::fold_from_loops::NubInitioMover
• max_tries() : protocols::moves::FilterMover
• max_tries_ : protocols::moves::FilterMover , protocols::recces::sampler::rna::MC_RNA_KIC_Sampler , protocols::simple_moves::DME_FilterMover , protocols::stepwise::sampler::rna::RNA_KIC_Sampler
• max_tries_for_random_sugar_setup_ : protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler
• max_tries_multiplier_for_ccd() : protocols::stepwise::options::StepWiseBasicOptions
• max_tries_multiplier_for_ccd_ : protocols::stepwise::options::StepWiseBasicOptions
• max_type_ : protocols::noesy_assign::PeakCalibrator
• max_type_direct_ : protocols::noesy_assign::PeakCalibrator
• max_unsat_Hpol_ : protocols::hbnet::HBNet
• max_valence_electrons_sp() : core::chemical::ElectronConfiguration
• max_value() : protocols::simple_moves::PSSM2BfactorMover
• max_value_ : protocols::simple_moves::PSSM2BfactorMover
• max_vdw_change_ : protocols::pose_length_moves::FixAllLoopsMover , protocols::pose_length_moves::NearNativeLoopCloser
• max_volume_contribution() : protocols::noesy_assign::CrossPeak
• max_weight_ : protocols::optimize_weights::WeightRangeConstraint
• MaxAngularMomentumQuantumNumber : core::chemical::ElectronConfiguration
• maxatoms_ : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• maxcycles() : protocols::moves::IteratedConvergenceMover
• maxcycles_ : protocols::moves::IteratedConvergenceMover
• maxd2 : core::scoring::etable::EtableParamsOnePair
• maxdis_ : protocols::ligand_docking::ga_ligand_dock::GridScorer
• maxdist_ : protocols::simple_filters::ResidueDepthFilter
• maxelts_ : protocols::loop_grower::LoopPartialSolutionStore
• maxfrac_ : protocols::mpi_refinement::WorkUnit_CombinePose
• maxfrac_crossover_ : protocols::simple_moves::CombinePoseMover
• maxfrag_ : protocols::loop_grower::LoopGrower
• maximum_clashes_allowed_ : protocols::sewing::requirements::ClashRequirement , protocols::sewing::requirements::LigandClashRequirement
• maximum_jobs_to_hold_in_memory_ : protocols::jd3::job_distributors::JobExtractor
• maximum_length_ : protocols::sewing::requirements::DsspSpecificLengthRequirement , protocols::sewing::requirements::LengthInResiduesRequirement
• maximum_size_ : protocols::sewing::requirements::SizeInSegmentsRequirement
• maximum_unpenalized_variance_ : protocols::sewing::scoring::IntraDesignTerminusMotifScorer , protocols::sewing::scoring::TerminusMotifScorer
• maxiter : protocols::ligand_docking::ga_ligand_dock::GADockStageParams
• maxiter_ : protocols::ligand_docking::ga_ligand_dock::GALigandDock , protocols::md::Rattle
• maxiter_minimize_ : protocols::ligand_docking::ga_ligand_dock::GridScorer
• maxLen_ : protocols::pockets::PocketGrid
• maxloopsize_ : protocols::loop_grower::FragmentExtension
• MAXNGB : protocols::constel::NeighTeller
• maxNominalRes() : core::scoring::electron_density::ElectronDensity
• maxouteriterations : core::pack::annealer::SimAnnealerBase
• maxpert_ : protocols::ligand_docking::ga_ligand_dock::EntropyEstimator
• maxPockSize_ : protocols::pockets::PocketGrid
• MaxPrincipleQuantumNumber : core::chemical::ElectronConfiguration
• maxRad_ : protocols::ligand_docking::ga_ligand_dock::GridScorer
• MaxSeqSepConstraintSet() : protocols::constraints_additional::MaxSeqSepConstraintSet
• maxsub : core::scoring::TMscoreStore
• maxsub_max : core::scoring::TMscoreStore
• maxsub_sum : core::scoring::TMscoreStore
• maxtrials() : protocols::monte_carlo::GenericMonteCarloMover
• maxtrials_ : protocols::monte_carlo::GenericMonteCarloMover
• maxX : protocols::pockets::CCluster , protocols::pockets::PCluster
• maxY : protocols::pockets::CCluster , protocols::pockets::PCluster
• maxZ : protocols::pockets::CCluster , protocols::pockets::PCluster
• maxz_ : core::scoring::ResidualDipolarCoupling
• may_change_aa() : core::chemical::ChiralFlipNaming , core::chemical::PatchCase , core::chemical::PatchOperation , core::chemical::Set_AA
• Mbhbond() : core::scoring::hbonds::HBondOptions
• Mbhbond_ : core::scoring::hbonds::HBondOptions
• mc() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio , protocols::loops::loop_closure::ccd::LoopClosure , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::minimization_packing::EnergyCutRotamerTrialsMover
• MC() : protocols::moves::DualMonteCarlo
• mc() : protocols::moves::TrialMover
• MC : protocols::sic_dock::Rose
• mc_ : protocols::abinitio::abscript::AbscriptMover , protocols::abinitio::abscript::AbscriptMover::StageTracker , protocols::abinitio::abscript::AbscriptStageMover , protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio , protocols::antibody::design::AntibodyDesignMover , protocols::antibody::GraftedStemOptimizer , protocols::antibody::H3PerturbCCD , protocols::antibody::H3RefineCCD , protocols::antibody::snugdock::SnugDock , protocols::canonical_sampling::CanonicalSamplingMover , protocols::carbohydrates::GlycanSampler , protocols::docking::DockingHighResLegacy , protocols::docking::DockingLowRes , protocols::docking::DockingProtocol , protocols::docking::DockMCMCycle , protocols::docking::DockMinMover , protocols::flexpep_docking::FlexPepDockingAbInitio , protocols::flexpep_docking::FlexPepDockingLowRes , protocols::flexpep_docking::FlexPepDockingProtocol , protocols::LoopRebuild , protocols::loops::loop_closure::ccd::LoopClosure , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::minimization_packing::EnergyCutRotamerTrialsMinMover , protocols::minimization_packing::EnergyCutRotamerTrialsMover
• MC_ : protocols::moves::DualMonteCarlo
• mc_ : protocols::moves::MCShowMover , protocols::moves::MonteCarloUtil , protocols::moves::RampingMover , protocols::moves::TrialMover , protocols::rbsegment_relax::RBSegmentRelax , protocols::relax::ClassicRelax , protocols::simple_moves::rational_mc::RationalMonteCarlo , protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockingLowRes , protocols::symmetric_docking::SymDockProtocol
• mc_accepted() : protocols::moves::MonteCarlo
• mc_accepted_ : protocols::monte_carlo::GenericMonteCarloMover , protocols::moves::MonteCarlo
• mc_accepted_string() : protocols::moves::MonteCarlo
• mc_accpeted() : protocols::monte_carlo::GenericMonteCarloMover
• mc_angle_weight_ : protocols::fold_from_loops::NubInitioMover
• MC_Any() : protocols::recces::sampler::MC_Any
• mc_binder_weight_ : protocols::fold_from_loops::NubInitioMover
• MC_branch_overlapping_networks() : protocols::hbnet::HBNet
• MC_Comb() : protocols::recces::sampler::MC_Comb
• mc_correction_weights_ : protocols::fold_from_loops::NubInitioMover
• mc_created : protocols::LoopRebuild
• mc_cycles_ : protocols::seeded_abinitio::SegmentHybridizer
• mc_dihedral_weight_ : protocols::fold_from_loops::NubInitioMover
• mc_filter_ : protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockRbTrialMover , protocols::symmetric_docking::SymFoldandDockRbTrialMover
• mc_initial_pose_ : protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• mc_interface_weight_ : protocols::antibody::design::AntibodyDesignMover
• mc_kt_ : protocols::backrub::BackrubProtocol , protocols::enzdes::BackboneSampler , protocols::protein_interface_design::movers::BackrubDDMover
• mc_kt_high_ : protocols::enzdes::EnzdesFlexBBProtocol
• mc_kt_low_ : protocols::enzdes::EnzdesFlexBBProtocol
• MC_Loop() : protocols::recces::sampler::MC_Loop
• MC_mover_ : protocols::monte_carlo::MonteCarloRecover , protocols::monte_carlo::MonteCarloReset , protocols::monte_carlo::MonteCarloTest
• MC_OneTorsion() : protocols::recces::sampler::MC_OneTorsion
• mc_optimize_dG_ : protocols::antibody::design::AntibodyDesignMover
• mc_ptr() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• MC_RNA_KIC_Sampler() : protocols::recces::sampler::rna::MC_RNA_KIC_Sampler
• MC_RNA_MultiSuite() : protocols::recces::sampler::rna::MC_RNA_MultiSuite
• MC_RNA_OneJump() : protocols::recces::sampler::rna::MC_RNA_OneJump
• MC_RNA_Sugar() : protocols::recces::sampler::rna::MC_RNA_Sugar
• MC_RNA_Suite() : protocols::recces::sampler::rna::MC_RNA_Suite
• MC_Sampler() : protocols::recces::sampler::MC_Sampler
• mc_scorefxn_ : protocols::hybridization::CartesianSampler
• mc_temp : protocols::simple_moves::ShakeStructureMover
• mc_temp_ : protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• mc_total_weight_ : protocols::antibody::design::AntibodyDesignMover
• MC_traverse_IG() : protocols::hbnet::HBNet
• mca_history_size_ : core::pack::task::PackerTask_
• MCAligner() : core::sequence::MCAligner
• mCen : protocols::cluster::calibur::Clustering
• mcfi() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList
• mcfi_ : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• mcfi_list() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• mcfi_list_vec_ : protocols::match::MatcherMover
• mcfi_lists_ : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• mcfi_lists_size() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• mcfis_ : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList
• mcfis_for_restype_ : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList
• mcfis_for_upstream_restype() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList
• mCluCen : protocols::cluster::calibur::Clustering
• mcm_cycles : protocols::flexpep_docking::FlexPepDockingFlags
• MCR : protocols::sic_dock::Rose
• MCShowMover() : protocols::moves::MCShowMover
• mD2C : protocols::cluster::calibur::Clustering
• md_energy_report_stepsize() : protocols::md::MDBase
• md_energy_report_stepsize_ : protocols::md::MDBase
• md_report_stepsize() : protocols::md::MDBase
• md_report_stepsize_ : protocols::md::MDBase
• md_rsr_update_stepsize() : protocols::md::MDBase
• md_rsr_update_stepsize_ : protocols::md::MDBase
• MDBase() : protocols::md::MDBase
• mdsch() : protocols::md::MDBase
• mdsch_ : protocols::md::MDBase
• mean() : core::scoring::dna::DNA_BasePotential
• Mean() : protocols::pack_daemon::Mean
• mean1_ : core::scoring::func::SoedingFunc
• mean2_ : core::scoring::func::SoedingFunc
• mean_ : core::chemical::AddChiRotamer , core::scoring::dna::DNA_BasePotential , core::scoring::func::GaussianFunc , core::scoring::methods::D2H_SA_Energy , protocols::ddg::ddGMover
• mean_backbone_torsion_ : core::scoring::dna::DNA_DihedralPotential
• mean_field_ : protocols::mean_field::GenMeanFieldMover
• MEAN_PROBABILITY : protocols::calc_taskop_filters::RotamerBoltzmannWeight2
• mean_sd : core::chemical::carbohydrates::LinkageConformerData
• mean_sugar_torsion_ : core::scoring::dna::DNA_DihedralPotential
• MeanField() : protocols::mean_field::MeanField
• means_ : core::scoring::disulfides::Cb_Distance_Func , core::scoring::func::SOGFunc_Impl , core::scoring::func::USOGFunc
• measure : core::io::CisPeptideInformation
• 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::pose_metric_calculators::SequenceComparison
• measure_sp3acc_BAH_from_hvy() : core::scoring::hbonds::HBondOptions
• measure_sp3acc_BAH_from_hvy_ : core::scoring::hbonds::HBDerivAssigner , core::scoring::hbonds::HBondOptions
• measure_specificities() : protocols::dna::DnaInterfacePacker
• measure_specificity() : protocols::dna::DnaInterfacePacker
• MED_AMBIG : protocols::noesy_assign::CrossPeak
• MedalExchangeMover() : protocols::medal::MedalExchangeMover
• MedalMover() : protocols::medal::MedalMover
• median() : protocols::filters::ReplicateFilter
• median_ : core::pack::dunbrack::BBIndNRChiSample< P > , protocols::filters::ReplicateFilter
• median_rms_ : protocols::cluster::ClusterBase
• meets_requirements() : core::chemical::Metapatch
• mem_ : protocols::membrane::HelixFromSequence
• mem_cbeta_2TM_den12() : core::scoring::membrane::MembraneData
• mem_cbeta_2TM_den12_ : core::scoring::membrane::MembraneData , core::scoring::MembranePotential
• mem_cbeta_2TM_den6() : core::scoring::membrane::MembraneData
• mem_cbeta_2TM_den6_ : core::scoring::membrane::MembraneData , core::scoring::MembranePotential
• mem_cbeta_4TM_den12() : core::scoring::membrane::MembraneData
• mem_cbeta_4TM_den12_ : core::scoring::membrane::MembraneData , core::scoring::MembranePotential
• mem_cbeta_4TM_den6() : core::scoring::membrane::MembraneData
• mem_cbeta_4TM_den6_ : core::scoring::membrane::MembraneData , core::scoring::MembranePotential
• mem_cbeta_den12() : core::scoring::membrane::MembraneData
• mem_cbeta_den12_ : core::scoring::membrane::MembraneData , core::scoring::MembranePotential
• mem_cbeta_den6() : core::scoring::membrane::MembraneData
• mem_cbeta_den6_ : core::scoring::membrane::MembraneData , core::scoring::MembranePotential
• mem_env_log10() : core::scoring::membrane::MembraneData
• mem_env_log10_ : core::scoring::membrane::FaMPEnvSmoothEnergy , core::scoring::membrane::MembraneData , core::scoring::MembranePotential , core::scoring::methods::MembraneEnvSmoothEnergy
• mem_env_log6() : core::scoring::membrane::MembraneData
• mem_env_log6_ : core::scoring::membrane::MembraneData , core::scoring::MembranePotential
• 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_from_topo_ : protocols::membrane::MPQuickRelaxMover
• mem_pair_log() : core::scoring::membrane::MembraneData
• mem_pair_log_ : core::scoring::membrane::MembraneData , core::scoring::MembranePotential
• mem_stats() : protocols::wum::WorkUnitQueue
• memb_center_search_ : core::scoring::MembranePotential
• memb_coord() : protocols::membrane::scoring::MEnvAtomParams
• memb_coord_ : protocols::membrane::scoring::MEnvAtomParams
• memb_dsolv1() : core::scoring::etable::MembEtable
• memb_dsolv1_ : core::scoring::etable::MembEtable , core::scoring::membrane::FaMPSolvEnergy , core::scoring::methods::Fa_MbsolvEnergy
• memb_dsolv2() : core::scoring::etable::MembEtable
• memb_dsolv2_ : core::scoring::etable::MembEtable , core::scoring::membrane::FaMPSolvEnergy , core::scoring::methods::Fa_MbsolvEnergy
• memb_etable() : core::scoring::ScoringManager
• memb_etable_ : core::scoring::membrane::FaMPEnvEnergy , core::scoring::membrane::FaMPSolvEnergy
• memb_etables_ : core::scoring::ScoringManager
• memb_lk_dgfree() : core::scoring::etable::MembEtable
• memb_lk_dgfree_ : core::scoring::etable::MembEtable
• memb_lk_dgrefce() : core::scoring::etable::MembEtable
• memb_lk_dgrefce_ : core::scoring::etable::MembEtable , core::scoring::membrane::FaMPEnvEnergy , core::scoring::methods::Fa_MbenvEnergy , protocols::membrane::scoring::FaWaterToBilayerEnergy
• memb_normal_search_ : core::scoring::MembranePotential
• memb_solv1() : core::scoring::etable::MembEtable
• memb_solv1_ : core::scoring::etable::MembEtable , core::scoring::membrane::FaMPSolvEnergy , core::scoring::methods::Fa_MbsolvEnergy
• memb_solv2() : core::scoring::etable::MembEtable
• memb_solv2_ : core::scoring::etable::MembEtable , core::scoring::membrane::FaMPSolvEnergy , core::scoring::methods::Fa_MbsolvEnergy
• MembAccesResidueLipophilicityFilter() : protocols::simple_filters::MembAccesResidueLipophilicityFilter
• Membed_init() : core::scoring::MembranePotential
• Membed_init_ : core::scoring::MembranePotential
• member : protocols::cluster::Cluster
• member_ : core::scoring::func::SOGFunc
• member_atoms_ : core::scoring::constraints::BasePairConstraint , core::scoring::constraints::MultiConstraint
• member_constraints() : core::scoring::constraints::MultiConstraint
• member_constraints_ : core::scoring::constraints::MultiConstraint
• member_residues_ : core::scoring::constraints::MultiConstraint
• MembEtable() : core::scoring::etable::MembEtable
• membrane() : core::import_pose::ImportPoseOptions
• membrane_ : core::import_pose::ImportPoseOptions , protocols::docking::DockingPrepackProtocol
• membrane_center() : core::conformation::membrane::MembraneInfo
• membrane_center_magnitude_ : core::scoring::MembranePotential
• membrane_center_max_delta_ : core::scoring::MembranePotential
• membrane_core() : core::conformation::membrane::MembraneInfo
• membrane_core_ : core::conformation::membrane::MembraneInfo , core::scoring::hbonds::HBondEnergy , protocols::membrane::AddMembraneMover
• MEMBRANE_EMBED : core::pose::datacache::CacheableDataType
• MEMBRANE_FAEMBED : core::pose::datacache::CacheableDataType
• 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_fapotential_ : core::scoring::ScoringManager
• membrane_from_topology() : protocols::membrane::MPQuickRelaxMover
• membrane_info() : core::conformation::Conformation , core::pose::Pose
• membrane_info_ : core::conformation::Conformation
• membrane_jump() : core::conformation::membrane::MembraneInfo
• membrane_jump_ : core::conformation::membrane::MembraneInfo
• membrane_jumps_ : protocols::abinitio::AbrelaxApplication
• membrane_normal() : core::conformation::membrane::MembraneInfo
• membrane_normal_cycles_ : core::scoring::MembranePotential
• membrane_normal_delta_angle_ : core::scoring::MembranePotential
• membrane_normal_magnitude_ : core::scoring::MembranePotential
• membrane_normal_max_angle_ : core::scoring::MembranePotential
• membrane_normal_start_angle_ : core::scoring::MembranePotential
• membrane_potential_ : core::scoring::Membrane_FAPotential , core::scoring::ScoringManager
• membrane_rsd_ : protocols::membrane::AddMembraneMover
• membrane_rsd_num() : core::conformation::membrane::MembraneInfo
• membrane_rsd_num_ : core::conformation::membrane::MembraneInfo
• membrane_steepness() : core::conformation::membrane::MembraneInfo
• membrane_thickness() : core::conformation::membrane::MembraneInfo
• MEMBRANE_TOPOLOGY : core::pose::datacache::CacheableDataType
• 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
• MembraneEnergyLandscapeSampler() : protocols::membrane_benchmark::MembraneEnergyLandscapeSampler
• 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
• MembraneSpanConstraint() : core::scoring::constraints::MembraneSpanConstraint
• MembraneSpanConstraintGenerator() : protocols::constraint_generator::MembraneSpanConstraintGenerator
• MembraneSpanTermZConstraint() : core::scoring::constraints::MembraneSpanTermZConstraint
• 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 , protocols::kinematic_closure::ClosureProblem::Memento
• memory_limit_ : protocols::wum::WorkUnitQueue , protocols::wum::WorkUnitQueue_Swapped
• memory_max_for_rpes_ : core::pack::interaction_graph::DoubleLazyInteractionGraph
• memory_offset_ : protocols::canonical_sampling::mc_convergence_checks::DataBuffer
• memory_usage_dynamic() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::SingleResidueDunbrackLibrary
• memory_usage_in_bytes() : core::pack::dunbrack::SingleResidueDunbrackLibrary
• memory_usage_static() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::SingleResidueDunbrackLibrary
• 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
• Menv_penalties_ : core::scoring::MembranePotential
• MEnvAtomParams() : protocols::membrane::scoring::MEnvAtomParams
• merge() : core::fragment::Frame , core::scoring::dssp::StrandPairing , core::scoring::dssp::StrandPairingSet , core::scoring::hbonds::graph::HBondGraph , core::scoring::ScoreFunction , protocols::comparative_modeling::AlignmentCluster , protocols::denovo_design::components::StructureData , protocols::loophash::LoopHashLibrary , protocols::wum::WorkUnitList
• merge_2_branched_networks() : protocols::hbnet::HBNet
• merge_atom_maps_ : core::io::pose_from_sfr::PoseFromSFRBuilder
• 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_behavior_manager_ : core::chemical::ResidueTypeSet
• merge_behaviors_ : core::chemical::MergeBehaviorManager , core::io::pose_from_sfr::PoseFromSFRBuilder
• merge_chains() : protocols::fold_from_loops::movers::SplitAndMixPoseMover
• merge_chains_ : protocols::fold_from_loops::movers::SplitAndMixPoseMover
• merge_data() : core::scoring::hbonds::graph::HBondEdge , core::scoring::hbonds::graph::HBondNode
• merge_helices() : protocols::helical_bundle_predict::HBPHelixAssignments
• merge_junction_sequence() : protocols::pose_creation::MergePDBatOverlapMover
• merge_poses() : protocols::fold_from_loops::movers::SplitAndMixPoseMover , protocols::pose_creation::MergePDBatOverlapMover
• merge_protein_surface_poses() : protocols::surface_docking::SurfaceDockingProtocol
• merge_segments() : protocols::denovo_design::components::StructureData
• mergeable() : core::scoring::dssp::StrandPairing
• MergeBehaviorManager() : core::chemical::MergeBehaviorManager
• MergeBehaviorMap : core::chemical::MergeBehaviorManager
• merged_vecs_ : protocols::hbnet::HBNet
• MergePDBatOverlapMover() : protocols::pose_creation::MergePDBatOverlapMover
• MergePDBMover() : protocols::pose_creation::MergePDBMover
• meridian_angle_degrees_ : protocols::legacy_sewing::Model
• mest_ : core::scoring::disulfides::FullatomDisulfidePotential
• metal_binding_atoms() : core::chemical::ResidueTypeBase
• metal_binding_atoms_ : core::chemical::ResidueTypeBase
• metal_bond_angle_constraint_multiplier() : core::import_pose::ImportPoseOptions
• metal_bond_angle_constraint_multiplier_ : core::import_pose::ImportPoseOptions
• metal_bond_dist_constraint_multiplier() : core::import_pose::ImportPoseOptions
• metal_bond_dist_constraint_multiplier_ : core::import_pose::ImportPoseOptions
• metal_bond_LJ_multiplier() : core::import_pose::ImportPoseOptions
• metal_bond_LJ_multiplier_ : core::import_pose::ImportPoseOptions
• metal_center_ : core::scoring::nmr::pcs::PCSTensor
• metal_coord_bounds_ : core::scoring::nmr::pcs::PCSSingleSet
• Metal_HelperBase() : protocols::cyclic_peptide::crosslinker::Metal_HelperBase
• metal_ion_label_ : core::scoring::nmr::pcs::PCSSingleSet
• metal_resnums_string_ : protocols::simple_moves::SetupMetalsMover
• metal_selector_ : protocols::simple_moves::SetupMetalsMover
• metal_set() : core::io::NomenclatureManager
• metal_set_ : core::io::NomenclatureManager
• metal_site_ : protocols::metal_interface::ZincHeterodimerMover
• metal_to_mobile_ : protocols::metal_interface::ZincHeterodimerMover
• metal_type() : protocols::cyclic_peptide::CrosslinkerMover
• metal_type_ : protocols::cyclic_peptide::crosslinker::Metal_HelperBase , protocols::cyclic_peptide::CrosslinkerMover
• metal_type_enum_from_string() : protocols::cyclic_peptide::crosslinker::Metal_HelperBase
• metal_type_string() : protocols::cyclic_peptide::crosslinker::Metal_HelperBase
• metal_type_string_from_enum() : protocols::cyclic_peptide::crosslinker::Metal_HelperBase
• metalbinding_constraint_energy() : core::scoring::constraints::ConstraintEdge
• metalbinding_constraint_energy_ : core::scoring::constraints::ConstraintEdge
• MetalContactsConstraintGenerator() : protocols::constraint_generator::MetalContactsConstraintGenerator
• MetalloClaimer() : protocols::topology_broker::MetalloClaimer
• metals_angle_constraint_multiplier_ : protocols::simple_moves::SetupMetalsMover
• metals_detection_LJ_multiplier_ : protocols::simple_moves::SetupMetalsMover
• metals_distance_constraint_multiplier_ : protocols::simple_moves::SetupMetalsMover
• MetalSiteResidue() : protocols::metal_interface::MetalSiteResidue
• Metapatch() : core::chemical::Metapatch
• metapatch() : core::chemical::PoseResidueTypeSet , core::chemical::ResidueTypeSet
• metapatch_map() : core::chemical::PoseResidueTypeSet , core::chemical::ResidueTypeSet
• metapatch_map_ : core::chemical::ResidueTypeSet
• metapatch_names_ : protocols::residue_optimization::MetapatchEnumeration
• MetapatchEnumeration() : protocols::residue_optimization::MetapatchEnumeration
• metapatches() : core::chemical::PoseResidueTypeSet , core::chemical::ResidueTypeSet
• metapatches_ : core::chemical::ResidueTypeSet
• MetaPoseEvaluator() : protocols::evaluation::MetaPoseEvaluator
• MetaPoseInputStream() : core::import_pose::pose_stream::MetaPoseInputStream
• method_ : core::scoring::sasa::SasaCalc , protocols::mpi_refinement::Clusterer
• method_creator_map_ : core::scoring::ScoringManager
• 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_type_ : core::scoring::sasa::SasaCalc
• method_weights() : core::scoring::methods::EnergyMethodOptions
• method_weights_ : core::scoring::methods::EnergyMethodOptions
• methodname() : protocols::mpi_refinement::Scheduler
• methodname_ : protocols::mpi_refinement::Scheduler
• methods_by_score_type_ : core::scoring::ScoreFunction
• methods_picked() : protocols::mpi_refinement::Scheduler
• methods_picked_ : protocols::mpi_refinement::Scheduler
• MethodWeights : core::scoring::methods::EnergyMethodOptions
• methyl_names_ : protocols::noesy_assign::MethylNameLibrary
• methyl_probe_dist_ : core::scoring::rna::data::RNA_DMS_Potential
• MethylNameLibrary() : protocols::noesy_assign::MethylNameLibrary
• MethylNames() : protocols::noesy_assign::MethylNames
• MethylNameTable : protocols::noesy_assign::MethylNameLibrary
• metric() : core::pose::Pose , core::simple_metrics::composite_metrics::CompositeEnergyMetric , core::simple_metrics::composite_metrics::ElectrostaticComplementarityMetric , core::simple_metrics::composite_metrics::ProtocolSettingsMetric , core::simple_metrics::CompositeRealMetric , core::simple_metrics::CompositeStringMetric , core::simple_metrics::metrics::CalculatorMetric , core::simple_metrics::metrics::DihedralDistanceMetric , core::simple_metrics::metrics::InteractionEnergyMetric , core::simple_metrics::metrics::ResidueSummaryMetric , core::simple_metrics::metrics::RMSDMetric , core::simple_metrics::metrics::SasaMetric , core::simple_metrics::metrics::SecondaryStructureMetric , core::simple_metrics::metrics::SelectedResidueCountMetric , core::simple_metrics::metrics::SelectedResiduesMetric , core::simple_metrics::metrics::SelectedResiduesPyMOLMetric , core::simple_metrics::metrics::SequenceMetric , core::simple_metrics::metrics::SequenceSimilarityMetric , core::simple_metrics::metrics::TimingProfileMetric , core::simple_metrics::metrics::TotalEnergyMetric , core::simple_metrics::per_residue_metrics::HbondMetric , core::simple_metrics::per_residue_metrics::PerResidueClashMetric , core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric , core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric , core::simple_metrics::per_residue_metrics::PerResidueGlycanLayerMetric , core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric , core::simple_metrics::per_residue_metrics::PerResidueSasaMetric , core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric , core::simple_metrics::PerResidueRealMetric , core::simple_metrics::PerResidueStringMetric , core::simple_metrics::RealMetric , core::simple_metrics::SimpleMetric , core::simple_metrics::StringMetric , core::simple_metrics::TestCompositeRealMetric , core::simple_metrics::TestCompositeStringMetric , core::simple_metrics::TestPerResidueRealMetric , core::simple_metrics::TestPerResidueStringMetric , core::simple_metrics::TestRealMetric , core::simple_metrics::TestStringMetric , protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric , protocols::analysis::simple_metrics::SequenceRecoveryMetric , protocols::cyclic_peptide::PeptideInternalHbondsMetric , protocols::filters::FilterValueMetric , protocols::quantum_annealing::InteractionGraphSummaryMetric
• metric_ : core::simple_metrics::metrics::ResidueSummaryMetric , protocols::filters::CalculatorFilter , protocols::simple_filters::PoseMetricEvaluator< T > , protocols::simple_filters::SimpleMetricFilter
• metric_calculators_ : core::pose::metrics::PoseMetricContainer
• metric_data() : protocols::jd3::job_summaries::StandardPoseJobSummary
• metric_data_ : protocols::jd3::job_summaries::StandardPoseJobSummary
• metric_for_evaluation() : protocols::multistage_rosetta_scripts::MRSJob
• metric_value() : protocols::multistate_design::SingleStateEntityData
• metric_value_getters() : protocols::multistate_design::MultiStateFitnessFunction
• metric_value_getters_ : protocols::multistate_design::MultiStateFitnessFunction
• metric_value_map() : protocols::multistate_design::SingleStateEntityData
• metric_value_map_ : protocols::multistate_design::SingleStateEntityData
• metric_value_template() : protocols::pose_metric_calculators::MetricValueGetter
• metric_value_template_ : protocols::pose_metric_calculators::MetricValueGetter
• MetricCalculatorFitnessFunction() : protocols::multistate_design::MetricCalculatorFitnessFunction
• MetricData() : protocols::features::MetricData
• MetricKey() : core::simple_metrics::MetricKey
• MetricRecorder() : protocols::canonical_sampling::MetricRecorder
• metrics_ : core::pose::Pose , core::simple_metrics::metrics::CalculatorMetric , protocols::analysis::simple_metrics::RunSimpleMetricsMover , protocols::features::SimpleMetricFeatures , protocols::jd3::jobs::MoverJob
• MetricValueBase : protocols::fldsgn::NcontactsCalculator , protocols::pose_metric_calculators::FragQualCalculator
• MetricValueGetter() : protocols::pose_metric_calculators::MetricValueGetter
• MetricValueGetterMap : protocols::multistate_design::MultiStateFitnessFunction
• MetricValueMap : protocols::multistate_design::SingleStateEntityData
• metropolis_hastings_mover() : protocols::canonical_sampling::ThermodynamicMover , protocols::simple_moves::sidechain_moves::SidechainMCMover
• metropolis_hastings_mover_ : protocols::simple_moves::sidechain_moves::SidechainMCMover
• MetropolisHastingsMover() : protocols::canonical_sampling::MetropolisHastingsMover
• mFinalClusters : protocols::cluster::calibur::Clustering
• mFinalDecoy : protocols::cluster::calibur::Clustering
• mg_calculation_annotated_sequence() : core::scoring::rna::RNA_ScoringInfo
• mg_calculation_annotated_sequence_ : core::scoring::rna::RNA_ScoringInfo
• mg_coord_cst_dist() : protocols::magnesium::MgMinimizer
• mg_coord_cst_dist_ : protocols::magnesium::MgMinimizer
• mg_lig_interaction_cutoff_ : core::scoring::magnesium::MgEnergy
• mg_lig_knowledge_based_potential_ : core::scoring::magnesium::MgEnergy
• mg_lj_radius_ : core::scoring::magnesium::MgEnergy
• mg_lk_coeff : core::scoring::magnesium::MgEnergy
• mg_lk_dgfree_ : core::scoring::magnesium::MgEnergy
• mg_lk_lambda_ : core::scoring::magnesium::MgEnergy
• mg_map_ : protocols::denovo_design::components::SolutionSorter
• mg_poses : protocols::magnesium::MgScanner
• mg_poses_ : protocols::magnesium::MgScanner
• mg_ref_score_ : core::scoring::magnesium::MgEnergy
• mg_res() : protocols::magnesium::MgMinimizer
• mg_res_ : protocols::magnesium::MgMinimizer
• mg_res_list_ : protocols::magnesium::MgHydrater , protocols::magnesium::MgWaterHydrogenPacker
• mg_sol_fade_func_ : core::scoring::magnesium::MgEnergy
• mg_sol_fade_zone_ : core::scoring::magnesium::MgEnergy
• mg_sol_interaction_cutoff_ : core::scoring::magnesium::MgEnergy
• mg_water_hydrogen_packer_ : protocols::magnesium::MgHydrater
• mg_water_pairs_ : protocols::magnesium::MgWaterHydrogenPacker
• 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
• mh_ : protocols::sic_dock::scores::MotifHashRigidScore
• mhc_csv_db_contents_map_ : core::scoring::ScoringManager
• mhc_epitope_energy_setup() : core::scoring::mhc_epitope_energy::MHCEpitopeConstraint
• mhc_epitope_setup_ : core::scoring::mhc_epitope_energy::MHCEpitopeConstraint
• mhc_epitope_setup_file() : core::scoring::methods::EnergyMethodOptions
• mhc_epitope_setup_file_count() : core::scoring::methods::EnergyMethodOptions
• mhc_epitope_setup_files_ : core::scoring::methods::EnergyMethodOptions
• mhc_epitope_setup_helpers_ : core::scoring::ScoringManager
• mhc_matrix_contents_map_ : core::scoring::ScoringManager
• mhc_sqlite_db_contents_map_ : core::scoring::ScoringManager
• MHCEpitopeConstraint() : core::scoring::mhc_epitope_energy::MHCEpitopeConstraint
• MHCEpitopeEnergy() : core::scoring::mhc_epitope_energy::MHCEpitopeEnergy
• MHCEpitopeEnergySetup() : core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup
• MHCEpitopePredictor() : core::scoring::mhc_epitope_energy::MHCEpitopePredictor
• MHCEpitopePredictorExternal() : core::scoring::mhc_epitope_energy::MHCEpitopePredictorExternal
• MHCEpitopePredictorMatrix() : core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix
• MHCEpitopePredictorPreLoaded() : core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded
• MHCEpitopePredictorSVM() : core::scoring::mhc_epitope_energy::MHCEpitopePredictorSVM
• mid_ : protocols::pockets::PocketGrid
• mid_dist_ : protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential
• mid_pos() : protocols::fldsgn::topology::SS_Base
• mid_pos_ : protocols::fldsgn::topology::SS_Base
• middle_offset_ : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger
• middle_pack_min_ : protocols::antibody::AntibodyModelerProtocol
• middle_res() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• middle_res_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger
• MidPhiOut() : protocols::frag_picker::scores::MidPhiOut
• midpoint() : protocols::loops::Loop
• MidPsiOut() : protocols::frag_picker::scores::MidPsiOut
• midway_dist_ : core::scoring::etable::count_pair::CountPair2B< CrossoverBehavior >
• might_be_designing_ : core::scoring::rna::RNA_PairwiseLowResolutionEnergy , core::scoring::rna::StackElecEnergy
• min() : core::id::DOF_ID_Range , core::id::TorsionID_Range , protocols::minimization_packing::PertMinMover
• min0_ : core::scoring::hbonds::FadeInterval
• min_ : core::id::DOF_ID_Range , core::id::TorsionID_Range , core::scoring::func::EtableFunc , protocols::cryst::DockLatticeMover , protocols::ddg::ddGMover , protocols::recces::Histogram , protocols::simple_filters::RepeatParameterFilter
• min_aa_probability_ : protocols::task_operations::SeqprofConsensusOperation
• min_after_repack_ : protocols::loops::loop_mover::refine::LoopMover_Refine_KIC
• min_after_stage1_ : protocols::hybridization::HybridizeProtocol
• min_all_jumps_ : protocols::enzdes::EnzdesBaseProtocol
• min_angle() : protocols::simple_filters::AngleToVector
• min_angle_ : protocols::rigid::RollMover , protocols::simple_filters::AngleToVector
• min_asp_glu_hbonds_ : protocols::hbnet::HBNetStapleInterface
• min_assembly_score_ : protocols::legacy_sewing::LegacyEnumerateAssemblyMover , protocols::legacy_sewing::LegacyMonteCarloAssemblyMover
• min_at_end_ : protocols::hybridization::FoldTreeHybridize
• min_atoms() : protocols::backrub::BackrubMover
• min_atoms_ : protocols::backrub::BackrubMover , protocols::backrub::BackrubProtocol
• min_backbone_ : protocols::electron_density::DockIntoDensityMover
• min_base_relax_ : protocols::antibody_legacy::CDRH3Modeler
• min_bb() : protocols::calc_taskop_movers::DesignRepackMover , protocols::protein_interface_design::movers::PrepackMover
• min_bb_ : protocols::calc_taskop_movers::DesignRepackMover , protocols::carbohydrates::GlycanTreeMinMover , protocols::enzdes::EnzRepackMinimize , protocols::minimization_packing::symmetry::TaskAwareSymMinMover , protocols::protein_interface_design::movers::PrepackMover
• min_bb_set() : protocols::calc_taskop_movers::DesignRepackMover
• min_bbrms() : protocols::loophash::LoopHashMoverWrapper
• min_bbrms_ : protocols::loophash::LoopHashMoverWrapper , protocols::loophash::LoopHashSampler
• min_bin_ : protocols::scoring::methods::saxs::PDDFEnergy
• min_bond_length() : core::io::StructFileRepOptions
• min_bond_length_ : core::io::StructFileRepOptions
• min_boundary_res_ : protocols::hbnet::HBNet
• min_bpy_contacts_ : protocols::sic_dock::scores::TrisBpyScore
• min_breakout_fast_loops_ : protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure
• min_breakout_good_loops_ : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• min_C_O_N_angle_ : protocols::features::strand_assembly::SandwichFeatures
• MIN_C_SIZE_LIMIT : core::chemical::carbohydrates::CarbohydrateInfo
• min_c_terminal_charges() : protocols::aa_composition::AddHelixSequenceConstraintsMover
• min_c_terminal_charges_ : protocols::aa_composition::AddHelixSequenceConstraintsMover
• min_CA_CA_dis_ : protocols::features::strand_assembly::SandwichFeatures
• min_cav_ball_radius : core::scoring::packstat::SasaOptions
• min_center_x_ : core::conformation::membrane::AqueousPoreParameters
• min_center_y_ : core::conformation::membrane::AqueousPoreParameters
• min_chi_ : protocols::carbohydrates::GlycanTreeMinMover , protocols::make_rot_lib::RotData , protocols::minimization_packing::symmetry::TaskAwareSymMinMover
• min_client_rank() : protocols::jd2::MPIFileBufJobDistributor
• min_client_rank_ : protocols::jd2::MPIFileBufJobDistributor
• min_cluster_overlap : core::scoring::packstat::SasaOptions
• min_com_vector_ang_cos_ : protocols::match::NumNeighborsMPM
• min_contacts_per_res_ : protocols::frag_picker::nonlocal::NonlocalFrags
• min_contribution_symmetric_peaks_ : protocols::noesy_assign::PeakAssignmentParameters
• min_core_res_ : protocols::hbnet::HBNet
• min_cst : protocols::simple_moves::ShakeStructureMover
• min_cst_ : protocols::ddg::ddGMover
• min_cst_mut_types_ : protocols::ddg::ddGMover
• min_cst_set_mut_ : protocols::ddg::ddGMover
• min_cst_set_wt_ : protocols::ddg::ddGMover
• min_cst_sfxn_ : protocols::ddg::ddGMover
• min_cst_sfxn_no_cst_weight_ : protocols::ddg::ddGMover
• min_cst_wt_types_ : protocols::ddg::ddGMover
• min_cycles_ : protocols::relax::RangeRelaxMover , protocols::seeded_abinitio::SegmentHybridizer , protocols::sewing::movers::AssemblyMover
• min_decoys_for_statistics_ : protocols::jd2::archive::NormalizedEvaluatedArchive
• 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_dis2_ : core::scoring::etable::coulomb::Coulomb , core::scoring::etable::Etable
• min_dis_ : core::scoring::etable::coulomb::Coulomb , core::scoring::etable::Etable
• min_dis_score_ : core::scoring::etable::coulomb::Coulomb
• min_dist() : core::scoring::mm::MMLJScore , protocols::noesy_assign::FragsToAtomDist::DistanceRecord
• min_dist_ : protocols::features::AtomAtomPairFeatures , protocols::noesy_assign::FragsToAtomDist::DistanceRecord , protocols::splice::RotLibOut
• min_dist_multiplier_ : protocols::simple_moves::DisulfideInsertionMover
• min_dist_squared_ : protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker
• min_distance() : protocols::constraint_generator::TerminiConstraintGenerator
• min_distance_ : protocols::constraint_generator::TerminiConstraintGenerator , protocols::simple_filters::TMsSpanMembraneFilter
• min_distance_grid_ : protocols::magnesium::SampleGrid
• min_disulfides_ : protocols::denovo_design::DisulfidizeMover
• min_diversity_list_ : protocols::abinitio::IterativeBase
• min_dwell_ : core::pack::annealer::FixbbPwatSimAnnealer
• min_edge_count : core::kinematics::FoldTree
• min_element_resis_ : protocols::fldsgn::filters::SecondaryStructureCountFilter
• min_env_energy_ : protocols::flxbb::InterlockAroma
• min_env_enrichment_ : core::scoring::dna::DNA_EnvPairPotential
• min_epsilon_ : protocols::make_rot_lib::RotData
• min_error_ : core::optimization::GA_Minimizer
• min_everything_ : protocols::ncbb::SecStructFinder
• min_fast_loops_ : protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure
• min_final_hbonds_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• min_frag_length() : protocols::splice::RotLibOut
• min_frag_length_ : protocols::simple_moves::ClassicFragmentMover , protocols::splice::RotLibOut
• min_genkic_hbonds_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• min_good_loops_ : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• min_hash_score : protocols::sewing::hashing::HasherSettings
• min_heap() : protocols::cluster::Exemplar
• min_helices_contacted_by_network_ : protocols::hbnet::HBNetStapleInterface
• min_helix_length() : protocols::aa_composition::AddHelixSequenceConstraintsMover
• min_helix_length_ : protocols::aa_composition::AddHelixSequenceConstraintsMover , protocols::fldsgn::filters::SecondaryStructureCountFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter
• min_helix_size_ : protocols::features::helixAssembly::HelixBundleFeatures , protocols::features::ModelFeatures
• min_hole_radius : core::scoring::packstat::SasaOptions
• min_inter_sheet_dis_CA_CA_ : protocols::features::strand_assembly::SandwichFeatures
• min_inter_ss_bbrms() : protocols::loophash::LoopHashDiversifier
• min_inter_ss_bbrms_ : protocols::loophash::LoopHashDiversifier
• min_interacting_set_fraction_ : protocols::features::helixAssembly::HelixBundleFeatures
• min_intermolecular_hbonds_ : protocols::hbnet::HBNetStapleInterface
• min_intra_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_helix_ : protocols::frags::TorsionFragmentMover
• min_len_strand() : protocols::frags::TorsionFragmentMover
• min_len_strand_ : protocols::frags::TorsionFragmentMover
• min_length() : protocols::antibody::CDRSetOptions , protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• min_length_ : protocols::antibody::CDRSetOptions , protocols::legacy_sewing::sampling::requirements::LegacyGlobalLengthRequirement , protocols::legacy_sewing::sampling::requirements::LegacySegmentLengthRequirement , protocols::ncbb::SecStructFinder , protocols::protein_interface_design::movers::LoopFinder , protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• min_lig_ : protocols::enzdes::EnzRepackMinimize
• min_loop_ : protocols::denovo_design::DisulfidizeMover
• min_loop_length() : protocols::features::LoopAnchorFeatures
• min_loop_length_ : protocols::features::LoopAnchorFeatures , protocols::fldsgn::filters::SecondaryStructureCountFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter , protocols::jumping::JumpSelector
• min_loop_size() : protocols::comparative_modeling::MultiThreadingMover , protocols::comparative_modeling::ThreadingMover
• min_loop_size_ : protocols::comparative_modeling::MultiThreadingMover , protocols::comparative_modeling::ThreadingMover , protocols::domain_assembly::AssembleLinkerMover , protocols::loophash::FastGapMover , protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure , protocols::topology_broker::RigidChunkClaimer
• min_major_radius_ : core::conformation::membrane::AqueousPoreParameters
• min_map() : core::optimization::AtomTreeMultifunc , core::optimization::CartesianMultifunc , protocols::cartesian::MolecularDynamics , protocols::normalmode::NormalModeMultifunc
• min_map_ : core::optimization::AtomTreeMultifunc , core::optimization::CartesianMultifunc , protocols::ligand_docking::ga_ligand_dock::GriddedAtomTreeMultifunc , protocols::md::CartesianMD , protocols::ncbb::SecStructMinimizeMultiFunc , protocols::normalmode::NormalModeMultifunc
• min_minor_radius_ : core::conformation::membrane::AqueousPoreParameters
• min_move() : protocols::abinitio::FoldConstraints
• min_move_ : protocols::abinitio::FoldConstraints
• min_movemap_ : protocols::dna::DnaInterfacePacker
• min_mover() : protocols::splice::SpliceOut
• min_mover_ : protocols::carbohydrates::GlycanSampler , protocols::carbohydrates::GlycanTreeMinMover , protocols::relax::ClassicRelax , protocols::symmetric_docking::SymDockingHiRes
• min_N_H_O_angle_between_two_sheets_ : protocols::features::strand_assembly::SandwichFeatures
• min_N_O_dis_between_two_sheets_ : protocols::features::strand_assembly::SandwichFeatures
• min_n_terminal_charges() : protocols::aa_composition::AddHelixSequenceConstraintsMover
• min_n_terminal_charges_ : protocols::aa_composition::AddHelixSequenceConstraintsMover
• min_nb_ : protocols::simple_moves::AddCavitiesMover
• min_neighbor_ : protocols::ligand_docking::ga_ligand_dock::GALigandDock
• min_neighbor_sc() : protocols::antibody::design::CDRGraftDesignOptions
• min_neighbor_sc_ : protocols::antibody::design::CDRGraftDesignOptions
• min_neighbors_ : protocols::match::NumNeighborsMPM
• min_network_size_ : protocols::hbnet::HBNet
• min_networks_per_pose_ : protocols::hbnet::HBNetStapleInterface
• min_num_south_sugar_filter_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• min_num_strands_in_sheet_ : protocols::features::strand_assembly::SandwichFeatures
• min_num_strands_to_deal_ : protocols::features::strand_assembly::SandwichFeatures , protocols::features::strand_assembly::StrandBundleFeatures
• min_O_N_dis_ : protocols::features::strand_assembly::StrandBundleFeatures
• min_occ_energy_ : core::scoring::geometric_solvation::DatabaseOccSolEne
• min_omega_ : protocols::make_rot_lib::RotData
• min_only : protocols::flexpep_docking::FlexPepDockingFlags
• min_options() : protocols::minimization_packing::MinMover , protocols::minimization_packing::SaneMinMover
• min_options_ : protocols::loop_modeling::refiners::MinimizationRefiner , protocols::loops::loop_mover::refine::ShearMinCCDTrial , protocols::minimization_packing::MinMover , protocols::minimization_packing::SaneMinMover
• min_orb_dist_enum_map_ : core::scoring::orbitals::OrbitalsScore
• min_overlap_ : protocols::simple_moves::ClassicFragmentMover
• min_pair_data_type() : core::scoring::etable::BaseEtableEnergy< Derived >
• min_pair_enrichment_ : core::scoring::dna::DNA_EnvPairPotential
• min_params : protocols::relax::CentroidRelax::parameters
• min_params_ : core::scoring::packing::HolesEnergy
• min_per_residue_fa_attr_ : protocols::features::helixAssembly::HelixBundleFeatures
• min_percent_hbond_capacity_ : protocols::hbnet::HBNet
• min_pos() : core::fragment::FragSet
• min_pos_ : core::fragment::FragSet
• min_primary_distance : protocols::indexed_structure_store::search::StructurePairQuery
• min_primary_seq_distance_diff_for_electrostatic_interactions_ : protocols::features::strand_assembly::SandwichFeatures
• MIN_PROBABILITY : protocols::calc_taskop_filters::RotamerBoltzmannWeight2
• min_rb() : protocols::antibody::design::CDRGraftDesignOptions , protocols::calc_taskop_movers::DesignRepackMover
• min_rb_ : protocols::antibody::design::CDRGraftDesignOptions , protocols::calc_taskop_movers::DesignRepackMover , protocols::enzdes::EnzRepackMinimize , protocols::minimization_packing::symmetry::TaskAwareSymMinMover
• min_rb_set() : protocols::calc_taskop_movers::DesignRepackMover
• min_rb_set_ : protocols::calc_taskop_movers::DesignRepackMover
• min_receptor_bb : protocols::flexpep_docking::FlexPepDockingFlags
• min_res_in_strand_ : protocols::features::strand_assembly::SandwichFeatures , protocols::features::strand_assembly::StrandBundleFeatures
• min_residue_count() : protocols::simple_filters::ResidueCountFilter
• min_residue_count_ : protocols::simple_filters::ResidueCountFilter
• min_rings_ : protocols::carbohydrates::GlycanSampler , protocols::carbohydrates::GlycanTreeMinMover , protocols::carbohydrates::GlycanTreeModeler
• min_rms() : protocols::loophash::FastGapMover , protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashMoverWrapper
• min_rms_ : protocols::enzdes::DiversifyStoredRBConfs , protocols::enzdes::MinimizeStoredRBConfs , protocols::loophash::FastGapMover , protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashMoverWrapper , protocols::loophash::LoopHashSampler
• MIN_ROT_PROB : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary
• min_rotation_angle_ : core::conformation::membrane::AqueousPoreParameters
• min_sc() : protocols::antibody::design::CDRGraftDesignOptions , protocols::calc_taskop_movers::DesignRepackMover
• min_sc_ : protocols::antibody::design::CDRGraftDesignOptions , protocols::calc_taskop_movers::DesignRepackMover , protocols::enzdes::EnzRepackMinimize
• min_sc_set() : protocols::calc_taskop_movers::DesignRepackMover
• min_score_ : core::scoring::MinScoreScoreFunction
• min_scorefxn : protocols::simple_moves::ShakeStructureMover
• min_scorefxn_ : protocols::antibody::design::GeneralAntibodyModeler , protocols::hybridization::CartesianHybridize , protocols::seeded_abinitio::SegmentHybridizer
• min_seg() : protocols::splice::SpliceIn , protocols::splice::SpliceInAntibody
• min_seg_ : protocols::splice::Splice , protocols::splice::SpliceIn
• min_segments() : protocols::legacy_sewing::sampling::requirements::LegacyRequirementSet
• min_segments_ : protocols::legacy_sewing::sampling::requirements::LegacyRequirementSet
• min_sep_ : protocols::simple_moves::AddCavitiesMover
• min_sep_d2_from_upstream_atoms_ : protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder
• min_seq_sep() : protocols::constraint_movers::AddConstraintsToCurrentConformationMover , protocols::fold_from_loops::constraint_generator::ConstraintConditions
• min_seq_sep_ : protocols::constraint_generator::AtomPairConstraintGenerator , protocols::constraint_movers::AddConstraintsToCurrentConformationMover , protocols::frag_picker::nonlocal::NonlocalFrags
• min_seq_separation_ : protocols::pose_metric_calculators::NonlocalContactsCalculator
• min_seq_separation_residue_assignment() : protocols::noesy_assign::CrossPeak
• MIN_SEQ_SEPARATIONS : core::scoring::methods::GoapEnergy
• min_seqsep_ : protocols::simple_filters::ContactMapEvaluator
• min_sfxn_ : protocols::relax::LocalRelax
• min_sheet_angle_ : protocols::features::strand_assembly::StrandBundleFeatures
• min_sheet_angle_by_four_term_cen_res_ : protocols::features::strand_assembly::SandwichFeatures
• min_sheet_dis_ : protocols::features::strand_assembly::SandwichFeatures , protocols::features::strand_assembly::StrandBundleFeatures
• min_sheet_length_ : protocols::fldsgn::filters::SecondaryStructureCountFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter
• min_sheet_torsion_ : protocols::features::strand_assembly::StrandBundleFeatures
• min_sheet_torsion_cen_res_ : protocols::features::strand_assembly::SandwichFeatures
• min_shortest_dis_sidechain_inter_sheet_ : protocols::features::strand_assembly::StrandBundleFeatures
• min_single_data_type() : core::scoring::etable::BaseEtableEnergy< Derived >
• min_size_ : protocols::simple_moves::AddCavitiesMover
• min_solution_count() : protocols::generalized_kinematic_closure::GeneralizedKIC
• min_solution_count_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• min_ss_cluster_size_ : protocols::features::ModelFeatures
• min_sse_count_ : protocols::pose_creation::SliceToMiniProteinMover
• min_sse_length_ : protocols::pose_creation::SliceToMiniProteinMover
• MIN_STRAND_LEN : protocols::denovo_design::components::SheetDB
• min_strand_size_ : protocols::features::ModelFeatures
• min_structures_for_acceptance_statistics_ : protocols::jd2::archive::ArchiveBase
• min_symm_dist2() : protocols::electron_density::DensitySymmInfo
• min_temperature() : protocols::helical_bundle_predict::HBP_TemperatureScheduleGenerator
• min_temperature_ : protocols::helical_bundle_predict::HBP_TemperatureScheduleGenerator , protocols::legacy_sewing::LegacyMonteCarloAssemblyMover
• min_threshold_ : protocols::antibody::LHRepulsiveRampLegacy
• min_time_ : protocols::ligand_docking::ga_ligand_dock::GridScorer
• min_tol_ : protocols::rna::denovo::movers::RNA_Minimizer
• min_tolerance : protocols::relax::ClassicRelax , protocols::stepwise::options::StepWiseBasicOptions
• min_tolerance_ : protocols::antibody::CDRsMinPackMin , protocols::antibody::H3RefineCCD , protocols::docking::DockingHighResLegacy , protocols::docking::DockMCMCycle , protocols::docking::DockMinMover , protocols::helical_bundle::FitSimpleHelix , protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer , protocols::stepwise::options::StepWiseBasicOptions , protocols::symmetric_docking::SymDockingHiRes , protocols::ub_e2c::ubi_e2c_modeler
• min_trial() : protocols::abinitio::FoldConstraints
• min_type() : core::import_pose::options::RNA_MinimizerOptions , core::optimization::MinimizerOptions , protocols::minimization_packing::MinMover , protocols::relax::ClassicRelax , protocols::relax::RelaxProtocolBase , protocols::stepwise::options::StepWiseBasicOptions
• min_type_ : core::import_pose::options::RNA_MinimizerOptions , core::optimization::MinimizerOptions , protocols::anchored_design::AnchoredPerturbMover , protocols::anchored_design::AnchoredRefineMover , protocols::antibody::CDRsMinPackMin , protocols::antibody::LHRepulsiveRampLegacy , protocols::antibody::LHSnugFitLegacy , protocols::docking::DockingHighResLegacy , protocols::docking::DockMCMCycle , protocols::docking::DockMinMover , protocols::helical_bundle::FitSimpleHelix , protocols::minimization_packing::symmetry::TaskAwareSymMinMover , protocols::relax::RelaxProtocolBase , protocols::relax::RepeatProteinRelax , protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer , protocols::stepwise::options::StepWiseBasicOptions , protocols::symmetric_docking::SymDockingHiRes , protocols::ub_e2c::ubi_e2c_modeler
• 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_type_to_enum_ : protocols::antibody::design::AntibodyDesignEnumManager
• min_type_to_string_ : protocols::antibody::design::AntibodyDesignEnumManager
• min_unique_networks_ : protocols::hbnet::HBNet
• min_value() : protocols::simple_moves::PSSM2BfactorMover
• min_value_ : protocols::simple_moves::PSSM2BfactorMover
• min_VC_to_write() : protocols::noesy_assign::PeakFileFormat_Base
• min_VC_to_write_ : protocols::noesy_assign::PeakFileFormat_Base
• min_volume_ : protocols::noesy_assign::PeakAssignmentParameters
• min_water_jump_ : protocols::simple_ddg::ddG
• min_weight_ : protocols::optimize_weights::WeightRangeConstraint
• mindata_from_pose() : core::scoring::methods::RG_Energy_Fast , core::scoring::methods::RG_LocalEnergy
• MinDebug() : core::optimization::symmetry::MinDebug
• mindist_ : protocols::electron_density::DockIntoDensityMover , protocols::simple_filters::ResidueDepthFilter
• mine() : core::pack::interaction_graph::InteractionGraphBase
• minE_ : core::select::residue_selector::SecondaryStructureSelector
• minfrac_ : protocols::mpi_refinement::WorkUnit_CombinePose
• minfrac_crossover_ : protocols::simple_moves::CombinePoseMover
• mingap_ : protocols::protein_interface_design::movers::LoopFinder
• minH_ : core::select::residue_selector::SecondaryStructureSelector
• mini_pose() : core::import_pose::libraries::ChunkSet
• mini_pose_list() : core::import_pose::libraries::BasePairStepLibrary
• mini_pose_list_ : core::import_pose::libraries::ChunkSet
• mini_pose_lists_ : core::import_pose::libraries::BasePairStepLibrary
• MinimalFragSet() : core::fragment::MinimalFragSet , core::fragment::MinimalFragSetIterator_
• MinimalFragSetIterator_() : core::fragment::MinimalFragSetIterator_
• MinimalistFlexbbEdge() : protocols::flexpack::interaction_graph::MinimalistFlexbbEdge
• MinimalistFlexbbInteractionGraph() : protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph
• MinimalistFlexbbNode() : protocols::flexpack::interaction_graph::MinimalistFlexbbNode
• MinimalRotamer() : protocols::minimization_packing::MinimalRotamer
• minimization_edge_pool_ : core::scoring::MinimizationGraph
• minimization_graph() : core::scoring::Energies
• minimization_graph_ : core::scoring::Energies
• minimization_mode_ : protocols::helical_bundle::FitSimpleHelixMultiFunc
• minimization_movers_ : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• minimization_rebuild_rounds_ : protocols::simple_moves::CyclizationMover
• minimization_repeats_after_placement_ : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• minimization_repeats_before_placement_ : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• minimization_score_function() : protocols::ddg::ddGMover
• minimization_scorefxns_ : protocols::protein_interface_design::movers::MapHotspot
• minimization_threshold() : protocols::mainchain_potential::GenerateMainchainPotentialOptions
• minimization_threshold_ : protocols::mainchain_potential::GenerateMainchainPotentialOptions
• minimization_type() : protocols::mainchain_potential::GenerateMainchainPotentialOptions
• minimization_type_ : protocols::antibody::H3RefineCCD , protocols::mainchain_potential::GenerateMainchainPotentialOptions
• MinimizationEdge() : core::scoring::MinimizationEdge
• MinimizationGraph() : core::scoring::MinimizationGraph
• MinimizationNode() : core::scoring::MinimizationNode
• MinimizationRefiner() : protocols::loop_modeling::refiners::MinimizationRefiner
• minimize() : protocols::forge::remodel::RemodelLigandHandler , protocols::magnesium::MgScanner , protocols::minimization_packing::MinMover , protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch , protocols::peptide_deriver::PeptideDeriverFilter
• minimize_ : protocols::dna::DnaInterfacePacker , protocols::hbnet::HBNet , protocols::ligand_docking::ga_ligand_dock::EntropyEstimator , protocols::loop_grower::FragmentExtension , protocols::loop_grower::LoopGrower , protocols::magnesium::MgScanner , protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch , protocols::mpi_refinement::StructAvrgMover , protocols::nmr::pre::PREMover , protocols::relax::RepeatProteinRelax , protocols::simple_moves::CyclizationMover , protocols::simple_moves::PeptideStapleMover
• minimize_after_delete() : protocols::stepwise::monte_carlo::mover::DeleteMover , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• minimize_after_delete_ : protocols::stepwise::monte_carlo::mover::DeleteMover , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• minimize_after_overlap_ : protocols::pose_creation::MergePDBatOverlapMover
• minimize_all() : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• minimize_all_ : core::import_pose::RNA_HelixAssembler
• minimize_all_ligand_torsions_ : protocols::enzdes::EnzdesBaseProtocol
• minimize_all_protein() : core::import_pose::options::RNA_MinimizerOptions
• minimize_all_protein_ : core::import_pose::options::RNA_MinimizerOptions
• minimize_all_rotamers() : protocols::make_rot_lib::MakeRotLibMover
• minimize_all_rsds_ : protocols::ligand_docking::LigandDockProtocol
• minimize_and_score_native_pose() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• minimize_and_score_native_pose_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• minimize_and_score_sugar() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• minimize_and_score_sugar_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• minimize_append_res() : core::import_pose::RNA_HelixAssembler
• minimize_backbone() : protocols::ligand_docking::MoveMapBuilder
• minimize_backbone_ : protocols::ligand_docking::LigandDockProtocol
• minimize_base_step() : core::import_pose::RNA_HelixAssembler
• minimize_bb_where_packing_ : protocols::hydrate::Hydrate
• minimize_best_tensor_ : protocols::scoring::methods::pcs::PCS_Energy_parameters_manager , protocols::scoring::methods::pcsTs1::PCS_Energy_parameters_manager_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_parameters_manager_Ts4
• minimize_best_tensor_stage1_ : protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• minimize_best_tensor_stage2_ : protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• minimize_best_tensor_stage3_ : protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• minimize_best_tensor_stage4_ : protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• minimize_bond_angles() : protocols::relax::RelaxProtocolBase
• minimize_bond_angles_ : protocols::relax::RelaxProtocolBase
• minimize_bond_lengths() : protocols::relax::RelaxProtocolBase
• minimize_bond_lengths_ : protocols::relax::RelaxProtocolBase
• minimize_bondangle_subset() : protocols::relax::RelaxProtocolBase
• minimize_bondangle_subset_ : protocols::relax::RelaxProtocolBase
• minimize_bondlength_subset() : protocols::relax::RelaxProtocolBase
• minimize_bondlength_subset_ : protocols::relax::RelaxProtocolBase
• minimize_bps() : core::import_pose::options::RNA_MinimizerOptions
• minimize_bps_ : core::import_pose::options::RNA_MinimizerOptions
• minimize_cats_ : protocols::enzdes::EnzdesFlexBBProtocol
• minimize_cdrs() : protocols::antibody::design::GeneralAntibodyModeler
• minimize_conformation() : protocols::vip::VIP_Mover
• minimize_dna_ : protocols::motifs::MotifDnaPacker
• minimize_during_scoring() : protocols::magnesium::MgScanner
• minimize_during_scoring_ : protocols::magnesium::MgScanner
• minimize_flexible_region() : protocols::enzdes::EnzdesFlexBBProtocol
• minimize_in_stages() : protocols::enzdes::EnzRepackMinimize
• 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::hbonds::NPDHBondEnergy , core::scoring::lkball::LK_BallEnergy , core::scoring::membrane::MPHelicalityEnergy , core::scoring::membrane::MPResidueLipophilicityEnergy , core::scoring::methods::AromaticBackboneRestraintEnergy , core::scoring::methods::AspartimidePenaltyEnergy , core::scoring::methods::carbohydrates::SugarBackboneEnergy , core::scoring::methods::CartesianBondedEnergy , core::scoring::methods::DNA_ReferenceEnergy , core::scoring::methods::EnergyMethod , core::scoring::methods::GenericBondedEnergy , core::scoring::methods::GoapEnergy , core::scoring::methods::HydroxylTorsionEnergy , 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::PointWaterEnergy , 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 , core::scoring::rna::TNA_SuiteEnergy
• minimize_interface() : protocols::antibody::design::GeneralAntibodyModeler
• minimize_jump_ : core::import_pose::RNA_HelixAssembler
• minimize_ligand_ : protocols::ligand_docking::LigandArea , protocols::ligand_docking::LigandDockProtocol
• minimize_ligand_torsions_ : protocols::enzdes::EnzdesBaseProtocol
• minimize_loop() : protocols::pose_length_moves::PossibleLoop
• minimize_mg_coord_constraint_distance() : protocols::magnesium::MgScanner
• minimize_mg_coord_constraint_distance_ : protocols::magnesium::MgScanner
• minimize_model_ : protocols::tcr::TCRmodel
• minimize_movemap_ : protocols::backrub::BackrubProtocol
• minimize_network() : protocols::hbnet::HBNet
• minimize_no_bb() : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• minimize_only() : protocols::flexpep_docking::FlexPepDockingProtocol
• minimize_options_ : protocols::dna::DnaInterfacePacker
• minimize_overlap() : protocols::pose_creation::MergePDBatOverlapMover
• minimize_pose() : protocols::relax::RepeatProteinRelax
• minimize_prepend_res() : core::import_pose::RNA_HelixAssembler
• minimize_prot_jumps_ : protocols::enzdes::EnzRepackMinimize
• minimize_protein() : protocols::rna::movers::ErraserMinimizerMover
• minimize_protein_ : protocols::rna::movers::ERRASER2Protocol , protocols::rna::movers::ErraserMinimizerMover
• minimize_protein_sc() : core::import_pose::options::RNA_MinimizerOptions
• minimize_protein_sc_ : core::import_pose::options::RNA_MinimizerOptions
• minimize_rebuild() : protocols::simple_moves::CyclizationMover
• minimize_region() : protocols::enzdes::EnzdesFlexibleRegion
• minimize_res_ : protocols::stepwise::monte_carlo::mover::TransientCutpointHandler
• minimize_rna_ : core::import_pose::RNA_DeNovoSetup , protocols::rna::denovo::movers::RNA_DeNovoProtocolMover
• minimize_rna_has_been_specified_ : core::import_pose::RNA_DeNovoSetup , protocols::rna::denovo::movers::RNA_DeNovoProtocolMover
• minimize_rotamer() : protocols::make_rot_lib::MakeRotLibMover
• minimize_rounds() : core::import_pose::options::RNA_MinimizerOptions
• minimize_rounds_ : core::import_pose::options::RNA_MinimizerOptions
• minimize_scorefxn() : protocols::magnesium::MgMinimizer
• minimize_scorefxn_ : protocols::magnesium::MgMinimizer , protocols::stepwise::modeler::StepWiseMinimizer
• minimize_segment() : protocols::splice::SpliceIn , protocols::splice::SpliceOut
• minimize_single_res() : protocols::stepwise::monte_carlo::mover::ResampleMover
• minimize_single_res_ : protocols::stepwise::monte_carlo::mover::AddMover , protocols::stepwise::monte_carlo::mover::ResampleMover , protocols::stepwise::monte_carlo::mover::StepWiseMasterMover
• minimize_single_res_frequency() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• minimize_single_res_frequency_ : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• minimize_structure() : core::import_pose::options::RNA_FragmentMonteCarloOptions
• minimize_structure_ : core::import_pose::options::RNA_FragmentMonteCarloOptions
• minimize_sugar() : protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler
• minimize_sugar_sets_legacy() : protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator
• minimize_tensors() : protocols::nmr::pcs::PCSEnergy
• 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_tolerance_ : core::optimization::GA_Minimizer , core::optimization::MinimizerOptions
• minimize_toward_stub() : protocols::protein_interface_design::movers::PlaceOnLoop
• minimize_toward_stub_ : protocols::protein_interface_design::movers::PlaceOnLoop
• minimize_trial_ : protocols::docking::DockMinMover
• minimize_w_pre_csts() : protocols::nmr::pre::PREMover
• minimize_water_ : protocols::ligand_docking::LigandDockProtocol , protocols::ligand_docking::MoveMapBuilder
• minimize_waters() : protocols::stepwise::options::StepWiseBasicOptions
• minimize_waters_ : protocols::stepwise::options::StepWiseBasicOptions
• minimize_with_constraints() : protocols::ddg::ddGMover , protocols::simple_moves::ShakeStructureMover , protocols::symmetry::SymShakeStructureMover
• MinimizeBackbone() : protocols::ligand_docking::MinimizeBackbone
• MinimizeHotspots() : protocols::protein_interface_design::movers::MapHotspot
• MinimizeLigand() : protocols::ligand_docking::MinimizeLigand
• Minimizer() : core::optimization::Minimizer
• minimizer() : protocols::loops::loop_mover::refine::ShearMinCCDTrial , protocols::loops::loop_mover::refine::SmallMinCCDTrial
• minimizer_ : core::import_pose::RNA_HelixAssembler , protocols::electron_density::BfactorFittingMover , protocols::electron_density::VoxelSpacingRefinementMover , protocols::flexpep_docking::FlexPepDockingAbInitio , protocols::flexpep_docking::FlexPepDockingLowRes , protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionSampler , protocols::loop_modeling::LoopBuilder , protocols::loops::loop_mover::refine::ShearMinCCDTrial , protocols::loops::loop_mover::refine::SmallMinCCDTrial , protocols::star::StarAbinitio
• minimizer_dofs_after_minimization_ : protocols::optimize_weights::IterativeOptEDriver
• minimizer_dofs_before_minimization_ : protocols::optimize_weights::IterativeOptEDriver
• minimizer_dofs_mixed_ : protocols::optimize_weights::IterativeOptEDriver
• minimizer_loop() : protocols::ligand_docking::ga_ligand_dock::GridScorer
• minimizer_mode() : protocols::stepwise::options::StepWiseBasicOptions
• minimizer_mode_ : protocols::stepwise::options::StepWiseBasicOptions
• minimizer_options() : protocols::loops::loop_mover::refine::SmallMinCCDTrial
• minimizer_options_ : core::import_pose::RNA_HelixAssembler , protocols::loops::loop_mover::refine::SmallMinCCDTrial , protocols::stepwise::modeler::StepWiseMinimizer
• minimizer_rename_tag() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• minimizer_rename_tag_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• minimizer_use_coordinate_constraints() : core::import_pose::options::RNA_MinimizerOptions
• minimizer_use_coordinate_constraints_ : core::import_pose::options::RNA_MinimizerOptions
• MinimizerMap() : core::optimization::MinimizerMap
• MinimizerMapBase() : core::kinematics::MinimizerMapBase
• MinimizerOptions() : core::optimization::MinimizerOptions
• MinimizerOptionsCOP : protocols::minimization_packing::MinMover , protocols::normalmode::NormalModeMinimizer
• MinimizerOptionsOP : protocols::minimization_packing::MinMover , protocols::normalmode::NormalModeMinimizer
• MinimizeStoredRBConfs() : protocols::enzdes::MinimizeStoredRBConfs
• MINIMIZING : core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty , core::scoring::util_methods::DumpTrajectoryEnergy
• minimizing_ : core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyEnergy
• minimum_hbond_energy() : protocols::task_operations::PruneBuriedUnsatsOperation
• minimum_hbond_energy_ : protocols::task_operations::PruneBuriedUnsats_RotamerSetsOperation , protocols::task_operations::PruneBuriedUnsatsOperation
• minimum_length_ : protocols::sewing::requirements::DsspSpecificLengthRequirement , protocols::sewing::requirements::LengthInResiduesRequirement
• minimum_peak_intensity() : protocols::noesy_assign::PeakFileFormat_Base
• minimum_peak_intensity_ : protocols::noesy_assign::PeakFileFormat_Base
• minimum_sampling_probability() : core::scoring::Ramachandran2B , core::scoring::Ramachandran
• minimum_size_ : protocols::sewing::requirements::SizeInSegmentsRequirement
• minimum_width_ : protocols::cluster::EnsembleConstraints_Simple
• minimumB : core::scoring::electron_density::ElectronDensity
• MiniPose() : core::pose::MiniPose
• miniPose_ : protocols::jumping::ResiduePairJump
• MiniRelax() : protocols::relax::MiniRelax
• minlen_ : protocols::hybridization::TMalign
• minmelt_ : protocols::loop_grower::FragmentExtension , protocols::loop_grower::LoopGrower
• MinMover() : protocols::minimization_packing::MinMover
• minmover_ : protocols::docking::SidechainMinMover , protocols::minimization_packing::symmetry::TaskAwareSymMinMover , protocols::minimization_packing::TaskAwareMinMover , protocols::symmetric_docking::SymSidechainMinMover
• MINMULT : core::scoring::electron_density::ElectronDensity
• minmult() : protocols::cryst::Spacegroup , protocols::cryst::WallpaperGroup
• MinMultiHarmonicFunc() : core::scoring::func::MinMultiHarmonicFunc
• minoption_ : protocols::normalmode::NormalModeRelaxMover
• MinPackMover() : protocols::minimization_packing::MinPackMover
• minPockSize_ : protocols::pockets::PocketGrid
• mInputFileName : protocols::cluster::calibur::Clustering
• minscorefxn_ : protocols::hybridization::FoldTreeHybridize
• MinScoreScoreFunction() : core::scoring::MinScoreScoreFunction
• mintolerance() : protocols::cyclic_peptide::TryDisulfPermutations
• mintolerance_ : protocols::cyclic_peptide::TryDisulfPermutations
• mintype() : protocols::antibody::design::CDRGraftDesignOptions , protocols::cyclic_peptide::TryDisulfPermutations , protocols::grafting::AnchoredGraftMover
• mintype_ : protocols::antibody::design::AntibodyDesignMover , protocols::antibody::design::CDRGraftDesignOptions , protocols::cyclic_peptide::TryDisulfPermutations , protocols::grafting::AnchoredGraftMover
• minval_ : core::scoring::loop_graph::evaluator::SixDTransRotPotential
• minX : protocols::pockets::CCluster , protocols::pockets::PCluster
• minY : protocols::pockets::CCluster , protocols::pockets::PCluster
• minZ : protocols::pockets::CCluster , protocols::pockets::PCluster
• mirror_symm() : protocols::cyclic_peptide::CycpepSymmetryFilter
• mirror_symm_ : protocols::cyclic_peptide::CycpepSymmetryFilter
• mirror_symmetry() : protocols::cyclic_peptide::SymmetricCycpepAlign
• mirror_symmetry_ : protocols::cyclic_peptide::SymmetricCycpepAlign
• mirror_z() : core::conformation::symmetry::SymmetryTransform
• mirror_z_ : core::conformation::symmetry::SymmetryTransform
• mirror_Z_ : core::conformation::symmetry::VirtualCoordinate
• mirror_z_transform : core::kinematics::Jump
• mirrored_relative_to_type() : core::conformation::Residue
• mirrored_relative_to_type_ : core::conformation::Residue
• MirrorSymmetricConformation() : core::conformation::symmetry::MirrorSymmetricConformation
• misc1_ : core::scoring::motif::ResPairMotif
• mismatch_probability_ : protocols::denovo_design::filters::SSPredictionFilter
• mismatch_score() : core::sequence::SimpleScoringScheme
• mismatch_score_ : core::sequence::SimpleScoringScheme
• misplaced() : core::conformation::Residue
• misplaced_ : core::conformation::Residue
• missing_ : core::io::pose_from_sfr::PoseFromSFRBuilder
• missing_atoms() : core::io::pose_from_sfr::PoseFromSFRBuilder
• missing_dens_as_jump() : core::io::StructFileRepOptions
• missing_dens_as_jump_ : core::io::StructFileRepOptions
• missing_in_pose() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters , protocols::toolbox::match_enzdes_util::EnzdesCstParamCache
• missing_pt_ : protocols::pockets::DarcParticleSwarmMinimizer , protocols::pockets::FingerprintMultifunc
• missing_residues() : core::scoring::loop_graph::LoopGraph
• missing_weight_ : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• missing_weight_interval_ : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• MissingDensityToJumpMover() : protocols::simple_moves::MissingDensityToJumpMover
• MissingEnergy() : core::scoring::methods::MissingEnergy
• mix_modes_ : protocols::normalmode::NormalModeRelaxMover
• mixed_disulfide() : protocols::denovo_design::DisulfidizeMover
• mixed_sliding_window_ : core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric
• mixing_factor_ : protocols::optimize_weights::IterativeOptEDriver
• mixture_param_ : core::scoring::func::MixtureFunc
• MixtureFunc() : core::scoring::func::MixtureFunc
• mkdir_pred() : protocols::sparta::Sparta::SpartaLib
• ml : core::scoring::cryst::XtalMLEnergy
• mLen : protocols::cluster::calibur::Clustering
• mm : protocols::cartesian::MolecularDynamics , protocols::protein_interface_design::movers::PrepackMover , protocols::splice::SpliceManager
• mm_ : protocols::frags::TorsionFragmentMover , protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionSampler , protocols::normalmode::NormalModeRelaxMover , protocols::protein_interface_design::movers::PrepackMover , protocols::recces::scratch::ThermalMinimizer , protocols::recces::scratch::ThermalSamplingMover , protocols::residue_optimization::MetapatchEnumeration , protocols::seeded_abinitio::SegmentHybridizer , protocols::splice::SpliceManager , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer
• mm_atom_name() : core::conformation::Residue
• mm_atom_set() : core::scoring::mm::MMLJLibrary
• mm_atom_set_ : core::scoring::mm::MMBondAngleLibrary , core::scoring::mm::MMBondLengthLibrary , core::scoring::mm::MMLJLibrary , core::scoring::mm::MMTorsionLibrary
• mm_atom_type() : core::chemical::ResidueType , core::scoring::mm::mmtrie::MMEnergyTableAtom
• mm_atom_type_index() : core::chemical::ResidueType
• mm_atom_type_index_ : core::chemical::ResidueType
• mm_atom_type_name() : core::chemical::Adduct
• mm_atom_type_name_ : core::chemical::AddAtom , core::chemical::Adduct , core::chemical::SetMMAtomType
• mm_atom_type_set() : core::chemical::ChemicalManager , core::chemical::PoseResidueTypeSet , core::chemical::ResidueTypeSet
• mm_atom_type_sets_ : core::chemical::ChemicalManager
• mm_atom_types_ : core::chemical::ResidueTypeBase , core::chemical::ResidueTypeSet
• mm_atom_types_ptr() : core::chemical::ResidueTypeBase
• mm_bend_weight_ : protocols::backrub::BackrubProtocol
• mm_bondangle_library() : core::scoring::mm::MMBondAngleResidueTypeParamSet
• mm_bondangle_library_ : core::scoring::mm::MMBondAngleResidueTypeParamSet , core::scoring::mm::MMBondAngleScore , core::scoring::ScoringManager , protocols::branch_angle::BranchAngleOptimizer
• mm_bondlength_library_ : core::scoring::mm::MMBondLengthLibrary , core::scoring::mm::MMBondLengthScore , core::scoring::ScoringManager
• mm_from_residues() : protocols::rna::movers::RNAThreadAndMinimizeMover
• mm_lj_energy_table_ : core::scoring::ScoringManager
• mm_lj_library() : core::scoring::mm::MMLJScore
• mm_lj_library_ : core::scoring::mm::MMLJLibrary , core::scoring::mm::MMLJScore , core::scoring::ScoringManager
• mm_lj_score() : core::scoring::mm::MMLJEnergyTable
• mm_lj_score_ : core::scoring::mm::MMLJEnergyTable
• mm_lj_three_bond_library_ : core::scoring::mm::MMLJLibrary
• mm_name() : core::chemical::Atom , core::chemical::ResidueType
• mm_name_ : core::chemical::Atom
• mm_torsion_library_ : core::scoring::mm::MMTorsionScore , core::scoring::ScoringManager , protocols::simple_moves::CyclizationMover
• mm_type() : core::conformation::Atom
• mm_type_ : core::conformation::Atom
• mman_ : core::scoring::methods::CenPairMotifDegreeEnergy , core::scoring::methods::CenPairMotifEnergy , core::scoring::methods::SSElementMotifContactEnergy , protocols::legacy_sewing::scoring::LegacyMotifScorer , protocols::sewing::scoring::MotifScorer , protocols::simple_filters::MotifScoreFilter , protocols::simple_filters::SSElementMotifContactFilter
• MMAtomType() : core::chemical::MMAtomType
• MMAtomTypeSet() : core::chemical::MMAtomTypeSet
• MMAtomTypeSets : core::chemical::ChemicalManager
• 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
• mmCIFJobOutputter() : protocols::jd2::mmCIFJobOutputter
• mmCIFParser() : core::chemical::mmCIF::mmCIFParser
• MMEnergyTableAtom() : core::scoring::mm::mmtrie::MMEnergyTableAtom
• mmf() : protocols::protein_interface_design::movers::PrepackMover
• mmf_ : protocols::cryst::SetCrystWeightMover , protocols::normalmode::NormalModeRelaxMover , protocols::protein_interface_design::movers::PrepackMover
• mmf_cat_in_datamap() : protocols::parser::MoveMapFactoryLoader
• mmf_ct_namer() : core::select::movemap::MoveMapFactory
• mmf_loader_ct_namer() : protocols::parser::MoveMapFactoryLoader
• MMJumpAction() : core::select::movemap::MoveMapFactory::MMJumpAction
• 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
• MMLJScoreTable : core::scoring::mm::MMLJEnergyTable
• MMResAction() : core::select::movemap::MoveMapFactory::MMResAction
• MMResIndexAction() : core::select::movemap::MoveMapFactory::MMResIndexAction
• mmt_ : protocols::simple_moves::TorsionDOFMover
• mmtf_extra_data_io() : core::io::StructFileReaderOptions , core::io::StructFileRepOptions
• mmtf_extra_data_io_ : core::io::StructFileReaderOptions , core::io::StructFileRepOptions
• mmtfJobOutputter() : protocols::jd2::mmtfJobOutputter
• mmTFPoseOutputSpecification() : protocols::jd3::pose_outputters::mmTFPoseOutputSpecification
• mmTFPoseOutputter() : protocols::jd3::pose_outputters::mmTFPoseOutputter
• MMTorsionEnergy() : core::scoring::methods::MMTorsionEnergy
• MMTorsionLibrary() : core::scoring::mm::MMTorsionLibrary
• MMTorsionScore() : core::scoring::mm::MMTorsionScore
• MNBRAK() : core::optimization::BrentLineMinimization
• mNumDecoy : protocols::cluster::calibur::PreloadedPDB
• mnx_ : core::scoring::packstat::Octree2D
• mny_ : core::scoring::packstat::Octree2D
• mobile_label_ : protocols::rigid::UniformRigidBodyCM
• mobile_residues_ : protocols::environment::CoMTrackerCM
• mobile_selector_ : protocols::environment::CoMTrackerCM
• MOD : core::scoring::Energies
• mod_depth_bounds() : core::scoring::epr_deer::DEERDecayData
• mod_depth_bounds_ : core::scoring::epr_deer::FittingInfo
• mod_distr() : core::scoring::epr_deer::DEERDecayData
• mod_reference_pose_local_ : protocols::stepwise::modeler::align::StepWisePoseAligner
• mod_segment_prod_ : protocols::fldsgn::MatchResidues
• mode() : core::chemical::AtomTypeSet , core::chemical::ResidueTypeBase , core::chemical::ResidueTypeSet
• Mode : core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty
• mode() : core::simple_metrics::per_residue_metrics::PerResidueSasaMetric , protocols::hbnet::UnsatSelector , protocols::matdes::SymUnsatHbondFilter , protocols::normalmode::NormalMode
• Mode : protocols::protein_interface_design::filters::AtomicContactCountFilter
• mode() : protocols::rosetta_scripts::ParsedProtocol , protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::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
• mode_ : core::chemical::AtomTypeSet , core::chemical::ResidueTypeBase , core::chemical::ResidueTypeSet , core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty , core::simple_metrics::per_residue_metrics::PerResidueSasaMetric , protocols::denovo_design::components::CompoundPerturber , protocols::enzdes::ValueEvaluator , protocols::ligand_docking::ComputeLigandRDF , protocols::matdes::SchemePlaceMotifsMover , protocols::matdes::SymUnsatHbondFilter , protocols::moves::MonteCarloUtil , protocols::normalmode::NormalMode , protocols::pdbinfo_manipulations::AlignPDBInfoToSequences , protocols::pose_reporters::RMSDReporter , protocols::rbsegment_relax::MakeStarTopologyMover , protocols::residue_optimization::MetapatchEnumeration , protocols::rosetta_scripts::ParsedProtocol , protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::simple_moves::ExplicitWaterMover , protocols::task_operations::SelectBySASAOperation , protocols::task_operations::StoreCompoundTaskMover
• MODE_all_atom_rmsd : protocols::pose_reporters::RMSDReporter
• MODE_CA_rmsd : protocols::pose_reporters::RMSDReporter
• mode_enum_from_name() : core::simple_metrics::metrics::SequenceMetric
• mode_lowres_ : protocols::docking::membrane::MPFindInterfaceMover
• mode_name_from_enum() : core::simple_metrics::metrics::SequenceMetric
• MODE_NONE : protocols::pose_reporters::RMSDReporter
• mode_scale_ : protocols::normalmode::NormalModeRelaxMover
• mode_tokens_ : core::pack::task::ResidueLevelTask_
• mode_using_ : protocols::normalmode::NormalModeRelaxMover
• Model : protocols::abinitio::PairingStatEntry , protocols::abinitio::PairingStatistics , protocols::legacy_sewing::Model
• model() : protocols::legacy_sewing::ModelNode
• model_ : core::pack::annealer::SmartFixbbSimAnnealer , protocols::legacy_sewing::ModelNode
• model_and_remove_capping_residues_ : core::import_pose::RNA_HelixAssembler
• model_begin() : protocols::legacy_sewing::Model
• model_cdrs_ : protocols::antibody::design::GeneralAntibodyModeler
• model_count : protocols::boinc::BoincSharedMemory , protocols::canonical_sampling::TrajectoryRecorder
• model_count_ : protocols::canonical_sampling::TrajectoryRecorder
• model_end() : protocols::legacy_sewing::Model
• model_file_from_options() : protocols::sewing::hashing::BasisMapGenerator
• model_file_name_ : protocols::sewing::movers::AssemblyMover
• model_h3() : protocols::antibody_legacy::CDRH3Modeler
• model_h3_ : protocols::antibody::AntibodyModelerProtocol , protocols::antibody_legacy::AntibodyModeler
• model_id : protocols::legacy_sewing::Basis , protocols::legacy_sewing::HashValue , protocols::legacy_sewing::sampling::requirements::LegacyResidueRetentionRequirement
• model_id_ : protocols::legacy_sewing::Model , protocols::legacy_sewing::sampling::requirements::LegacyResidueRetentionRequirement , protocols::legacy_sewing::SewSegment
• model_ids() : protocols::legacy_sewing::Assembly
• model_ids_ : protocols::legacy_sewing::LegacyGivenPathAssemblyMover
• model_index : core::io::mmtf::sd_index
• model_indices_ : protocols::legacy_sewing::SewGraph
• 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_low_energy : protocols::boinc::BoincSharedMemory
• model_low_energy_rmsd : protocols::boinc::BoincSharedMemory
• model_resnum() : protocols::legacy_sewing::HashEdge
• model_tag() : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• model_tag_ : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• model_weight_ : protocols::abinitio::PairingStatistics
• model_with_density() : core::import_pose::options::RNA_BasicOptions , protocols::rna::denovo::RNA_DeNovoPoseInitializer
• model_with_density_ : core::import_pose::options::RNA_BasicOptions , protocols::rna::denovo::RNA_DeNovoPoseInitializer
• ModelConstIterator() : protocols::legacy_sewing::ModelConstIterator< T >
• modeler_ : protocols::antibody::design::AntibodyDesignMover
• modeler_scorefxn_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection
• modeler_sugar() : protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator
• modeler_sugar_at_chain_break() : protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator
• ModelFeatures() : protocols::features::ModelFeatures
• ModelFileReader() : protocols::sewing::hashing::ModelFileReader
• ModelFreq : protocols::abinitio::PairingStatistics
• ModelIterator() : protocols::legacy_sewing::ModelIterator< T >
• ModelList : protocols::abinitio::PairingStatEntry
• ModelNode() : protocols::legacy_sewing::ModelNode
• models() : protocols::abinitio::PairingStatEntry , protocols::legacy_sewing::LegacyEnumerateAssemblyMover
• models_ : protocols::abinitio::PairingStatEntry , protocols::legacy_sewing::LegacyAppendAssemblyMover
• models_per_file_ : protocols::contact_map::ContactMap
• modeltag() : core::io::StructFileRep , core::pose::PDBInfo
• modeltag_ : core::io::StructFileRep , core::pose::PDBInfo
• ModelWeight : protocols::abinitio::PairingStatistics
• modes_using_ : protocols::normalmode::NormalModeMinimizer , protocols::normalmode::NormalModeMultifunc
• modifiable() : protocols::moves::ResId
• modifiable_ : protocols::moves::ResId
• modifiable_residue_type_set_for_conf() : core::conformation::Conformation
• modifiable_terminus_ : protocols::sewing::data_storage::SmartAssembly , protocols::sewing::movers::AppendAssemblyMover
• modifications_ : core::chemical::carbohydrates::CarbohydrateInfo
• Modified2Original : protocols::forge::build::BuildManager
• modified2original_interval_endpoints() : protocols::forge::build::BuildManager
• modified2original_intervals() : protocols::forge::build::BuildManager
• MODIFIED_DDG : protocols::calc_taskop_filters::RotamerBoltzmannWeight2
• 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
• modifieddensity() : protocols::loop_grower::LoopGrower
• modifiedscore() : protocols::loop_grower::LoopGrower
• modify() : protocols::forge::build::BuildInstruction , protocols::forge::build::BuildManager
• modify_after_jump() : protocols::task_operations::ProteinInterfaceDesignOperation
• modify_after_jump_ : protocols::task_operations::ProteinInterfaceDesignOperation
• modify_and_add_permutation() : protocols::denovo_design::architects::BetaSheetArchitect
• modify_before_jump() : protocols::task_operations::ProteinInterfaceDesignOperation
• modify_before_jump_ : protocols::task_operations::ProteinInterfaceDesignOperation
• modify_foldtree() : protocols::splice::RBInMover
• modify_foldtree_ : protocols::splice::RBInMover
• 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_pdb_segments_with_current_segment() : protocols::splice::Splice , protocols::splice::SpliceManager
• 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::calc_taskop_filters::Operator
• modify_symmetry_and_exit_ : protocols::relax::RepeatProteinRelax
• modify_task() : core::pack::task::TaskFactory
• modify_tors_params() : core::scoring::GenericBondedPotential
• modify_torsion_params_from_cmd_line() : core::scoring::GenericBondedPotential
• modify_unselected_residues() : protocols::task_operations::SelectResiduesWithinChainOperation
• modify_unselected_residues_ : protocols::task_operations::SelectResiduesWithinChainOperation
• modify_was_successful() : protocols::forge::build::BuildInstruction
• modify_was_successful_ : protocols::forge::build::BuildManager
• ModifyAnnealer() : protocols::task_operations::ModifyAnnealer
• ModifyStoredRBConfs() : protocols::enzdes::ModifyStoredRBConfs
• ModifyVariantTypeMover() : protocols::simple_moves::ModifyVariantTypeMover
• modomics_map() : core::io::NomenclatureManager
• modres_map() : core::io::StructFileRep
• modres_map_ : core::io::StructFileRep
• modulation_depth_fit() : core::scoring::epr_deer::DEERDecayData
• modules_ : core::kinematics::jacobian::SeriesJacobians
• ModuleType1() : core::kinematics::jacobian::ModuleType1
• MOL_ID : core::io::HeaderInformation
• 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
• MOLECULE : core::io::HeaderInformation
• molecule : core::scoring::sc::Atom
• molecule_atoms_ : core::scoring::sc::ElectrostaticComplementarityCalculator
• molecule_string_data_ : core::chemical::sdf::MolFileIOMolecule
• MolFileIOAtom() : core::chemical::sdf::MolFileIOAtom
• MolFileIOBond() : core::chemical::sdf::MolFileIOBond
• MolFileIOMolecule() : core::chemical::sdf::MolFileIOMolecule
• MolFileIOReader() : core::chemical::sdf::MolFileIOReader
• molgraph_ : core::chemical::sdf::MolFileIOMolecule
• molName : protocols::pockets::SmallMol
• moltenres() : core::scoring::hbonds::graph::HBondNode
• moltenres_2_flexseg_ : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• moltenres_2_resid() : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubsets , core::pack_basic::RotamerSetsBase , protocols::flexpack::rotamer_set::FlexbbRotamerSets
• moltenres_2_resid_ : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubsets , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::flexpack::rotamer_set::FlexbbRotamerSets
• moltenres_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::RotamerSubsets , core::pack_basic::RotamerSetsBase , protocols::flexpack::rotamer_set::FlexbbRotamerSets
• moltenres_for_rotamer_ : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubsets , protocols::flexpack::rotamer_set::FlexbbRotamerSets
• moltenres_for_sample_rot() : core::pack::rotamer_set::ContinuousRotamerSets
• moltenres_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::RotamerSubsets , core::pack_basic::RotamerSetsBase , protocols::flexpack::rotamer_set::FlexbbRotamerSets
• moltenres_sample_rot_offset_ : core::pack::rotamer_set::ContinuousRotamerSets
• moltenresid : core::pack::annealer::RotSub
• moltenresid_2_resid() : core::pack::rotamer_set::ContinuousRotamerSets
• moltenresid_2_resid_ : core::pack::rotamer_set::ContinuousRotamerSets , core::pack::scmin::AtomTreeCollection
• 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
• monopole_ : core::scoring::MultipoleElecResidueInfo , core::scoring::MultipoleParameter
• monoub_all_dof_map_ : protocols::ub_e2c::ubi_e2c_modeler
• 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_ctr_of_mass_ : protocols::ub_e2c::ubi_e2c_modeler
• monoub_docking_map_ : protocols::ub_e2c::ubi_e2c_modeler
• monoub_end_ : protocols::ub_e2c::ubi_e2c_modeler
• monoub_first_perturbation() : protocols::ub_e2c::ubi_e2c_modeler
• monoub_flex_cter_map_ : 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_mode_ : 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 , protocols::ligand_docking::TransformEnsemble
• monte_carlo_ : protocols::canonical_sampling::MetropolisHastingsMover , protocols::canonical_sampling::TemperatureController , protocols::loop_modeling::LoopProtocol , protocols::loop_modeling::utilities::AcceptanceCheck , protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::FullatomRelaxMover
• monte_carlo_branch_ : protocols::hbnet::HBNet
• monte_carlo_cycles() : core::import_pose::options::RNA_FragmentMonteCarloOptions
• monte_carlo_cycles_ : core::import_pose::options::RNA_FragmentMonteCarloOptions , protocols::rna::denovo::RNA_FragmentMonteCarlo
• monte_carlo_cycles_max_default_ : protocols::rna::denovo::RNA_FragmentMonteCarlo
• monte_carlo_loader_ct_namer() : protocols::parser::MonteCarloLoader
• monte_carlo_net_clash() : protocols::hbnet::HBNet
• monte_carlo_seed() : protocols::hbnet::NetworkState
• monte_carlo_seed_ : protocols::hbnet::NetworkState
• monte_carlo_seed_is_dead_end() : protocols::hbnet::HBNet
• monte_carlo_seed_must_be_buried_ : protocols::hbnet::HBNet
• monte_carlo_seed_must_be_fully_buried_ : protocols::hbnet::HBNet
• monte_carlo_seed_threshold_ : protocols::hbnet::HBNet
• monte_carlo_seeds_ : protocols::hbnet::HBNet
• MonteCarlo : protocols::forge::remodel::RemodelLoopMover , protocols::moves::MonteCarlo
• MonteCarloInterface() : protocols::monte_carlo::MonteCarloInterface
• MonteCarloLoader() : protocols::parser::MonteCarloLoader
• MonteCarloRecover() : protocols::monte_carlo::MonteCarloRecover
• MonteCarloReset() : protocols::monte_carlo::MonteCarloReset
• montecarlorounds_ : protocols::loop_grower::FragmentExtension
• MonteCarloTest() : protocols::monte_carlo::MonteCarloTest
• MonteCarloUtil() : protocols::moves::MonteCarloUtil
• more_ancient_ptr : core::pack::interaction_graph::history_queue_struct
• more_dump_stuff() : protocols::recces::RECCES_Mover
• more_precise_base_pair_classification() : core::scoring::rna::RNA_LowResolutionPotential
• more_precise_base_pair_classification_ : core::scoring::rna::RNA_LowResolutionPotential
• more_recent_ptr : core::pack::interaction_graph::history_queue_struct
• morpheme_from_ring_size() : core::chemical::carbohydrates::CarbohydrateInfoManager
• most_probable_bin() : protocols::frag_picker::quota::ABEGO_SS_Config
• most_recent_cluster_results_ : protocols::multistage_rosetta_scripts::MRSJobQueen
• most_recent_pose_id_ : protocols::multistage_rosetta_scripts::MRSJobQueen
• most_recent_request_ : protocols::multistage_rosetta_scripts::TagManager
• Motif : core::scoring::motif::MotifHash
• motif : core::scoring::motif::MotifHit
• Motif : protocols::denovo_design::architects::DeNovoMotifArchitect , protocols::denovo_design::components::IdealAbegoGenerator , protocols::motifs::Motif
• motif_ : protocols::calc_taskop_movers::CreateSequenceMotifMover , protocols::task_operations::SequenceMotifTaskOperation
• motif_bin_hash() : core::scoring::motif::ResPairMotifMetaBinner
• motif_bin_label() : core::scoring::motif::ResPairMotifMetaBinner
• motif_cuts : protocols::simple_filters::SymmetricMotifFilter
• motif_expansion_inner_loop() : protocols::motifs::MotifDnaPacker
• motif_forward_ : protocols::motifs::IRCollection
• motif_fragments_RMSD : protocols::motif_grafting::movers::motif2scaffold_data , protocols::motif_grafting::movers::MotifMatch
• motif_hash() : protocols::sic_dock::scores::MotifHashRigidScore
• motif_hash_BB_BB_ : core::scoring::motif::MotifHashManager
• motif_hash_BB_PH_ : core::scoring::motif::MotifHashManager
• motif_hash_BB_PO_ : core::scoring::motif::MotifHashManager
• motif_hash_SC_BB_ : core::scoring::motif::MotifHashManager
• motif_hash_SC_SC_ : core::scoring::motif::MotifHashManager
• motif_hits_ : protocols::matdes::MotifHitsRotamersOperation
• motif_label() : protocols::fold_from_loops::utils::Nub
• motif_library() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• motif_library_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• motif_match_results_ : protocols::motif_grafting::movers::MotifGraftMover
• motif_mover_ : protocols::carbohydrates::CreateGlycanSequonMover
• motif_operation_ : protocols::calc_taskop_movers::CreateSequenceMotifMover
• motif_search_ : protocols::enzdes::AddLigandMotifRotamers , protocols::motifs::MotifDnaPacker
• motif_selector_ : protocols::simple_moves::FoldTreeFromMotif
• motif_set_names() : core::scoring::motif::MotifHashManager
• motif_set_names_ : core::scoring::motif::MotifHashManager
• motif_sets_ : protocols::matdes::SchemePlaceMotifsMover
• motif_source_ : protocols::motifs::IRCollection
• motif_umap_ : core::scoring::motif::MotifHash
• motifAtomIDs : protocols::motifs::Motif
• MotifCOP : protocols::denovo_design::architects::DeNovoMotifArchitect
• motifcop() : protocols::motifs::MotifHit
• motifcop_ : protocols::motifs::MotifHit
• MotifCOPs : protocols::denovo_design::architects::DeNovoMotifArchitect
• MotifDnaPacker() : protocols::motifs::MotifDnaPacker
• MotifDockEnergy() : core::scoring::methods::MotifDockEnergy
• MotifGraftMover() : protocols::motif_grafting::movers::MotifGraftMover
• MotifHash() : core::scoring::motif::MotifHash , core::scoring::motif::ResPairMotifQuery
• MotifHashManager() : core::scoring::motif::MotifHashManager
• MotifHashRigidScore() : protocols::sic_dock::scores::MotifHashRigidScore
• motifHigh : protocols::motif_grafting::movers::motif2scaffold_indexes
• MotifHit() : core::scoring::motif::MotifHit , protocols::motifs::MotifHit
• MotifHitsRotamersOperation() : protocols::matdes::MotifHitsRotamersOperation
• MotifLibrary() : protocols::motifs::MotifLibrary
• motifLow : protocols::motif_grafting::movers::motif2scaffold_indexes
• MotifMap : core::scoring::motif::MotifHash
• MotifMatch() : protocols::motif_grafting::movers::MotifMatch
• MotifOP : protocols::denovo_design::architects::DeNovoMotifArchitect , protocols::denovo_design::components::IdealAbegoGenerator
• MotifOPs : protocols::denovo_design::components::IdealAbegoGenerator
• motifs_ : protocols::denovo_design::architects::DeNovoMotifArchitect , protocols::denovo_design::architects::HelixArchitect , protocols::denovo_design::architects::StrandArchitect , protocols::denovo_design::connection::ConnectionArchitect
• motifs_begin() : protocols::denovo_design::architects::DeNovoMotifArchitect , protocols::denovo_design::architects::HelixArchitect , protocols::denovo_design::architects::StrandArchitect
• motifs_by_fname_ : core::scoring::motif::MotifHashManager
• motifs_end() : protocols::denovo_design::architects::DeNovoMotifArchitect , protocols::denovo_design::architects::HelixArchitect , protocols::denovo_design::architects::StrandArchitect
• motifs_for_pair() : protocols::denovo_design::connection::ConnectionArchitect
• MotifScoreFilter() : protocols::simple_filters::MotifScoreFilter
• MotifScorer() : protocols::sewing::scoring::MotifScorer
• MotifSearch() : protocols::motifs::MotifSearch
• movable_ : protocols::nonlocal::BiasedFragmentMover , protocols::nonlocal::Chunk , protocols::nonlocal::SingleFragmentMover
• movable_chains() : protocols::simple_task_operations::InterfaceTaskOperation
• movable_chains_ : protocols::simple_task_operations::InterfaceTaskOperation
• movable_group() : protocols::denovo_design::components::Segment , protocols::denovo_design::components::StructureData
• movable_group_ : protocols::denovo_design::components::Segment
• movable_groups() : 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::simple_task_operations::InterfaceTaskOperation
• movable_jumps_ : protocols::docking::DockingHighRes , protocols::docking::DockingHighResFilter , protocols::docking::DockingInitialPerturbation , protocols::docking::DockingLowRes , protocols::docking::DockingProtocol , protocols::docking::DockMCMCycle , protocols::docking::DockSetupMover , protocols::docking::RigidBodyInfo , protocols::docking::TemperedDocking , protocols::protein_interface_design::filters::FNatFilter , protocols::protein_interface_design::filters::IRmsdFilter , protocols::protein_interface_design::filters::LRmsdFilter , protocols::rigid::RigidBodyPerturbMover , protocols::rigid::RigidBodyPerturbNoCenterMover , protocols::simple_task_operations::InterfaceTaskOperation , protocols::symmetric_docking::SymDockProtocol
• movable_reducing_ends_ : protocols::carbohydrates::TautomerizeAnomerMover
• movable_residues() : protocols::fold_from_loops::movers::NubInitioLoopClosureMover
• movable_scs_ : protocols::ligand_docking::ga_ligand_dock::LigandAligner
• movable_torsion_pairs_ : protocols::carbohydrates::RingPlaneFlipMover
• MovableGroupSet : protocols::denovo_design::connection::AreConnectablePredicate
• MovableGroupToSegmentNameListMap : protocols::denovo_design::components::FoldGraph
• move() : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• move_ : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• move_all_inserted() : protocols::abinitio::MembraneAbinitio
• move_apart_first() : protocols::docking::SlideIntoContact
• move_apart_first_ : protocols::docking::SlideIntoContact
• move_atoms_to_collcheck_begin() : protocols::toolbox::match_enzdes_util::LigandConformer
• move_away() : protocols::docking::DockingEnsemblePrepackProtocol
• move_back() : protocols::docking::DockingEnsemblePrepackProtocol
• move_distance : protocols::ligand_docking::Transform_info , protocols::ligand_docking::TransformEnsemble_info
• move_element() : protocols::stepwise::monte_carlo::mover::StepWiseMove
• move_element_ : protocols::stepwise::monte_carlo::mover::StepWiseMove
• move_first_rigid_body() : core::import_pose::options::RNA_BasicOptions
• move_first_rigid_body_ : core::import_pose::options::RNA_BasicOptions , protocols::rna::denovo::movers::RNA_HelixMover
• move_forward_to_next_model() : protocols::rna::setup::RNA_MonteCarloJobDistributor
• move_jump_points_away() : protocols::stepwise::monte_carlo::mover::TransientCutpointHandler
• move_jump_points_away_ : protocols::stepwise::monte_carlo::mover::TransientCutpointHandler
• move_jumps_between_chains() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• move_jumps_between_chains_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer , protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• move_ligand_and_update_rhos_() : protocols::pockets::PlaidFingerprint
• move_ligand_close_to_surface() : protocols::nmr::pcs::PCSLigandTransformMover
• move_ligand_to_desired_centroid() : protocols::ligand_docking::LigandBaseProtocol
• move_map() : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::minimization_packing::SaneMinMover
• move_map_ : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::simple_moves::CyclizationMover , protocols::simple_moves::RandomOmegaFlipMover , protocols::simple_moves::RandomTorsionMover , protocols::surface_docking::FullatomRelaxMover
• move_map_factory_ : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• move_map_torsion_id_map_ : core::kinematics::MoveMap
• move_pos_list_ : protocols::simple_moves::BackboneMover
• move_pose_to_standard_orie() : protocols::pockets::PocketGrid
• move_positions_ : protocols::coupled_moves::CoupledMovesProtocol
• move_segment() : protocols::denovo_design::components::StructureData
• move_segments() : protocols::denovo_design::components::StructureData
• move_side_chain() : protocols::stepwise::modeler::StepWiseMinimizer
• move_spans() : protocols::topology_broker::TMHTopologySamplerClaimer
• move_str_ : protocols::stepwise::monte_carlo::mover::AddMover , protocols::stepwise::monte_carlo::mover::DeleteMover , protocols::stepwise::monte_carlo::mover::FromScratchMover
• move_takeoff_torsions_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer
• move_to_boundary() : protocols::ligand_docking::ga_ligand_dock::GridScorer
• move_tolerance_sqr_ : core::scoring::NeighborList
• move_type() : protocols::rna::denovo::movers::RNA_DeNovoMasterMover , protocols::stepwise::monte_carlo::mover::StepWiseMove
• move_type_ : protocols::coupled_moves::CoupledMovesProtocol , protocols::rna::denovo::movers::RNA_DeNovoMasterMover , protocols::stepwise::monte_carlo::mover::StepWiseMove
• move_type_string() : protocols::stepwise::monte_carlo::mover::StepWiseMasterMover
• move_type_string_ : protocols::stepwise::monte_carlo::mover::StepWiseMasterMover
• move_water_ : protocols::ligand_docking::ga_ligand_dock::GALigandDock
• move_with_rama() : protocols::simple_moves::BackboneMover , protocols::simple_moves::ShearMover , protocols::simple_moves::SmallMover
• move_with_scorefxn() : protocols::simple_moves::BackboneMover , protocols::simple_moves::ShearMover , protocols::simple_moves::SmallMover
• MoveBeforeFilter() : protocols::filters::MoveBeforeFilter
• moved() : core::pack::interaction_graph::SimpleNode , core::scoring::EnergyNode
• moved_ : core::pack::interaction_graph::SimpleNode , core::scoring::EnergyNode , protocols::md::Rattle
• moveFromStubFrame() : protocols::hotspot_hashing::StubGenerator
• moveIntoStubFrame() : protocols::hotspot_hashing::StubGenerator
• MoveMap : core::fragment::IndependentBBTorsionSRFD , core::kinematics::MoveMap
• movemap() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::KinematicControl , protocols::abinitio::MembraneAbinitio , protocols::carbohydrates::RingPlaneFlipMover
• MoveMap : protocols::fldsgn::CircularPermutation
• movemap() : protocols::fold_from_loops::utils::Nub
• MoveMap : protocols::forge::build::Bridge
• movemap() : protocols::forge::build::Bridge
• MoveMap : protocols::forge::build::BuildInstruction
• movemap() : protocols::forge::build::BuildInstruction , protocols::forge::build::BuildManager
• MoveMap : protocols::forge::build::BuildManager
• movemap() : protocols::forge::build::ConnectRight
• MoveMap : protocols::forge::build::ConnectRight
• movemap() : protocols::forge::build::GrowLeft
• MoveMap : protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight
• movemap() : protocols::forge::build::GrowRight
• MoveMap : protocols::forge::build::RelativeConnectRight
• movemap() : protocols::forge::build::SegmentInsert
• MoveMap : protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild
• movemap() : protocols::forge::build::SegmentRebuild
• MoveMap : protocols::forge::build::SegmentSwap
• movemap() : protocols::forge::build::SegmentSwap
• MoveMap : protocols::forge::components::VarLengthBuild , protocols::forge::remodel::RemodelAccumulator , protocols::forge::remodel::RemodelDesignMover , protocols::forge::remodel::RemodelGlobalFrame , protocols::forge::remodel::RemodelLigandHandler , protocols::forge::remodel::RemodelLoopMover
• movemap() : 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::MDBase , protocols::minimization_packing::MinMover , protocols::minimization_packing::PertMinMover , protocols::moves::MoveMapMover , protocols::moves::NullMover , protocols::nonlocal::SingleFragmentMover , protocols::simple_moves::BackboneMover , protocols::simple_moves::BBGaussianMover , protocols::simple_moves::FragmentMover , protocols::simple_moves::RandomOmegaFlipMover , protocols::simple_moves::RandomTorsionMover , protocols::simple_moves::RingConformationMover
• movemap_ : protocols::abinitio::abscript::AbscriptLoopCloserCM , protocols::abinitio::ClassicAbinitio , protocols::abinitio::KinematicControl , protocols::abinitio::MembraneAbinitio , protocols::antibody::CloseOneCDRLoop , protocols::antibody::LHRepulsiveRamp , protocols::carbohydrates::RingPlaneFlipMover , protocols::docking::DockingHighResLegacy , protocols::docking::DockingLowRes , protocols::docking::DockMCMCycle , protocols::docking::DockMCMProtocol , protocols::docking::DockMinMover , protocols::docking::SidechainMinMover , protocols::flexpep_docking::FlexPepDockingAbInitio , protocols::flexpep_docking::FlexPepDockingLowRes , protocols::flexpep_docking::FlexPepDockingProtocol , protocols::floppy_tail::FloppyTailMover , protocols::flxbb::FlxbbDesign , protocols::fold_from_loops::movers::MoveMapFactoryToNamedMoveMapMover , protocols::fold_from_loops::utils::Nub , protocols::grafting::AnchoredGraftMover , protocols::LoopRebuild , protocols::loops::loop_closure::ccd::CCDLoopClosureMover , protocols::loops::loop_closure::ccd::LoopClosure , protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure , protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover , protocols::loops::loop_closure::kinematic_closure::KinematicPerturber , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::md::MDBase , protocols::membrane::MPQuickRelaxMover , protocols::minimization_packing::MinMover , protocols::minimization_packing::SaneMinMover , protocols::rbsegment_relax::AutoRBMover , protocols::rbsegment_relax::CCDMoveWrapper , protocols::relax::CentroidRelax , protocols::relax::RangeRelaxMover , protocols::relax::RelaxProtocolBase , protocols::simple_moves::BackboneMover , protocols::simple_moves::BBGaussianMover , protocols::simple_moves::FragmentMover , protocols::simple_moves::RingConformationMover , protocols::splice::TailSegmentMover , protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockingLowRes , protocols::symmetric_docking::SymSidechainMinMover , protocols::task_operations::RestrictToMoveMapChiOperation , protocols::topology_broker::FragmentClaimer
• movemap_as_OP() : protocols::forge::build::BuildManager
• movemap_builder_ : protocols::ligand_docking::FinalMinimizer , protocols::ligand_docking::HighResDocker , protocols::ligand_docking::HighResEnsemble
• movemap_builder_ct_namer() : protocols::ligand_docking::MoveMapBuilderLoader
• movemap_cen() : protocols::anchored_design::AnchorMoversData
• movemap_cen_all() : protocols::anchored_design::AnchorMoversData
• movemap_cen_all_ : protocols::anchored_design::AnchorMoversData
• movemap_cen_omegafixed() : protocols::anchored_design::AnchorMoversData
• movemap_disables_packing_of_fixed_chi_positions() : protocols::relax::FastRelax
• movemap_disables_packing_of_fixed_chi_positions_ : protocols::relax::FastRelax
• movemap_fa() : protocols::anchored_design::AnchorMoversData
• movemap_fa_all() : protocols::anchored_design::AnchorMoversData
• movemap_fa_all_ : protocols::anchored_design::AnchorMoversData
• movemap_fa_omegafixed() : protocols::anchored_design::AnchorMoversData
• movemap_factory() : protocols::carbohydrates::RingPlaneFlipMover , protocols::fold_from_loops::movers::DisplayPoseLabelsMover , protocols::minimization_packing::MinMover , protocols::minimization_packing::PertMinMover , protocols::nonlocal::SingleFragmentMover , protocols::simple_moves::BackboneMover , protocols::simple_moves::BBGaussianMover , protocols::simple_moves::RandomOmegaFlipMover , protocols::simple_moves::RandomTorsionMover , protocols::simple_moves::RingConformationMover
• movemap_factory_ : protocols::carbohydrates::RingPlaneFlipMover , protocols::flxbb::FlxbbDesign , protocols::fold_from_loops::movers::DisplayPoseLabelsMover , protocols::md::CartesianMD , protocols::minimization_packing::MinMover , protocols::minimization_packing::PertMinMover , protocols::nonlocal::SingleFragmentMover , protocols::normalmode::NormalModeMinimizer , protocols::relax::RelaxProtocolBase , protocols::seeded_abinitio::SeedSetupMover , protocols::simple_moves::BackboneMover , protocols::simple_moves::BBGaussianMover , protocols::simple_moves::DisulfideInsertionMover , protocols::simple_moves::RandomOmegaFlipMover , protocols::simple_moves::RandomTorsionMover , protocols::simple_moves::RingConformationMover
• movemap_from_blueprint() : protocols::flxbb::FlxbbDesign
• movemap_from_blueprint_ : protocols::flxbb::FlxbbDesign
• movemap_from_pose() : protocols::fold_from_loops::movers::DisplayPoseLabelsMover
• movemap_lesstail_ : protocols::floppy_tail::FloppyTailMover , protocols::splice::TailSegmentMover
• movemap_minimizer_ : protocols::flexpep_docking::FlexPepDockingProtocol
• movemap_ptr() : protocols::abinitio::KinematicControl
• movemap_reset_ : protocols::docking::DockMCMProtocol
• movemap_set_ : protocols::task_operations::RestrictToMoveMapChiOperation
• movemap_setup() : protocols::rna::movers::ErraserMinimizerMover
• movemap_smallmover_ : protocols::backrub::BackrubProtocol
• movemap_torsion_id_begin() : core::kinematics::MoveMap
• movemap_torsion_id_end() : core::kinematics::MoveMap
• MoveMapBuilder() : protocols::ligand_docking::MoveMapBuilder
• MoveMapBuilderLoader() : protocols::ligand_docking::MoveMapBuilderLoader
• MoveMapFactory() : core::select::movemap::MoveMapFactory
• movemapfactory() : protocols::fold_from_loops::utils::Nub
• movemapfactory_ : protocols::fold_from_loops::movers::MoveMapFactoryToNamedMoveMapMover
• MoveMapFactoryLoader() : protocols::parser::MoveMapFactoryLoader
• MoveMapFactoryToNamedMoveMapMover() : protocols::fold_from_loops::movers::MoveMapFactoryToNamedMoveMapMover
• MoveMapMover() : protocols::moves::MoveMapMover
• MoveMapOP : protocols::fldsgn::CircularPermutation , protocols::flxbb::FlxbbDesign , protocols::forge::build::BuildManager , protocols::loops::loop_mover::LoopMover , protocols::nonlocal::Chunk , protocols::nonlocal::SingleFragmentMover , protocols::parser::BluePrint
• MoveMapTorsionID : core::kinematics::MoveMap
• MoveMapTorsionID_Map : core::kinematics::MoveMap
• MovePoseToMembraneCenterMover() : protocols::rigid::MovePoseToMembraneCenterMover
• mover() : core::environment::DofPassport , protocols::abinitio::abscript::FragmentCM , protocols::abinitio::FragmentSampler
• Mover : protocols::fldsgn::MatchResidues , protocols::fldsgn::MatchResiduesMover
• mover() : protocols::flxbb::DesignTask , protocols::jd3::chunk_library::MoverAndChunkLibraryJob , protocols::jd3::jobs::MoverJob , protocols::monte_carlo::GenericMonteCarloMover
• Mover() : protocols::moves::Mover
• mover() : protocols::moves::MoverApplyingMover , protocols::moves::TrialMover , protocols::multistage_rosetta_scripts::mover_or_filter
• Mover : protocols::nonlocal::SingleFragmentMover
• mover : protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair , protocols::simple_moves::ChangeAndResetFoldTreeMover , protocols::simple_moves::ContingentAcceptMover , protocols::simple_moves::rational_mc::RationalMonteCarlo , protocols::topology_broker::FragmentClaimer , protocols::topology_broker::TopologyBroker
• mover_ : core::environment::DofPassport , protocols::abinitio::abscript::FragmentCM , protocols::comparative_modeling::RecoverSideChainsMover , protocols::enzdes::RemoveLigandFilter , protocols::flxbb::DesignTask , protocols::jd3::chunk_library::MoverAndChunkLibraryJob , protocols::jd3::jobs::MoverJob , protocols::loop_modeling::samplers::LegacyKicSampler , protocols::loops::loop_mover::LoopCM , protocols::monte_carlo::GenericMonteCarloMover , protocols::moves::FilterReporterMover , protocols::moves::RampingMover , protocols::moves::RepeatMover , protocols::moves::TrialMover , protocols::moves::WhileMover , protocols::protein_interface_design::movers::LoopOver , protocols::protein_interface_design::movers::SubroutineMover , protocols::rigid::UniformRigidBodyCM , protocols::rosetta_scripts::MultipleOutputWrapper , protocols::rotamer_recovery::RRProtocolMover , protocols::simple_moves::ContingentAcceptMover , protocols::simple_moves::rational_mc::RationalMonteCarlo , protocols::topology_broker::FragmentClaimer
• mover_by_index() : protocols::canonical_sampling::MetropolisHastingsMover
• mover_creator_map() : protocols::moves::MoverFactory
• mover_creator_map_ : protocols::moves::MoverFactory
• mover_cycles_ : protocols::loop_modeling::LoopProtocol
• mover_exists() : protocols::moves::MoverFactory
• mover_is_unpublished() : protocols::cyclic_peptide::SymmetricCycpepAlign , protocols::cyclic_peptide::TryDisulfPermutations , protocols::generalized_kinematic_closure::GeneralizedKIC , protocols::helical_bundle::BackboneGridSampler , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::PerturbBundle , protocols::moves::Mover , protocols::relax::RelaxProtocolBase , protocols::rosetta_scripts::ParsedProtocol , protocols::simple_moves::SetupMetalsMover
• mover_list_ : protocols::wum::MoverList
• Mover_LoopHashRefine() : protocols::loophash::Mover_LoopHashRefine
• mover_mc_trial_count : protocols::boinc::BoincSharedMemory
• mover_name() : protocols::aa_composition::AddCompositionConstraintMover , protocols::aa_composition::AddHelixSequenceConstraintsMover , protocols::aa_composition::AddMHCEpitopeConstraintMover , protocols::aa_composition::AddNetChargeConstraintMover , protocols::aa_composition::ClearCompositionConstraintsMover , protocols::abinitio::abscript::AbscriptLoopCloserCM , protocols::abinitio::abscript::AbscriptMover , protocols::abinitio::abscript::ConstraintPreparer , protocols::abinitio::abscript::FragmentCM , protocols::abinitio::abscript::FragmentJumpCM , protocols::abinitio::abscript::RigidChunkCM , protocols::abinitio::abscript::StructPerturberCM , protocols::abinitio::DomainAssembly , protocols::analysis::GlycanInfoMover , protocols::analysis::InterfaceAnalyzerMover , protocols::analysis::LoopAnalyzerMover , protocols::analysis::simple_metrics::RunSimpleMetricsMover , protocols::antibody::AntibodyCDRGrafter , protocols::antibody::AntibodyNumberingConverterMover , protocols::antibody::constraints::CDRDihedralConstraintMover , protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover , protocols::antibody::constraints::ParatopeSiteConstraintMover , protocols::antibody::design::AntibodyDesignMover , protocols::antibody::design::MutateFrameworkForClusterCreator , protocols::antibody::snugdock::SnugDock , protocols::backbone_moves::local_backbone_mover::LocalBackboneMover , protocols::backbone_moves::RandomizeBBByRamaPrePro , protocols::backrub::BackrubMover , protocols::backrub::BackrubProtocol , protocols::backrub::BackrubSidechainMover , protocols::calc_taskop_movers::ConsensusDesignMover , protocols::calc_taskop_movers::CreateSequenceMotifMover , protocols::calc_taskop_movers::ForceDisulfidesMover , protocols::canonical_sampling::DbTrajectoryRecorderCreator , protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::MetropolisHastingsMover , protocols::canonical_sampling::ParallelTempering , protocols::canonical_sampling::PDBTrajectoryRecorder , protocols::canonical_sampling::ProgressBarObserverCreator , protocols::canonical_sampling::SidechainMetropolisHastingsMoverCreator , protocols::canonical_sampling::SilentTrajectoryRecorder , protocols::canonical_sampling::SimulatedTempering , protocols::canonical_sampling::TrialCounterObserver , protocols::carbohydrates::CreateGlycanSequonMover , protocols::carbohydrates::GlycanSampler , protocols::carbohydrates::GlycanTreeModeler , protocols::carbohydrates::IdealizeAnomericHydrogens , protocols::carbohydrates::LinkageConformerMover , protocols::carbohydrates::RingPlaneFlipMover , protocols::carbohydrates::SimpleGlycosylateMover , protocols::carbohydrates::TautomerizeAnomerMover , protocols::chemically_conjugated_docking::UBQ_GTPaseMover , protocols::comparative_modeling::LoopRelaxMover , protocols::constraint_generator::AddConstraints , protocols::constraint_generator::RemoveConstraints , protocols::constraint_movers::AddConstraintsToCurrentConformationMover , protocols::constraint_movers::ClearConstraintsMover , protocols::constraint_movers::ConstraintSetMover , protocols::constraint_movers::CstInfoMover , protocols::constraint_movers::ResidueTypeConstraintMover , protocols::contact_map::ContactMap , protocols::coupled_moves::CoupledMovesProtocol , protocols::cryst::CrystRMS , protocols::cryst::DockLatticeMover , protocols::cryst::FitBfactorsMover , protocols::cryst::LoadDensityMapMover , protocols::cryst::MakeLatticeMover , protocols::cryst::MakeLayerMover , protocols::cryst::RecomputeDensityMapMover , protocols::cryst::ReportGradientsMover , protocols::cryst::SetCrystWeightMover , protocols::cryst::SetRefinementOptionsMover , protocols::cryst::TagPoseWithRefinementStatsMover , protocols::cryst::UpdateCrystInfo , protocols::cryst::UpdateSolventMover , protocols::cutoutdomain::CutOutDomain , protocols::cyclic_peptide::CreateAngleConstraint , protocols::cyclic_peptide::CreateDistanceConstraint , protocols::cyclic_peptide::CreateTorsionConstraint , protocols::cyclic_peptide::CrosslinkerMover , protocols::cyclic_peptide::DeclareBond , protocols::cyclic_peptide::FlipChiralityMover , protocols::cyclic_peptide::PeptideCyclizeMover , protocols::cyclic_peptide::PeptideStubMover , protocols::cyclic_peptide::SymmetricCycpepAlign , protocols::cyclic_peptide::TryDisulfPermutations , protocols::denovo_design::DisulfidizeMover , protocols::denovo_design::movers::AddSegmentDataMover , protocols::denovo_design::movers::AlignResiduesMover , protocols::denovo_design::movers::BridgeChainsMover , protocols::denovo_design::movers::BuildDeNovoBackboneMover , protocols::denovo_design::movers::DeclareStructureDataCovalentBondMover , protocols::denovo_design::movers::ExtendChainMover , protocols::denovo_design::movers::FastDesign , protocols::denovo_design::movers::MakeAsymmetricStructureDataMover , protocols::denovo_design::movers::SetResidueAliasMover , protocols::design_opt::GreedyOptMutationMover , protocols::dna::DesignProteinBackboneAroundDNA , protocols::dna::DnaInterfaceMinMover , protocols::dna::DnaInterfaceMultiStateDesign , protocols::dna::DnaInterfacePacker , protocols::dna::SeparateDnaFromNonDna , protocols::docking::ConformerSwitchMover , protocols::docking::DockingHighResLegacy , protocols::docking::DockingInitialPerturbation , protocols::docking::DockingPrepackProtocol , protocols::docking::DockingProtocol , protocols::docking::DockingSlideIntoContact , protocols::docking::DockMCMProtocol , protocols::docking::DockMinMover , protocols::docking::DockSetupMover , protocols::docking::membrane::MPDockingMover , protocols::docking::membrane::MPDockingSetupMover , protocols::docking::membrane::MPFindInterfaceMoverCreator , protocols::docking::membrane::QuickRelaxPartnersSeparatelyCreator , protocols::docking::TemperedDockingCreator , protocols::electron_density::BfactorFittingMover , protocols::electron_density::ReportFSC , protocols::electron_density::ScaleMapIntensities , protocols::electron_density::SetupForDensityScoringMover , protocols::electron_density::VoxelSpacingRefinementMover , protocols::environment::CoMTrackerCM , protocols::environment::EnvMover , protocols::environment::ScriptCM , protocols::enzdes::AddOrRemoveMatchCsts , protocols::enzdes::BackboneSampler , protocols::enzdes::EnzRepackMinimize , protocols::enzdes::PackRotamersMoverPartGreedy , protocols::enzdes::PredesignPerturbMover , protocols::enzdes::UpdateEnzdesHeaderMover , protocols::enzymatic_movers::DNAMethyltransferaseMover , protocols::enzymatic_movers::GlycosyltransferaseMover , protocols::enzymatic_movers::KinaseMover , protocols::enzymatic_movers::NTerminalAcetyltransferaseMover , protocols::evolution::EvolutionaryDynamicsMover , protocols::evolution::NucleotideMutation , protocols::farnesyl::InstallFarnesylMover , protocols::farnesyl::SampleFarnesylMover , protocols::features::InterfaceDdGMover , protocols::features::InterfaceDdGMoverCreator , protocols::features::ReportToDB , protocols::features::TrajectoryReportToDB , protocols::fldsgn::BluePrintBDR , protocols::fldsgn::CircularPermutation , protocols::fldsgn::MatchResiduesMover , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::fldsgn::SheetRemodelConstraintGenerator , protocols::flexpep_docking::FlexPepDockingProtocol , protocols::flxbb::FlxbbDesign , protocols::flxbb::InterlockAroma , protocols::fold_from_loops::movers::AlignByResidueSelectorMover , protocols::fold_from_loops::movers::DisplayPoseLabelsMover , protocols::fold_from_loops::movers::LabelPoseFromResidueSelectorMover , protocols::fold_from_loops::movers::MoveMapFactoryToNamedMoveMapMover , protocols::fold_from_loops::movers::NubInitioLoopClosureMover , protocols::fold_from_loops::movers::ReleaseConstraintFromResidueMover , protocols::fold_from_loops::movers::ResidueLabelsToPymolSelectionMover , protocols::fold_from_loops::movers::SavePDBInfoMover , protocols::fold_from_loops::movers::SplitAndMixPoseMover , protocols::fold_from_loops::NubInitioMover , protocols::forge::constraints::InverseRotamersRCG , protocols::forge::constraints::InvrotTreeRCG , protocols::forge::constraints::NtoCConstraintGenerator , protocols::forge::constraints::RemoveRemodelCsts , protocols::forge::remodel::RemodelMover , protocols::forge::remodel::ResidueVicinityRCG , protocols::generalized_kinematic_closure::GeneralizedKIC , protocols::grafting::AnchoredGraftMover , protocols::grafting::CCDEndsGraftMover , protocols::grafting::simple_movers::DeleteRegionMover , protocols::grafting::simple_movers::InsertPoseIntoPoseMover , protocols::grafting::simple_movers::KeepRegionMover , protocols::grafting::simple_movers::ReplaceRegionMover , protocols::hbnet::HBNet , protocols::hbnet::HBNetStapleInterface , protocols::helical_bundle::BackboneGridSampler , protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::FitSimpleHelix , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::PerturbBundle , protocols::helical_bundle::PerturbBundleHelix , protocols::hotspot_hashing::movers::PlaceSurfaceProbe , protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionSampler , protocols::hybridization::CartesianSampler , protocols::hybridization::HybridizeProtocol , protocols::idealize::IdealizeMover , protocols::indexed_structure_store::movers::DirectSegmentLookupMover , protocols::indexed_structure_store::movers::SegmentSequenceProfileMover , protocols::kinematic_closure::KicMover , protocols::legacy_sewing::LegacyAddStartnodeFragments , protocols::legacy_sewing::LegacyAppendAssemblyMover , protocols::legacy_sewing::LegacyAssemblyConstraintsMover , protocols::legacy_sewing::LegacyAssemblyMover , protocols::legacy_sewing::LegacyEnumerateAssemblyMover , protocols::legacy_sewing::LegacyGivenPathAssemblyMover , protocols::legacy_sewing::LegacyGreedyAssemblyMover , protocols::legacy_sewing::LegacyMonteCarloAssemblyMover , protocols::legacy_sewing::LegacyRepeatAssemblyMover , protocols::ligand_docking::AddHydrogens , protocols::ligand_docking::CompoundTranslate , protocols::ligand_docking::ComputeLigandRDF , protocols::ligand_docking::FinalMinimizer , protocols::ligand_docking::ga_ligand_dock::GALigandDock , protocols::ligand_docking::GrowLigand , protocols::ligand_docking::HighResDocker , protocols::ligand_docking::HighResEnsemble , protocols::ligand_docking::InterfaceScoreCalculator , protocols::ligand_docking::LigandDesign , protocols::ligand_docking::MinimizeBackbone , protocols::ligand_docking::ProtLigEnsemble , protocols::ligand_docking::RandomConformers , protocols::ligand_docking::Rotate , protocols::ligand_docking::Rotates , protocols::ligand_docking::SlideTogether , protocols::ligand_docking::StartFrom , protocols::ligand_docking::Transform , protocols::ligand_docking::TransformEnsemble , protocols::ligand_docking::Translate , protocols::ligand_docking::WriteLigandMolFile , protocols::loop_build::LoopmodelWrapper , protocols::loop_build::LoopMover_SlidingWindow , protocols::loop_grower::FragmentExtension , protocols::loop_modeler::LoopModeler , protocols::loop_modeling::LoopBuilder , protocols::loop_modeling::LoopProtocol , protocols::loop_modeling::refiners::MinimizationRefiner , protocols::loop_modeling::refiners::RepackingRefiner , protocols::loop_modeling::refiners::RotamerTrialsRefiner , protocols::loop_modeling::samplers::LegacyKicSampler , protocols::loop_modeling::utilities::PrepareForCentroid , protocols::loop_modeling::utilities::PrepareForFullatom , protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashMoverWrapper , protocols::loops::FoldTreeFromLoops , protocols::loops::loop_closure::ccd::CCDLoopClosureMover , protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover , protocols::loops::loop_mover::LoopCM , 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 , protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub , protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::loops::loop_mover::refine::LoopMover_Refine_KIC , protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer , protocols::loops::loop_mover::refine::RepackTrial , protocols::loops::loop_mover::refine::ShearMinCCDTrial , protocols::loops::loop_mover::refine::SmallMinCCDTrial , protocols::match::MatcherMover , protocols::matdes::ExtractSubposeMover , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::SchemePlaceMotifsMover , protocols::matdes::SymDofMover , protocols::md::CartesianMD , protocols::mean_field::GenMeanFieldMover , protocols::membrane::AddMembraneMover , protocols::membrane::AddMembraneSpanConstraint , protocols::membrane::AddMembraneSpanTermZConstraint , protocols::membrane::AddMPLigandMover , protocols::membrane::AqueousPoreFinder , protocols::membrane::benchmark::MakeCanonicalHelix , protocols::membrane::benchmark::SampleTiltAngles , protocols::membrane::FlipMover , protocols::membrane::HelixFromSequenceCreator , protocols::membrane::MembranePositionFromTopologyMover , protocols::membrane::MPLipidAccessibility , protocols::membrane::MPMutateRelaxMoverCreator , protocols::membrane::MPQuickRelaxMoverCreator , protocols::membrane::OptimizeMembranePositionMoverCreator , protocols::membrane::OptimizeProteinEmbeddingMoverCreator , protocols::membrane::RotationMoverCreator , protocols::membrane::SetMembraneCenterMoverCreator , protocols::membrane::SetMembraneNormalMoverCreator , protocols::membrane::SetMembranePositionMover , protocols::membrane::SpinAroundPartnerMoverCreator , protocols::membrane::symmetry::SymmetricAddMembraneMover , protocols::membrane::TiltMoverCreator , protocols::membrane::TransformIntoMembraneMover , protocols::membrane::TranslationMoverCreator , protocols::membrane::TranslationRotationMoverCreator , protocols::membrane::visualize::VisualizeEmbeddingMover , protocols::membrane::visualize::VisualizeMembraneMover , protocols::membrane_benchmark::MembraneEnergyLandscapeSampler , protocols::membrane_benchmark::PeptideOrientationMover , protocols::minimization_packing::BoltzmannRotamerMover , protocols::minimization_packing::DisulfideOptimizationMover , protocols::minimization_packing::MinMover , protocols::minimization_packing::MinMoverCreator , protocols::minimization_packing::MinPackMover , protocols::minimization_packing::PackRotamersMover , protocols::minimization_packing::PackRotamersMoverCreator , protocols::minimization_packing::PackRotamersMoverLazyCreator , protocols::minimization_packing::PertMinMover , protocols::minimization_packing::RepackSidechainsMoverCreator , protocols::minimization_packing::RotamerTrialsMinMover , protocols::minimization_packing::RotamerTrialsMover , protocols::minimization_packing::SaneMinMover , protocols::minimization_packing::symmetry::SymMinMover , protocols::minimization_packing::symmetry::SymPackRotamersMover , protocols::minimization_packing::symmetry::SymRotamerTrialsMover , protocols::minimization_packing::symmetry::TaskAwareSymMinMover , protocols::minimization_packing::TaskAwareMinMover , protocols::monte_carlo::GenericMonteCarloMover , protocols::monte_carlo::GenericSimulatedAnnealer , protocols::monte_carlo::MonteCarloRecover , protocols::monte_carlo::MonteCarloReset , protocols::monte_carlo::MonteCarloTest , protocols::monte_carlo::ResetBaselineMover , protocols::motif_grafting::movers::MotifGraftMover , protocols::motifs::MotifDnaPacker , protocols::moves::DsspMover , protocols::moves::FilterReportAsPoseExtraScoresMover , protocols::moves::IfMover , protocols::moves::IteratedConvergenceMover , protocols::moves::PyMOLMover , protocols::moves::RampingMover , protocols::moves::RandomMover , protocols::moves::SwitchMover , protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopCreatorMover , protocols::ncbb::oop::OopDockDesignProtocol , protocols::ncbb::ResidueReplacementRebuildMover , protocols::ncbb::SecStructFinderCreator , protocols::ncbb::SecStructMinimizeMover , protocols::nmr::ParaNMRScoreMover , protocols::nmr::pcs::PCSLigandTransformMover , protocols::nmr::pre::PREMover , protocols::nonlocal::SingleFragmentMover , protocols::normalmode::NormalModeMinimizer , protocols::normalmode::NormalModeRelaxMover , protocols::pb_potential::SetupPoissonBoltzmannPotential , protocols::pdbinfo_manipulations::AlignPDBInfoToSequences , protocols::pose_creation::ExtendedPoseMover , protocols::pose_creation::MakeJunctionsMover , protocols::pose_creation::MakePolyXMover , protocols::pose_creation::MergePDBatOverlapMover , protocols::pose_creation::MergePDBMover , protocols::pose_creation::PoseFromSequenceMover , protocols::pose_creation::SliceToMiniProteinMover , protocols::pose_length_moves::AnalyzeLoopModeling , protocols::pose_length_moves::ConnectChainsMover , protocols::pose_length_moves::FixAllLoopsMover , protocols::pose_length_moves::InsertResMover , protocols::pose_length_moves::NearNativeLoopCloser , protocols::protein_interface_design::movers::AddChainBreak , protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots , protocols::protein_interface_design::movers::BackrubDDMover , protocols::protein_interface_design::movers::BestHotspotCstMover , protocols::protein_interface_design::movers::BuildAlaPose , protocols::protein_interface_design::movers::DesignMinimizeHbonds , protocols::protein_interface_design::movers::DisulfideMover , protocols::protein_interface_design::movers::DockAndRetrieveSidechains , protocols::protein_interface_design::movers::DockWithHotspotMover , protocols::protein_interface_design::movers::FavorNativeResiduePreCycle , protocols::protein_interface_design::movers::FavorNonNativeResiduePreCycle , protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover , protocols::protein_interface_design::movers::HotspotHasherMover , protocols::protein_interface_design::movers::InterfaceRecapitulationMover , protocols::protein_interface_design::movers::LoopFinder , protocols::protein_interface_design::movers::LoopLengthChange , protocols::protein_interface_design::movers::LoopLengthChangeCreator , protocols::protein_interface_design::movers::LoopMoverFromCommandLine , protocols::protein_interface_design::movers::LoopOver , protocols::protein_interface_design::movers::LoopRemodel , protocols::protein_interface_design::movers::MapHotspot , protocols::protein_interface_design::movers::PatchdockTransform , protocols::protein_interface_design::movers::PeptideStapleDesignMover , protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::protein_interface_design::movers::PlacementMinimizationMover , protocols::protein_interface_design::movers::PlaceOnLoop , protocols::protein_interface_design::movers::PlaceSimultaneouslyMover , protocols::protein_interface_design::movers::PlaceStubMover , protocols::protein_interface_design::movers::PrepackMover , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover , protocols::protein_interface_design::movers::RandomMutation , protocols::protein_interface_design::movers::RepackMinimize , protocols::protein_interface_design::movers::SaveAndRetrieveSidechains , protocols::protein_interface_design::movers::SetAtomTree , protocols::protein_interface_design::movers::SetTemperatureFactor , protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover , protocols::protein_interface_design::movers::SetupHotspotConstraintsMover , protocols::protein_interface_design::movers::ShoveResidueMover , protocols::protein_interface_design::movers::SpinMover , protocols::protein_interface_design::movers::SubroutineMover , protocols::protein_interface_design::movers::TaskAwareCsts , protocols::protein_interface_design::movers::TopologyBrokerMover , protocols::protein_interface_design::movers::TryRotamers , protocols::protein_interface_design::movers::VLB , protocols::qsar::qsarCreator , protocols::qsar::RenderGridsToKinemage , protocols::quantum_annealing::ExternalPackerResultLoader , protocols::rbsegment_relax::IdealizeHelicesMover , protocols::rbsegment_relax::MakeStarTopologyMover , protocols::rbsegment_relax::OptimizeThreadingMover , protocols::recces::scratch::ThermalMinimizer , protocols::recces::scratch::ThermalSamplingMover , protocols::recon_design::FindConsensusSequenceCreator , protocols::recon_design::MSDMoverCreator , protocols::relax::AcceptToBestMover , protocols::relax::AcceptToBestMoverCreator , protocols::relax::AtomCoordinateCstMover , protocols::relax::AtomCoordinateCstMoverCreator , protocols::relax::ClassicRelaxCreator , protocols::relax::FastRelax , protocols::relax::LocalRelax , protocols::relax::membrane::MPFastRelaxMover , protocols::relax::RepeatProteinRelax , protocols::residue_selectors::StoreResidueSubsetMover , protocols::rigid::RigidBodyPerturbNoCenterMover , protocols::rigid::RigidBodyTiltMover , protocols::rigid::RigidBodyTransMover , protocols::rigid::RollMover , protocols::rigid::UniformRigidBodyCM , protocols::rigid::UniformRigidBodyMover , protocols::rna::denovo::movers::RNA_DeNovoProtocolMover , protocols::rna::denovo::RNA_DeNovoProtocol , protocols::rna::movers::ERRASER2Protocol , protocols::rna::movers::ErraserMinimizerMover , protocols::rna::movers::RNAIdealizeMover , protocols::rosetta_scripts::AdditionalOutputWrapperCreator , protocols::rosetta_scripts::MultipleOutputWrapper , protocols::rosetta_scripts::MultiplePoseMover , protocols::rosetta_scripts::ParsedProtocol , protocols::rosetta_scripts::SavePoseMover , protocols::rotamer_recovery::RotamerRecoveryMover , protocols::seeded_abinitio::CAcstGenerator , protocols::seeded_abinitio::CloseFold , protocols::seeded_abinitio::CoordinateCst , protocols::seeded_abinitio::DefineMovableLoops , protocols::seeded_abinitio::GrowPeptides , protocols::seeded_abinitio::SeedFoldTree , protocols::seeded_abinitio::SeedSetupMover , protocols::seeded_abinitio::SegmentHybridizer , protocols::seeded_abinitio::SwapSegment , protocols::sewing::hashing::AlignmentFileGeneratorMoverCreator , protocols::sewing::movers::AppendAssemblyMoverCreator , protocols::sewing::movers::AssemblyMover , protocols::sewing::movers::LigandBindingAssemblyMoverCreator , protocols::simple_ddg::ddG , protocols::simple_moves::AddChainMover , protocols::simple_moves::AddJobPairData , protocols::simple_moves::AddPDBInfoMover , protocols::simple_moves::AddResidueCouplingConstraint , protocols::simple_moves::AddResidueLabelMoverCreator , protocols::simple_moves::AlignChainMover , protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockMoveRbJumpMover , protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockRbTrialMover , protocols::simple_moves::BBDihedralSamplerMoverCreator , protocols::simple_moves::BBGaussianMover , protocols::simple_moves::bin_transitions::InitializeByBins , protocols::simple_moves::bin_transitions::PerturbByBins , protocols::simple_moves::ChangeAndResetFoldTreeMover , protocols::simple_moves::ConcatenatePosesMover , protocols::simple_moves::ContingentAcceptMover , protocols::simple_moves::ConvertRealToVirtualMover , protocols::simple_moves::ConvertVirtualToRealMover , protocols::simple_moves::CopyRotamerMover , protocols::simple_moves::CoupledMover , protocols::simple_moves::CutChainMoverCreator , protocols::simple_moves::DeleteChainMover , protocols::simple_moves::DeleteChainsMover , protocols::simple_moves::DisulfideInsertionMover , protocols::simple_moves::DumpPdb , protocols::simple_moves::DumpSingleResidueRotamers , protocols::simple_moves::ExplicitWaterMover , protocols::simple_moves::ExplicitWaterMoverCreator , protocols::simple_moves::FavorSequenceProfile , protocols::simple_moves::FavorSymmetricSequence , protocols::simple_moves::FoldTreeFromMotif , protocols::simple_moves::LoadPDBMover , protocols::simple_moves::LoadUnboundRotMover , protocols::simple_moves::MembraneTopology , protocols::simple_moves::ModifyVariantTypeMover , protocols::simple_moves::MutateResidue , protocols::simple_moves::PDBReloadMover , protocols::simple_moves::PeriodicBoxMover , protocols::simple_moves::PoseFromPoseResourceMover , protocols::simple_moves::PSSM2BfactorMover , protocols::simple_moves::RandomOmegaFlipMover , protocols::simple_moves::RandomTorsionMover , protocols::simple_moves::RepeatPropagationMover , protocols::simple_moves::ReportEffectivePKA , protocols::simple_moves::ReportXYZ , protocols::simple_moves::ResetFoldTree , protocols::simple_moves::ResetFullModelInfoMover , protocols::simple_moves::RingConformationMover , protocols::simple_moves::SaveSequenceToCommentsMover , protocols::simple_moves::ScoreMover , protocols::simple_moves::SequenceProfileMover , protocols::simple_moves::SetTorsion , protocols::simple_moves::SetupMetalsMover , protocols::simple_moves::SetupMetalsMoverCreator , protocols::simple_moves::ShearMover , protocols::simple_moves::ShortBackrubMover , protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover , protocols::simple_moves::sidechain_moves::PerturbChiSidechainMover , protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover , protocols::simple_moves::sidechain_moves::SetChiMover , protocols::simple_moves::sidechain_moves::SidechainMCMover , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::SimpleThreadingMover , protocols::simple_moves::SmallMover , protocols::simple_moves::StorePoseSnapshot , protocols::simple_moves::StructProfileMover , protocols::simple_moves::SuperimposeMover , protocols::simple_moves::SwitchChainOrderMover , protocols::simple_moves::SwitchResidueTypeSetMover , protocols::simple_moves::Tumble , protocols::simple_moves::VirtualRootMover , protocols::simple_moves::WriteFiltersToPose , protocols::simple_moves::WriteSSEMover , protocols::splice::AlignEndsMover , protocols::splice::RBInMover , protocols::splice::RBOutMover , protocols::splice::RotLibOut , protocols::splice::RotLibOutCreator , protocols::splice::Splice , protocols::splice::SpliceCreator , protocols::splice::SpliceIn , protocols::splice::SpliceInAntibody , protocols::splice::SpliceInAntibodyCreator , protocols::splice::SpliceInCreator , protocols::splice::SpliceInTail , protocols::splice::SpliceInTailCreator , protocols::splice::SpliceManager , protocols::splice::SpliceOut , protocols::splice::SpliceOutAntibody , protocols::splice::SpliceOutAntibodyCreator , protocols::splice::SpliceOutCreator , protocols::splice::SpliceOutTail , protocols::splice::SpliceOutTailCreator , protocols::splice::TailSegmentMover , protocols::splice::TailSegmentMoverCreator , protocols::stepwise::monte_carlo::mover::AddMover , protocols::stepwise::monte_carlo::mover::DeleteMover , protocols::stepwise::monte_carlo::mover::FromScratchMover , protocols::stepwise::monte_carlo::mover::ResampleMover , protocols::struct_fragment::StructFragmentMover , protocols::switches::GraftSwitchMover , protocols::symmetric_docking::membrane::MPSymDockMover , protocols::symmetric_docking::SymDockProtocol , protocols::symmetric_docking::SymFoldandDockMoveRbJumpMover , protocols::symmetric_docking::SymFoldandDockRbTrialMover , protocols::symmetric_docking::SymFoldandDockSlideTrialMover , protocols::symmetry::DetectSymmetry , protocols::symmetry::ExtractAsymmetricPoseMover , protocols::symmetry::ExtractAsymmetricUnitMover , protocols::symmetry::SetupForSequenceSymmetryMover , protocols::symmetry::SetupForSymmetryMover , protocols::symmetry::SetupNCSMover , protocols::task_operations::StoreCombinedStoredTasksMover , protocols::task_operations::StoreCompoundTaskMover , protocols::task_operations::StoreTaskMover , protocols::testing::BenchmarkBuildRotamersMover , protocols::testing::BenchmarkBuildRotamersMoverCreator , protocols::vardist_solaccess::LoadVarSolDistSasaCalculatorMover
• mover_name_ : protocols::splice::Splice , protocols::splice::SpliceManager
• mover_names_ : protocols::moves::SwitchMover
• mover_or_add_group_name() : protocols::canonical_sampling::MetropolisHastingsMover
• mover_or_filter() : protocols::multistage_rosetta_scripts::mover_or_filter
• mover_provides_citation_info() : protocols::analysis::GlycanInfoMover , protocols::analysis::simple_metrics::RunSimpleMetricsMover , protocols::antibody::AntibodyCDRGrafter , protocols::antibody::AntibodyNumberingConverterMover , protocols::antibody::constraints::CDRDihedralConstraintMover , protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover , protocols::antibody::constraints::ParatopeSiteConstraintMover , protocols::antibody::design::AntibodyDesignMover , protocols::antibody::design::MutateFrameworkForCluster , protocols::calc_taskop_movers::CreateSequenceMotifMover , protocols::carbohydrates::CreateGlycanSequonMover , protocols::carbohydrates::GlycanSampler , protocols::carbohydrates::GlycanTreeMinMover , protocols::carbohydrates::GlycanTreeModeler , protocols::carbohydrates::IdealizeAnomericHydrogens , protocols::carbohydrates::LinkageConformerMover , protocols::carbohydrates::RingPlaneFlipMover , protocols::carbohydrates::SimpleGlycosylateMover , protocols::carbohydrates::TautomerizeAnomerMover , protocols::denovo_design::movers::FastDesign , protocols::enzymatic_movers::EnzymaticMover , protocols::enzymatic_movers::GlycosyltransferaseMover , protocols::enzymatic_movers::KinaseMover , protocols::features::ReportToDB , protocols::generalized_kinematic_closure::GeneralizedKIC , protocols::grafting::AnchoredGraftMover , protocols::grafting::CCDEndsGraftMover , protocols::grafting::simple_movers::DeleteRegionMover , protocols::grafting::simple_movers::InsertPoseIntoPoseMover , protocols::grafting::simple_movers::KeepRegionMover , protocols::grafting::simple_movers::ReplaceRegionMover , protocols::helical_bundle::BundleGridSampler , protocols::ligand_docking::FinalMinimizer , protocols::ligand_docking::HighResDocker , protocols::ligand_docking::HighResEnsemble , protocols::ligand_docking::InterfaceScoreCalculator , protocols::ligand_docking::ProtLigEnsemble , protocols::ligand_docking::StartFrom , protocols::ligand_docking::Transform , protocols::ligand_docking::TransformEnsemble , protocols::loop_grower::FragmentExtension , protocols::loop_grower::LoopGrower , protocols::loop_grower::SheetSampler , protocols::monte_carlo::GenericMonteCarloMover , protocols::moves::Mover , protocols::protein_interface_design::movers::LoopOver , protocols::relax::FastRelax , protocols::relax::RelaxProtocolBase , protocols::rosetta_scripts::ParsedProtocol , protocols::simple_moves::BBDihedralSamplerMover , protocols::simple_moves::ConvertRealToVirtualMover , protocols::simple_moves::ConvertVirtualToRealMover , protocols::simple_moves::DeleteChainsMover , protocols::simple_moves::RingConformationMover , protocols::simple_moves::SetupMetalsMover , protocols::simple_moves::SimpleThreadingMover
• mover_stopping_condition() : protocols::monte_carlo::GenericMonteCarloMover
• mover_stopping_condition_ : protocols::monte_carlo::GenericMonteCarloMover
• mover_tag() : protocols::topology_broker::FragmentClaimer
• mover_tag_ : protocols::monte_carlo::GenericMonteCarloMover , protocols::rosetta_scripts::AdditionalOutputWrapper , protocols::rosetta_scripts::MultipleOutputWrapper , protocols::splice::Splice , protocols::splice::SpliceOut , protocols::topology_broker::FragmentClaimer
• mover_tags : protocols::multistage_rosetta_scripts::ParsedTagCache
• mover_type_ : protocols::splice::SpliceOut
• mover_type_text : protocols::boinc::BoincSharedMemory
• mover_user_name : protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair
• mover_weight() : protocols::topology_broker::TopologyClaimer
• mover_xml_schema_group_name() : protocols::moves::MoverFactory
• MoverAndChunkLibraryJob() : protocols::jd3::chunk_library::MoverAndChunkLibraryJob
• MoverApplyingMover() : protocols::moves::MoverApplyingMover
• moverclass : protocols::simple_moves::bin_transitions::InitializeByBins , protocols::simple_moves::bin_transitions::PerturbByBins
• MoverContainer() : protocols::moves::MoverContainer
• MoverCreator() : protocols::moves::MoverCreator
• MoverFactory() : protocols::moves::MoverFactory
• MoverFilterPair() : protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair
• MoverFilterVector : protocols::rosetta_scripts::ParsedProtocol
• MoverForPoseList() : protocols::moves::MoverForPoseList
• MoverJob() : protocols::jd3::jobs::MoverJob
• moverkey() : protocols::abinitio::abscript::FragmentJumpCM , protocols::abinitio::abscript::JumpSampleData
• moverkey_ : protocols::abinitio::abscript::FragmentJumpCM , protocols::abinitio::abscript::JumpSampleData
• MoverList() : protocols::wum::MoverList
• MoverMap : protocols::moves::MoverFactory
• MoverOP : protocols::calc_taskop_movers::ConsensusDesignMover , protocols::enzdes::RemoveLigandFilter , protocols::evolution::EvolutionaryDynamicsMover , protocols::fldsgn::BluePrintBDR , protocols::fldsgn::CircularPermutation , protocols::fldsgn::MatchResidues , protocols::fldsgn::MatchResiduesMover , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::flxbb::DesignTask , protocols::flxbb::FlxbbDesign , protocols::flxbb::InterlockAroma , protocols::forge::components::BDR , protocols::forge::components::VarLengthBuild , protocols::forge::remodel::RemodelAccumulator , protocols::forge::remodel::RemodelDesignMover , protocols::forge::remodel::RemodelGlobalFrame , protocols::forge::remodel::RemodelLigandHandler , protocols::forge::remodel::RemodelLoopMover , protocols::forge::remodel::RemodelMover , protocols::match::MatcherMover , protocols::matdes::SymDofMover , protocols::minimization_packing::BoltzmannRotamerMover , protocols::minimization_packing::RotamerTrialsMover , protocols::monte_carlo::GenericMonteCarloMover , protocols::monte_carlo::MonteCarloRecover , protocols::monte_carlo::MonteCarloReset , protocols::monte_carlo::MonteCarloTest , protocols::moves::DsspMover , protocols::moves::FilterMover , protocols::nmr::pre::PREMover , protocols::nonlocal::SingleFragmentMover , protocols::pose_creation::MakePolyXMover , protocols::rosetta_scripts::RosettaScriptsParser , protocols::simple_moves::CoupledMover , protocols::simple_moves::ShortBackrubMover
• MoverOPs : protocols::denovo_design::movers::BuildDeNovoBackboneMover
• MoverPassMap : protocols::environment::EnvClaimBroker
• MoverRealPair : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• MoverRegistrator() : protocols::moves::MoverRegistrator< T >
• Movers : protocols::moves::CyclicMover
• movers() : protocols::moves::MoverContainer
• movers_ : protocols::abinitio::abscript::AbscriptStageMover , protocols::canonical_sampling::MetropolisHastingsMover , protocols::environment::EnvMover , protocols::loop_modeling::LoopProtocol , protocols::moves::CompositionMover , protocols::moves::CyclicMover , protocols::moves::MoverContainer , protocols::rosetta_scripts::ParsedProtocol , protocols::rosetta_scripts::XmlObjects
• movers_and_passes_ : protocols::environment::EnvClaimBroker
• movers_setup_ : protocols::docking::DockingEnsemblePrepackProtocol , protocols::docking::DockingPrepackProtocol
• MoverSet : protocols::abinitio::abscript::AbscriptMover , protocols::abinitio::abscript::AbscriptStageMover
• MoverStatistics() : protocols::moves::MoverStatistics
• movertype : protocols::mpi_refinement::MethodParams
• moves_ : protocols::membrane::MPQuickRelaxMover , protocols::relax::RangeRelaxMover
• moves_for_pose() : protocols::stepwise::monte_carlo::mover::StepWiseMasterMover
• moves_residue() : core::fragment::Frame , core::fragment::NonContinuousFrame
• moveset_phase1_ : protocols::relax::ClassicRelax
• moveset_phase2_ : protocols::relax::ClassicRelax
• moveset_phase3_ : protocols::relax::ClassicRelax
• movie_file_accepted_ : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• movie_file_trial_ : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• moving_atom_name_ : protocols::stepwise::screener::AnchorSugarScreener
• moving_atoms_ : core::optimization::CartesianMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , protocols::electron_density::BfactorMultifunc
• moving_distance_ : protocols::normalmode::NormalModeRelaxMover
• moving_dofids_ : core::optimization::CartesianMinimizerMap
• moving_lattice_ : protocols::cryst::MakeLayerMover
• moving_ligand_ : protocols::stepwise::modeler::StepWiseConnectionSampler
• moving_partition_res() : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler
• moving_partition_res_ : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler , protocols::stepwise::modeler::StepWiseConnectionSampler , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler
• moving_phosphate_virtualized_ : protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler
• moving_res : protocols::stepwise::modeler::rna::sugar::SugarModeling , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters , protocols::stepwise::monte_carlo::mover::StepWiseMove , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler
• moving_res_ : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup , protocols::stepwise::modeler::rna::bulge::BulgeApplyMover , protocols::stepwise::modeler::rna::bulge::BulgeUnApplyMover , protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker , protocols::stepwise::modeler::rna::o2prime::O2PrimePacker , protocols::stepwise::modeler::rna::sugar::SugarInstantiateMover , protocols::stepwise::modeler::rna::sugar::SugarVirtualizeMover , protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator , protocols::stepwise::modeler::StepWiseConnectionSampler , protocols::stepwise::modeler::StepWiseModeler , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler , protocols::stepwise::screener::CentroidDistanceScreener , protocols::stepwise::screener::FastForwardToNextResidueAlternative , protocols::stepwise::screener::SugarInstantiator , protocols::stepwise::screener::TagDefinition , protocols::stepwise::screener::VDW_BinScreener , protocols::topology_broker::AsymFoldandDockClaimer
• moving_res_base_state : protocols::stepwise::modeler::rna::sugar::SugarModeling
• moving_res_base_stub_ : protocols::stepwise::modeler::StepWiseConnectionSampler , protocols::stepwise::screener::BaseCentroidScreener , protocols::stepwise::screener::RNA_ChainClosableGeometryStubBasedScreener , protocols::stepwise::screener::StubDistanceScreener , protocols::stepwise::screener::VDW_BinScreener
• moving_res_contact_dist_cutoff_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• moving_res_contact_filter() : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• moving_res_legacy_ : protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator
• moving_res_list_ : protocols::rna::AlignmentEnergy , protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup , protocols::stepwise::legacy::screener::SimplePoseSelection , protocols::stepwise::modeler::protein::checker::ProteinAtrRepChecker , protocols::stepwise::modeler::StepWiseConnectionSampler , protocols::stepwise::modeler::StepWiseModeler , protocols::stepwise::screener::AlignRMSD_Screener , protocols::stepwise::screener::PartitionContactScreener
• moving_res_pucker_state : protocols::stepwise::modeler::rna::sugar::SugarModeling
• moving_res_stub_ : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler
• moving_res_to_base_contact_only_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• moving_residue_at_origin() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler
• moving_residue_at_origin_ : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler
• moving_residues_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_MultiPoseCloser , protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler , protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• moving_residues_input_ : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• moving_rsd_ : protocols::stepwise::sampler::StepWiseSamplerRingConformer
• moving_rsd_at_origin : protocols::stepwise::screener::SampleApplier
• moving_rsd_at_origin_ : protocols::stepwise::screener::RNA_ChainClosableGeometryStubBasedScreener
• moving_rsd_at_origin_list : protocols::stepwise::screener::SampleApplier
• moving_rsd_at_origin_list_ : protocols::stepwise::screener::RNA_ChainClosableGeometryStubBasedScreener
• moving_scs() : protocols::ligand_docking::ga_ligand_dock::LigandConformer
• moving_suite_ : protocols::recces::sampler::rna::MC_RNA_KIC_Sampler , protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser , protocols::stepwise::sampler::rna::RNA_KIC_Sampler , protocols::stepwise::sampler::rna::RNA_KinematicCloser
• moving_torsionids_ : core::optimization::CartesianMinimizerMap
• moving_torsions_ : protocols::simple_moves::BackboneMover
• movingscs_ : protocols::ligand_docking::ga_ligand_dock::LigandConformer
• mp_base_potential_ : core::scoring::ScoringManager
• mp_param() : core::scoring::MultipoleElecResidueInfo
• mp_param_ : core::scoring::MultipoleElecResidueInfo
• mp_span_ins_ : core::scoring::membrane::MPSpanAngleEnergy
• MPCbetaEnergy() : core::scoring::membrane::MPCbetaEnergy
• mpdata_ : core::scoring::membrane::MPCbetaEnergy , core::scoring::membrane::MPEnvEnergy , core::scoring::membrane::MPNonHelixPenalty , core::scoring::membrane::MPPairEnergy , core::scoring::membrane::MPTerminiPenalty , core::scoring::membrane::MPTMProjPenalty
• mPDB : protocols::cluster::calibur::Stru
• 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
• mphbond_ : core::scoring::hbonds::HBondOptions
• MPHelicalityEnergy() : core::scoring::membrane::MPHelicalityEnergy
• MPI_bcast_ : protocols::canonical_sampling::CanonicalSamplingMover
• 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_channel_ : protocols::jd2::SingleFileBuffer
• mpi_feedback() : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• 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_master_save_score_only_ : protocols::loophash::MPI_LoopHashRefine_Master , protocols::mpi_refinement::MPI_Refine_Master
• mpi_metropolis_temp_ : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• MPI_nprocs_ : protocols::optimize_weights::IterativeOptEDriver
• mpi_nprocs_ : protocols::optimize_weights::OptEMultifunc
• MPI_nprocs_ : protocols::pack_daemon::MPIMultistateFitnessFunction , protocols::pmut_scan::PointMutScanDriver
• MPI_rank_ : protocols::optimize_weights::IterativeOptEDriver
• mpi_rank_ : protocols::optimize_weights::OptEMultifunc
• MPI_rank_ : protocols::pmut_scan::PointMutScanDriver
• MPI_ranks_handling_message() : protocols::cyclic_peptide_predict::HierarchicalHybridJD_ResultsSummaryBase
• mpi_ranks_handling_message_ : protocols::cyclic_peptide_predict::HierarchicalHybridJD_ResultsSummaryBase
• 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_resume_ : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• MPI_synchronize_pools_ : protocols::canonical_sampling::CanonicalSamplingMover
• MPI_TIMING : protocols::wum::MPI_WorkUnitManager
• MPI_WorkUnitManager() : protocols::wum::MPI_WorkUnitManager , protocols::wum::WorkUnitBase
• MPI_WorkUnitManager_Slave() : protocols::wum::MPI_WorkUnitManager_Slave , protocols::wum::WorkUnitBase
• MPIArchiveJobDistributor() : protocols::jd2::archive::MPIArchiveJobDistributor
• MpiFileBuffer() : protocols::jd2::MpiFileBuffer
• MPIFileBufJobDistributor() : protocols::jd2::MPIFileBufJobDistributor
• MPIMultiCommJobDistributor() : protocols::jd2::MPIMultiCommJobDistributor
• MPIMultistateFitnessFunction() : protocols::pack_daemon::MPIMultistateFitnessFunction
• MPIWorkPartitionJobDistributor() : protocols::jd2::MPIWorkPartitionJobDistributor
• MPIWorkPoolJobDistributor() : protocols::jd2::MPIWorkPoolJobDistributor
• MPLipidAccessibility() : protocols::membrane::MPLipidAccessibility
• MPMutateRelaxMover() : protocols::membrane::MPMutateRelaxMover
• MPNonHelixPenalty() : core::scoring::membrane::MPNonHelixPenalty
• mpose() : core::scoring::motif::MotifHit
• mpose_ : core::scoring::motif::MotifHit
• mposeptr() : core::scoring::motif::MotifHit
• MPPairEnergy() : core::scoring::membrane::MPPairEnergy
• MPQuickRelaxMover() : protocols::membrane::MPQuickRelaxMover
• MPRangeRelaxMover() : protocols::relax::membrane::MPRangeRelaxMover
• MPResidueLipophilicityEnergy() : core::scoring::membrane::MPResidueLipophilicityEnergy
• MPSpanAngleEnergy() : core::scoring::membrane::MPSpanAngleEnergy
• MPSpanAngleFilter() : protocols::simple_filters::MPSpanAngleFilter
• MPSpanInsertionEnergy() : core::scoring::membrane::MPSpanInsertionEnergy
• MPSymDockMover() : protocols::symmetric_docking::membrane::MPSymDockMover
• MPTerminiPenalty() : core::scoring::membrane::MPTerminiPenalty
• MPTMProjPenalty() : core::scoring::membrane::MPTMProjPenalty
• mRemainingSize : protocols::cluster::calibur::Clustering
• mres : core::pack::annealer::Key
• mres_has_heavy_unsats() : protocols::hbnet::NetworkState
• mres_has_unsats() : protocols::hbnet::NetworkState
• mres_id_ : core::scoring::hbonds::graph::HBondNode
• mrlod_ : protocols::make_rot_lib::MakeRotLibJob , protocols::make_rot_lib::MakeRotLibJobInputter
• MRMover() : protocols::hybridization::MRMover
• MRSJob() : protocols::multistage_rosetta_scripts::MRSJob
• MRSJobQueen() : protocols::multistage_rosetta_scripts::MRSJobQueen
• MRSJobQueenChecker() : protocols::multistage_rosetta_scripts::MRSJobQueenChecker
• MRSJobSummary() : protocols::multistage_rosetta_scripts::MRSJobSummary
• ms_whenfail_ : protocols::moves::FilterMover , protocols::protein_interface_design::movers::LoopOver
• msa() : core::scoring::packstat::PackingScoreResData
• msa_ : core::scoring::packstat::PackingScoreResData
• msas_for_atom() : protocols::vardist_solaccess::VarSolDRotamerDots
• msas_radii_ : protocols::vardist_solaccess::VarSolDistSasaCalculator , protocols::vardist_solaccess::VarSolDRotamerDots
• MSDMover() : protocols::recon_design::MSDMover
• mseq_ : protocols::hybridization::DDomainParse
• msg_ : protocols::rpc::JSON_RPC
• msg_tag : protocols::jd2::archive::MPIArchiveJobDistributor::CompletionMessage
• msr_ : protocols::metal_interface::AddZincSiteConstraints , protocols::metal_interface::ZincSiteFinder
• mtzfile_ : core::scoring::cryst::PhenixInterface
• mu() : core::pose::Pose , core::scoring::methods::BBDepCartBondedParameters , core::scoring::methods::BBIndepCartBondedParameters , core::scoring::methods::CartBondedParameters
• mu0_ : core::scoring::methods::BBIndepCartBondedParameters
• mulfactor_ : protocols::mpi_refinement::StructAvrgMover
• MulliganPNearEvaluator() : protocols::toolbox::MulliganPNearEvaluator
• mult_ : core::scoring::GenTorsionParams , core::scoring::SpringParams , protocols::cryst::DockLatticeMover
• multi_component() : protocols::hbnet::HBNet
• multi_component_ : protocols::hbnet::HBNet
• multi_cool_annealer() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• multi_cool_annealer_ : core::pack::task::PackerTask_
• multi_cool_annealer_history_size() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• multi_fast_relax() : protocols::abinitio::AbrelaxApplication
• multi_ligands_maxRad_ : protocols::ligand_docking::ga_ligand_dock::GALigandDock
• multi_origin_list() : protocols::pockets::FingerprintBase
• multi_origin_list_ : protocols::pockets::FingerprintBase
• multi_relative() : protocols::calc_taskop_filters::Operator
• multi_relative_ : protocols::calc_taskop_filters::Operator
• multi_threading_inner_job() : protocols::jd2::MultiThreadingJob
• multi_use() : protocols::protein_interface_design::movers::SaveAndRetrieveSidechains
• multi_use_ : protocols::protein_interface_design::movers::SaveAndRetrieveSidechains
• multi_water_fade_ : core::scoring::lkball::LK_BallEnergy
• multicomp() : protocols::matdes::InterfacePackingFilter , protocols::matdes::OligomericAverageDegreeFilter , protocols::simple_filters::ShapeComplementarityFilter
• multicomp_ : protocols::matdes::InterfacePackingFilter , protocols::matdes::OligomericAverageDegreeFilter , protocols::simple_filters::ShapeComplementarityFilter
• multicomponent_ : protocols::matdes::BuildingBlockInterfaceOperation
• MultiConstraint() : core::scoring::constraints::MultiConstraint
• MultiConstraintCreator() : core::scoring::constraints::MultiConstraintCreator
• MultiCoolAnnealer() : core::pack::annealer::MultiCoolAnnealer
• Multifunc() : core::optimization::Multifunc
• multifunc_ : protocols::optimize_weights::WrappedOptEExpressionCreator , protocols::optimize_weights::WrapperOptEMultifunc
• MultiObjective() : protocols::mpi_refinement::MultiObjective
• MultiPhosphateSampler() : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• multiple_jumps_ : protocols::docking::DockingInitialPerturbation
• multiple_ligands_ : protocols::ligand_docking::ga_ligand_dock::GALigandDock
• MultipleDomainMover() : protocols::rna::denovo::coarse::MultipleDomainMover
• MultipleOutputSpecification() : protocols::jd3::output::MultipleOutputSpecification
• MultipleOutputter() : protocols::jd3::output::MultipleOutputter
• MultipleOutputWrapper() : protocols::rosetta_scripts::MultipleOutputWrapper
• MultiplePoseMover() : protocols::rosetta_scripts::MultiplePoseMover
• MultipleSigmoids() : protocols::calc_taskop_filters::MultipleSigmoids
• MultiplexedAnnealableGraph() : core::pack::interaction_graph::MultiplexedAnnealableGraph
• MultiplicitiveFactor() : core::scoring::FACTSPotential
• MultiplicitiveFactor_ : core::scoring::FACTSPotential
• multiplicity() : core::scoring::constraints::AmbiguousNMRDistanceConstraint , core::scoring::GenTorsionParams , core::scoring::SpringParams
• multiplier_ : protocols::optimize_weights::PNatLigPoseOptEData , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection
• multipole_elec_potential_ : core::scoring::ScoringManager
• multipole_info_ : core::scoring::MultipoleElecPotential
• MULTIPOLE_POSE_INFO : core::pose::datacache::CacheableDataType
• 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
• MultipoleParameterOP : core::scoring::MultipoleParameter
• MultiProbePerSphereAccumulator() : core::scoring::packstat::MultiProbePerSphereAccumulator
• MultiProbePoseAccumulator() : core::scoring::packstat::MultiProbePoseAccumulator
• multistate_packer_ : protocols::dna::DnaInterfaceMultiStateDesign , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• MultiStateAggregateFunction() : protocols::multistate_design::MultiStateAggregateFunction
• MultistateAggregateFunction() : protocols::pack_daemon::MultistateAggregateFunction
• MultiStateEntity() : protocols::multistate_design::MultiStateEntity
• 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
• Multivec : core::pack::scmin::CartSCMinMultifunc , core::pack::scmin::SCMinMultifunc , protocols::nmr::pcs::PCSTensorOptimizer , protocols::optimize_weights::OptEData , protocols::optimize_weights::OptEMultifunc , protocols::optimize_weights::OptEPositionData , protocols::optimize_weights::WrapperOptEMultifunc
• multivec2poseBfacts() : protocols::electron_density::BfactorMultifunc
• mus_spline_ : core::scoring::methods::BBDepCartBondedParameters
• MUST_CONTROL : protocols::environment::claims::ClaimStrength
• must_switch_bins() : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber , protocols::simple_moves::bin_transitions::PerturbByBins
• must_switch_bins_ : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber , protocols::simple_moves::bin_transitions::PerturbByBins
• mut_aa_ : protocols::optimize_weights::DDGMutationOptEData , protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover
• MUT_COMPLEXES_LIST_FILE : protocols::optimize_weights::DDGBindOptEData
• mut_res_ : protocols::membrane::MPMutateRelaxMover
• mut_resid : protocols::ligand_docking::ProtLigPair_info
• mut_residue() : protocols::pmut_scan::MutationData
• mut_residue_ : protocols::pmut_scan::MutationData
• mut_save_pose_mover_ : protocols::features::InterfaceDdGMover
• mut_target : protocols::ligand_docking::ProtLigPair_info
• mut_to_gly() : protocols::analysis::InterfaceAnalyzerMover
• MUT_UNBOUNDS_LIST_FILE : protocols::optimize_weights::DDGBindOptEData
• mut_unfolded_energies_emap_ : protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData
• MutableChiRecord() : core::chemical::MutableChiRecord
• MutableICoorRecord() : core::chemical::MutableICoorRecord
• MutableResidueConnection() : core::chemical::MutableResidueConnection
• MutableResidueType : core::chemical::Atom , core::chemical::MutableResidueType
• Mutant() : protocols::pmut_scan::Mutant , protocols::pmut_scan::MutationData
• mutant_complexes_ : protocols::optimize_weights::DDGBindOptEData
• mutant_components_ : protocols::ddg::ddGMover
• mutant_file_ : protocols::membrane::MPMutateRelaxMover
• mutant_info_ : protocols::antibody::design::MutateFrameworkForCluster
• mutant_score_components() : protocols::ddg::ddGMover
• mutant_unbound_components_ : protocols::ddg::ddGMover
• mutant_unbounds_ : protocols::optimize_weights::DDGBindOptEData
• mutants_ : protocols::ddg::ddGMover
• mutants_allowed_ : protocols::antibody::design::MutantPosition
• mutants_begin() : protocols::pmut_scan::PointMutScanDriver
• mutants_end() : protocols::pmut_scan::PointMutScanDriver
• mutants_list_ : protocols::pmut_scan::PointMutScanDriver
• mutants_list_file_ : 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 , protocols::ligand_docking::ga_ligand_dock::LigandConformer
• mutate_all_at_once() : protocols::rna::movers::RNAThreadAndMinimizeMover
• mutate_and_relax() : protocols::design_opt::PointMutationCalculator , protocols::matdes::MatDesPointMutationCalculator
• mutate_disulfides_to_ala() : protocols::denovo_design::DisulfidizeMover
• mutate_framework_for_cluster_ : protocols::antibody::design::AntibodyDesignMover
• mutate_gly_ : protocols::denovo_design::DisulfidizeMover
• mutate_pro_ : protocols::denovo_design::DisulfidizeMover
• mutate_rate_ : protocols::dna::DnaInterfaceMultiStateDesign , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• mutate_residues() : protocols::kinematic_closure::ClosureProblem
• mutate_self_ : protocols::simple_moves::MutateResidue
• mutate_to_ala_ : protocols::energy_based_clustering::EnergyBasedClusteringOptions
• mutate_to_alanine() : protocols::energy_based_clustering::EnergyBasedClusteringProtocol
• mutate_to_glycine_ : protocols::simple_moves::RepulsiveOnlyMover
• MutateFrameworkForCluster() : protocols::antibody::design::MutateFrameworkForCluster
• MutateResidue() : protocols::simple_moves::MutateResidue
• MUTATION : core::io::HeaderInformation
• mutation_ddGs() : core::io::PositionDdGInfo::PositionDdGInfo
• mutation_ddGs_ : core::io::PositionDdGInfo::PositionDdGInfo
• mutation_label() : protocols::ddg::ddGMover
• mutation_list() : protocols::features::InterfaceDdGMover
• mutation_list_ : protocols::rna::movers::RNAThreadAndMinimizeMover
• mutation_probability_ : core::optimization::GA_Minimizer
• mutation_rate() : protocols::evolution::EvolutionaryDynamicsMover , protocols::genetic_algorithm::EntityRandomizer
• mutation_rate_ : protocols::evolution::EvolutionaryDynamicsMover , protocols::genetic_algorithm::EntityRandomizer
• mutation_sets_ : protocols::task_operations::MutationSetDesignOperation
• 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
• 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_ : protocols::optimize_weights::DDGBindOptEData , protocols::pmut_scan::Mutant , protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::simple_filters::MutationsFilter
• mutations_begin() : protocols::pmut_scan::Mutant
• mutations_end() : protocols::pmut_scan::Mutant
• MutationSetDesignOperation() : protocols::task_operations::MutationSetDesignOperation
• MutationsFilter() : protocols::simple_filters::MutationsFilter
• muts_ : protocols::optimize_weights::DDGMutationOptEData
• MutTyp : protocols::constel::SingResCnlCrea
• mxr_ : core::scoring::packstat::Octree2D
• mxx_ : core::scoring::packstat::Octree2D
• mxy_ : core::scoring::packstat::Octree2D
• my_constraints_ : protocols::ligand_docking::ResidueTorsionRestraints
• my_csts_ : core::scoring::constraints::BigBinConstraint
• my_emperor() : protocols::loophash::MPI_LoopHashRefine_Master , protocols::mpi_refinement::MPI_Refine_Master
• my_emperor_ : protocols::loophash::MPI_LoopHashRefine_Master , protocols::mpi_refinement::MPI_Refine_Master
• my_filter_ : protocols::moves::FilterMover
• my_frag_id_ : core::fragment::FragID_Iterator
• my_group() : core::scoring::MultipoleElecResidueInfo
• my_group_ : core::scoring::MultipoleElecResidueInfo
• my_group_members() : core::scoring::MultipoleParameter
• my_hits_for_target_hit_map_ : protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• my_itr() : core::scoring::power_diagram::PDvertex
• my_itr_ : core::scoring::power_diagram::PDvertex
• my_local_coord_frame() : core::scoring::MultipoleElecResidueInfo
• my_local_coord_frame_ : core::scoring::MultipoleElecResidueInfo
• my_master_ : protocols::wum::MPI_WorkUnitManager_Slave
• my_mover_ : protocols::moves::FilterMover , protocols::simple_moves::DME_FilterMover
• my_provider_ : protocols::frag_picker::VallChunk
• my_rank_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication , protocols::jd2::MpiFileBuffer
• my_residue_pair_energy() : core::scoring::methods::DirectReadoutEnergy
• MY_TYPE : protocols::constraint_generator::ConstraintsManager
• MyAtom() : protocols::fldsgn::MyAtom
• myslaves_ : protocols::mpi_refinement::MPI_Refine_Master