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

- m -

• M : 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_done_all : protocols::simple_moves::TailsScoreMover
• m_hill_size : protocols::simple_moves::TailsScoreMover
• m_number_of_hill_points : protocols::simple_moves::TailsScoreMover
• m_Temperature : protocols::relax::ClassicRelax
• m_Temperature_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::RNA_DeNovoProtocol , protocols::LoopRebuild
• machine_letter_ : protocols::wum::MPI_WorkUnitManager
• mag_rot_ : protocols::rigid::RigidBodyMotionMover
• mag_trans_ : protocols::rigid::RigidBodyMotionMover
• 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_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_mover_ : protocols::simple_moves::ChangeAndResetFoldTreeMover
• mainchain_torsion_diff_threshold_ : protocols::dna::PDBOutput
• MainChainTorsionSet() : protocols::stepwise::modeler::protein::MainChainTorsionSet
• maintain_cap_seq_and_structure_ : protocols::simple_moves::RepeatPropagationMover
• maintain_cap_sequence_alone_ : protocols::simple_moves::RepeatPropagationMover
• make() : protocols::frag_picker::scores::MakeABEGO_SS_Score , protocols::frag_picker::scores::MakeAmbigCSScore , protocols::frag_picker::scores::MakeAtomPairConstraintsScore , protocols::frag_picker::scores::MakeBFactor , protocols::frag_picker::scores::MakeConstScore , protocols::frag_picker::scores::MakeCSScore , protocols::frag_picker::scores::MakeDihedralConstraintsScore , protocols::frag_picker::scores::MakeDisulfideDistance , protocols::frag_picker::scores::MakeDisulfideIdentity , protocols::frag_picker::scores::MakeFragmentAllAtomCrmsd , protocols::frag_picker::scores::MakeFragmentChunkCrms , protocols::frag_picker::scores::MakeFragmentCrmsd , protocols::frag_picker::scores::MakeFragmentCrmsdResDepth , protocols::frag_picker::scores::MakeFragmentDME , protocols::frag_picker::scores::MakeFragmentScoringMethod , protocols::frag_picker::scores::MakeGunnCostScore , protocols::frag_picker::scores::MakeHydrophobicityProfileSimilarity , protocols::frag_picker::scores::MakeHydrophobicitySimilarity , protocols::frag_picker::scores::MakeInterbondAngleScore , protocols::frag_picker::scores::MakeJCoupling , protocols::frag_picker::scores::MakeLAMBEGO_Similarity , protocols::frag_picker::scores::MakeMidPhiOut , protocols::frag_picker::scores::MakeMidPsiOut , protocols::frag_picker::scores::MakePartialSecondarySimilarity , protocols::frag_picker::scores::MakePCS_FragDistance , protocols::frag_picker::scores::MakePhi , protocols::frag_picker::scores::MakePhiPsiRmsd , protocols::frag_picker::scores::MakePhiPsiSquareWell , protocols::frag_picker::scores::MakeProfileScore , protocols::frag_picker::scores::MakeProfileScoreBlosum62 , protocols::frag_picker::scores::MakeProfileScoreDistWeight , protocols::frag_picker::scores::MakeProfileScoreL1 , protocols::frag_picker::scores::MakeProfileScoreStructL1 , protocols::frag_picker::scores::MakeProfileScoreSubMatrix , protocols::frag_picker::scores::MakeProlinePhiScore , protocols::frag_picker::scores::MakePsi , protocols::frag_picker::scores::MakeRamaScore , protocols::frag_picker::scores::MakeRDCScore , protocols::frag_picker::scores::MakeScoreEValuator , protocols::frag_picker::scores::MakeSecondaryIdentity , protocols::frag_picker::scores::MakeSecondarySimilarity , protocols::frag_picker::scores::MakeSequenceIdentity , protocols::frag_picker::scores::MakeSolventAccessibility , protocols::frag_picker::scores::MakeTalosSSSimilarity , protocols::frag_picker::scores::MakeTorsionBinSimilarity
• make_bundle_ : protocols::helical_bundle::BundleGridSampler
• make_bundle_helix_movers_ : protocols::helical_bundle::MakeBundle
• make_calculator() : protocols::toolbox::task_operations::RestrictToInterfaceOperation , protocols::toolbox::task_operations::RestrictToNeighborhoodOperation
• make_chi_move() : protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover , protocols::simple_moves::sidechain_moves::PerturbChiSidechainMover , protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• make_claim() : protocols::environment::claims::EnvClaim
• make_compatible_with_ROCS_custom_ForceField() : protocols::pockets::GenPharmacophore
• make_complete_chunks() : protocols::hybridization::HybridizeFoldtreeDynamic
• make_constraint_covalent() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• make_constraint_covalent_helper() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• make_disjointed_foldtree() : protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover
• make_disulfide() : protocols::forge::remodel::RemodelDesignMover
• make_disulfide_fast() : protocols::forge::remodel::RemodelDesignMover
• 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_fragment_moves() : protocols::farna::RNA_Relaxer
• make_full_pose() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• make_Hessian_ANM() : protocols::normalmode::NormalMode
• make_Hessian_TNM() : protocols::normalmode::NormalMode
• make_inner_cycle_from_string_name() : protocols::loops::loop_mover::refine::LoopRefineInnerCycleFactory
• make_interface_combos() : protocols::features::InterfaceFeatures
• make_interface_set() : protocols::analysis::InterfaceAnalyzerMover
• make_local_bb_change() : protocols::loophash::LocalInserter , protocols::loophash::LocalInserter_SimpleMin
• make_local_bb_change_close_gaps() : protocols::loophash::LocalInserter , protocols::loophash::LocalInserter_SimpleMin
• make_local_bb_change_include_cut() : protocols::loophash::LocalInserter , protocols::loophash::LocalInserter_SimpleMin
• make_motif_filename() : protocols::motifs::IRCollection
• make_move() : protocols::simple_moves::BackboneMover , protocols::simple_moves::BBConRotMover , protocols::simple_moves::ShearMover , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase , protocols::simple_moves::SmallMover
• make_movemap() : protocols::ligand_docking::LigandBaseProtocol
• make_movie() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• make_movie_ : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• make_multichain_interface_set() : protocols::analysis::InterfaceAnalyzerMover
• make_mutant_structure() : protocols::pmut_scan::PointMutScanDriver
• make_mutants() : protocols::pmut_scan::PointMutScanDriver
• make_name() : protocols::toolbox::task_operations::RestrictToInterfaceOperation , protocols::toolbox::task_operations::RestrictToNeighborhoodOperation
• make_new_grid() : protocols::qsar::scoring_grid::GridManager
• make_packer_task() : protocols::ligand_docking::HighResDocker , protocols::ligand_docking::LigandBaseProtocol
• make_packer_task_from_vector() : protocols::ligand_docking::HighResDocker
• make_packer_task_ligand_only() : protocols::ligand_docking::LigandBaseProtocol
• make_pose() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• make_pymol_script() : protocols::flxbb::LayerDesignOperation
• make_pymol_script_ : protocols::flxbb::LayerDesignOperation
• make_rasmol_format_file() : protocols::toolbox::SelectResiduesByLayer
• make_rasmol_format_file_ : protocols::toolbox::SelectResiduesByLayer
• make_rotwell_jump() : protocols::simple_moves::sidechain_moves::SidechainMover
• make_sec() : protocols::hybridization::TMalign
• make_separated_pose() : protocols::analysis::InterfaceAnalyzerMover
• make_sequence_claim() : protocols::topology_broker::SequenceClaimer
• make_sequence_shift() : protocols::loops::Loops
• make_sequence_symmetric() : protocols::topology_broker::TopologyBroker
• make_simple_ssd_from_pdb() : protocols::optimize_weights::IterativeOptEDriver
• make_specific_mutant() : protocols::pmut_scan::PointMutScanDriver
• make_strand_neighbor_two() : protocols::fldsgn::topology::StrandPairingSet
• make_symmetric_task() : protocols::simple_moves::symmetry::SymEnergyCutRotamerTrialsMover , protocols::simple_moves::symmetry::SymPackRotamersMover , protocols::simple_moves::symmetry::SymRotamerTrialsMover
• make_tail() : protocols::simple_moves::TailsScoreMover
• make_three_fold_symmetry_90_210_330() : protocols::make_rot_lib::MakeRotLibMover
• make_tweaked_scorefxn() : protocols::ligand_docking::LigandBaseProtocol
• make_two_fold_symmetry_0_180() : protocols::make_rot_lib::MakeRotLibMover
• make_two_fold_symmetry_135_315() : protocols::make_rot_lib::MakeRotLibMover
• MakeABEGO_SS_Score() : protocols::frag_picker::scores::MakeABEGO_SS_Score
• MakeAmbigCSScore() : protocols::frag_picker::scores::MakeAmbigCSScore
• MakeAtomPairConstraintsScore() : protocols::frag_picker::scores::MakeAtomPairConstraintsScore
• MakeBFactor() : protocols::frag_picker::scores::MakeBFactor
• makebinary() : protocols::sic_dock::XfoxmScore
• MakeBundle() : protocols::helical_bundle::MakeBundle
• MakeBundleHelix() : protocols::helical_bundle::MakeBundleHelix
• MakeConstScore() : protocols::frag_picker::scores::MakeConstScore
• MakeCSScore() : protocols::frag_picker::scores::MakeCSScore
• MakeDihedralConstraintsScore() : protocols::frag_picker::scores::MakeDihedralConstraintsScore
• MakeDisulfideDistance() : protocols::frag_picker::scores::MakeDisulfideDistance
• MakeDisulfideIdentity() : protocols::frag_picker::scores::MakeDisulfideIdentity
• MakeFragmentAllAtomCrmsd() : protocols::frag_picker::scores::MakeFragmentAllAtomCrmsd
• MakeFragmentChunkCrms() : protocols::frag_picker::scores::MakeFragmentChunkCrms
• MakeFragmentCrmsd() : protocols::frag_picker::scores::MakeFragmentCrmsd
• MakeFragmentCrmsdResDepth() : protocols::frag_picker::scores::MakeFragmentCrmsdResDepth
• MakeFragmentDME() : protocols::frag_picker::scores::MakeFragmentDME
• MakeFragmentScoringMethod() : protocols::frag_picker::scores::MakeFragmentScoringMethod
• MakeGunnCostScore() : protocols::frag_picker::scores::MakeGunnCostScore
• MakeHydrophobicityProfileSimilarity() : protocols::frag_picker::scores::MakeHydrophobicityProfileSimilarity
• MakeHydrophobicitySimilarity() : protocols::frag_picker::scores::MakeHydrophobicitySimilarity
• MakeInterbondAngleScore() : protocols::frag_picker::scores::MakeInterbondAngleScore
• MakeJCoupling() : protocols::frag_picker::scores::MakeJCoupling
• MakeLAMBEGO_Similarity() : protocols::frag_picker::scores::MakeLAMBEGO_Similarity
• MakeMidPhiOut() : protocols::frag_picker::scores::MakeMidPhiOut
• MakeMidPsiOut() : protocols::frag_picker::scores::MakeMidPsiOut
• MakePartialSecondarySimilarity() : protocols::frag_picker::scores::MakePartialSecondarySimilarity
• MakePCS_FragDistance() : protocols::frag_picker::scores::MakePCS_FragDistance
• MakePhi() : protocols::frag_picker::scores::MakePhi
• MakePhiPsiRmsd() : protocols::frag_picker::scores::MakePhiPsiRmsd
• MakePhiPsiSquareWell() : protocols::frag_picker::scores::MakePhiPsiSquareWell
• MakePolyXMover() : protocols::simple_moves::MakePolyXMover
• MakeProfileScore() : protocols::frag_picker::scores::MakeProfileScore
• MakeProfileScoreBlosum62() : protocols::frag_picker::scores::MakeProfileScoreBlosum62
• MakeProfileScoreDistWeight() : protocols::frag_picker::scores::MakeProfileScoreDistWeight
• MakeProfileScoreL1() : protocols::frag_picker::scores::MakeProfileScoreL1
• MakeProfileScoreStructL1() : protocols::frag_picker::scores::MakeProfileScoreStructL1
• MakeProfileScoreSubMatrix() : protocols::frag_picker::scores::MakeProfileScoreSubMatrix
• MakeProlinePhiScore() : protocols::frag_picker::scores::MakeProlinePhiScore
• MakePsi() : protocols::frag_picker::scores::MakePsi
• MakeRamaScore() : protocols::frag_picker::scores::MakeRamaScore
• MakeRDCScore() : protocols::frag_picker::scores::MakeRDCScore
• MakeRotLibJob() : protocols::make_rot_lib::MakeRotLibJob
• MakeRotLibJobInputter() : protocols::make_rot_lib::MakeRotLibJobInputter
• MakeRotLibMover() : protocols::make_rot_lib::MakeRotLibMover
• MakeRotLibOptionsData() : protocols::make_rot_lib::MakeRotLibOptionsData
• MakeScoreEValuator() : protocols::frag_picker::scores::MakeScoreEValuator
• MakeSecondaryIdentity() : protocols::frag_picker::scores::MakeSecondaryIdentity
• MakeSecondarySimilarity() : protocols::frag_picker::scores::MakeSecondarySimilarity
• MakeSequenceIdentity() : protocols::frag_picker::scores::MakeSequenceIdentity
• MakeSolventAccessibility() : protocols::frag_picker::scores::MakeSolventAccessibility
• MakeStarTopologyMover() : protocols::rbsegment_relax::MakeStarTopologyMover
• MakeTalosSSSimilarity() : protocols::frag_picker::scores::MakeTalosSSSimilarity
• MakeTorsionBinSimilarity() : protocols::frag_picker::scores::MakeTorsionBinSimilarity
• MALARKEY : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• 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 , protocols::protein_interface_design::movers::VLB
• manager_ptr() : protocols::jd2::archive::AbstractArchiveBase
• manager_type() : protocols::jd2::JD2ResourceManagerCreator
• manipulate_cut_bias() : protocols::topology_broker::CutBiasClaimer , protocols::topology_broker::RigidChunkClaimer , protocols::topology_broker::TopologyClaimer
• manual_call() : protocols::loophash::LoopHashRelaxProtocol
• manual_jump_pairs_ : protocols::seeded_abinitio::SeedFoldTree
• manualPackerTaskGen() : protocols::forge::remodel::RemodelWorkingSet
• map2keyvector() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• map2target() : protocols::abinitio::Template
• map2template() : protocols::abinitio::Template
• map_ : protocols::comparative_modeling::StealSideChainsMover , protocols::noesy_assign::ResonanceList
• map_cst_from_centroid_to_fa_ : protocols::abinitio::ResolutionSwitcher
• map_DOF_to_NM_ : protocols::normalmode::NormalModeMultifunc
• map_helix_pairings_ : protocols::fldsgn::topology::HelixPairingSet
• map_name_ : protocols::qsar::qsarMap
• map_NM_to_DOF_ : protocols::normalmode::NormalModeMultifunc
• map_pairing() : protocols::abinitio::Template
• map_pairings2target() : protocols::abinitio::Template
• map_pairings2template() : protocols::abinitio::Template
• map_pdb_info_number() : protocols::hybridization::FoldTreeHybridize
• map_ss_segments() : protocols::fldsgn::MatchResidues
• map_strand_pairings_ : protocols::fldsgn::topology::StrandPairingSet
• map_to_cen_atom_ : protocols::noesy_assign::PeakAssignmentParameters
• map_to_original_ : protocols::toolbox::AllowInsert
• map_type_ : 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::modeler::options::StepWiseProteinModelerOptions
• mapfile_activated_ : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• MapHotspot() : protocols::protein_interface_design::movers::MapHotspot
• mapping_ : protocols::abinitio::Template , protocols::simple_moves::symmetry::NCSResMapping
• maps_ : protocols::frag_picker::scores::ABEGO_SS_Score
• 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_current_job_id_for_repetition() : protocols::jd2::BOINCJobDistributor , protocols::jd2::FileSystemJobDistributor , protocols::jd2::JobDistributor , protocols::jd2::MPIFileBufJobDistributor , protocols::jd2::MPIWorkPartitionJobDistributor , protocols::jd2::MPIWorkPoolJobDistributor , protocols::jd2::MSDJobDistributor , protocols::jd2::ShuffleFileSystemJobDistributor
• mark_designable() : protocols::toolbox::task_operations::DatabaseThread
• mark_entity_as_unimportant() : protocols::pack_daemon::DaemonSet , protocols::pack_daemon::PackDaemon
• 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::toolbox::task_operations::DatabaseThread
• mark_loop_moveable() : protocols::forge::remodel::RemodelLoopMover
• mark_loops_moveable() : protocols::forge::remodel::RemodelLoopMover
• mark_protein_espGrid_points() : protocols::pockets::ElectrostaticpotentialGrid
• mark_structure_as_sampled() : protocols::features::StructureFeatures
• mark_tags() : protocols::toolbox::KClusterData
• markDepth() : protocols::pockets::PocketGrid
• markEdgeDepth() : protocols::pockets::PocketGrid
• markNativeInterface() : protocols::flexpep_docking::FlexPepDockingProtocol
• markOneEdgeDepth() : protocols::pockets::PocketGrid
• markPocketDepth() : protocols::pockets::PocketGrid
• markpsp_ : protocols::pockets::PocketGrid
• marksps_ : protocols::pockets::PocketGrid
• mask() : protocols::electron_density::SetupForDensityScoringMover
• mask_ : protocols::electron_density::ReportFSC , protocols::electron_density::ScaleMapIntensities
• mask_from_offsets() : protocols::match::Bool3DGrid
• mask_output_ : protocols::electron_density::ScaleMapIntensities
• mask_reses_ : protocols::electron_density::SetupForDensityScoringMover
• mass : protocols::cartesian::CartesianAtom
• mass_ : protocols::md::MDBase
• mass_limit_ : protocols::ligand_docking::MolarMassFilter , protocols::ligand_docking::MolecularMassFilter
• master() : protocols::match::output::ResidueKinemageWriter , protocols::wum2::WorkUnit
• master_ : protocols::match::Bool3DGridKinemageWriter , protocols::match::output::ResidueKinemageWriter , protocols::match::output::SingleDownstreamResidueWriter , protocols::match::output::WriteUpstreamHitKinemage , protocols::wum2::WorkUnit
• master_add_unfolded_energy_data() : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor
• master_gather_new_coords() : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD
• master_get_new_job_id() : protocols::jd2::MPIFileBufJobDistributor , protocols::jd2::MPIWorkPoolJobDistributor
• master_go() : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD , protocols::jd2::MPIFileBufJobDistributor , protocols::jd2::MPIWorkPoolJobDistributor , protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor
• master_job_succeeded() : protocols::jd2::MPIFileBufJobDistributor , protocols::jd2::MPIWorkPoolJobDistributor
• master_mark_current_job_id_for_repetition() : protocols::jd2::MPIFileBufJobDistributor , protocols::jd2::MPIWorkPoolJobDistributor
• master_node_ : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD
• 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::inputter::InputterStream , protocols::jd2::MPIFileBufJobDistributor , protocols::loophash::MPI_LoopHashRefine_Master , protocols::mpi_refinement::MPI_Refine_Master
• master_remove_bad_inputs_from_job_list() : protocols::jd2::MPIFileBufJobDistributor , protocols::jd2::MPIWorkPoolJobDistributor
• master_set_energy_terms() : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor
• master_to_archive() : protocols::jd2::archive::MPIArchiveJobDistributor
• master_weight() : protocols::toolbox::pose_metric_calculators::EnergiesData
• master_weight_ : protocols::toolbox::pose_metric_calculators::EnergiesData
• master_weight_vector() : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• masters_done_ : protocols::mpi_refinement::MPI_Refine_Emperor
• Mat : protocols::sic_dock::RigidScore
• Mat3VecMult() : protocols::sparta::PDB
• match() : protocols::noesy_assign::Resonance
• match2D() : protocols::noesy_assign::FloatingResonance , protocols::noesy_assign::LabelResonance , protocols::noesy_assign::ProtonResonance , protocols::noesy_assign::Resonance
• match_algorithm_ : protocols::match::output::WriteUpstreamCoordinateKinemage
• 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_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_score_writer_ : protocols::match::output::MatchProcessor
• match_scores_ : protocols::match::output::MatchScoreWriter
• match_variants() : protocols::environment::ProtectedConformation
• 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
• Matcher() : protocols::match::Matcher
• matcher_ : protocols::match::output::UpstreamHitCacher
• MatcherMover() : protocols::match::MatcherMover
• MatcherOutputStats() : protocols::match::MatcherOutputStats
• MatcherTask() : protocols::match::MatcherTask
• matches() : protocols::topology_broker::ClaimerMessage
• matches_output_count_ : protocols::match::output::WriteUpstreamHitKinemage
• MatchFilter() : protocols::match::output::MatchFilter
• MatchGrafter() : protocols::metal_interface::MatchGrafter
• MatchGrouper() : protocols::match::output::MatchGrouper
• MatchHash : protocols::match::MatchOutputTracker
• matchingFrags_ : protocols::forge::remodel::RemodelMover::instruction_flags
• MatchList : protocols::canonical_sampling::AsyncMPITemperingBase
• MatchOutputter() : protocols::match::output::MatchOutputter
• MatchOutputTracker() : protocols::match::MatchOutputTracker
• MatchPositionModifier() : protocols::match::MatchPositionModifier
• MatchProcessor() : protocols::match::output::MatchProcessor
• 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 : protocols::evaluation::PCA , protocols::frag_picker::LAMBEGO_IO , protocols::frag_picker::TorsionBinIO
• Matrix : protocols::hotspot_hashing::StubGenerator , protocols::simple_moves::BBGaussianMover
• matrix3f_to_xyzMatrix() : protocols::forge::remodel::RemodelGlobalFrame , protocols::simple_filters::RepeatParameterFilter
• matrix_ : protocols::simple_moves::FavorSequenceProfile
• matrix_A : protocols::simple_moves::BBGaussianMover
• matrix_dRdPhi : protocols::simple_moves::BBGaussianMover
• matrix_G : protocols::simple_moves::BBGaussianMover
• max_ : protocols::simple_filters::RepeatParameterFilter
• max_abs_inter_strand_dihedral_to_not_be_same_direction_strands_ : protocols::features::strand_assembly::SandwichFeatures
• max_allowed_conserved_pos_mutations_ : protocols::simple_filters::ConservedPosMutationFilter
• max_angle() : protocols::simple_filters::AngleToVector
• max_angle_ : protocols::rigid::RollMover , protocols::simple_filters::AngleToVector , protocols::simple_moves::RandomTorsionMover
• 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_atoms() : protocols::backrub::BackrubMover
• max_atoms_ : protocols::backrub::BackrubMover
• max_attempts_ : protocols::loop_modeling::LoopBuilder , protocols::rosetta_scripts::MultipleOutputWrapper
• max_bbrms() : protocols::loophash::LoopHashMoverWrapper
• max_bbrms_ : protocols::loophash::LoopHashMoverWrapper , protocols::loophash::LoopHashSampler
• max_bfactor_ : protocols::match::BfactorMPM
• max_bin_ : protocols::scoring::methods::saxs::PDDFEnergy
• max_buried_sasa_ : protocols::toolbox::task_operations::CrystalContactsOperation
• max_CA_CA_dis_ : protocols::features::strand_assembly::SandwichFeatures
• max_cache_size() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel , protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• max_cache_size_ : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• 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_chainbreak_ : protocols::analysis::LoopAnalyzerMover
• max_chi_considered_ : protocols::rotamer_recovery::RRComparerChiDiff
• max_chunk_size_ : protocols::frag_picker::scores::GunnCostScore
• 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_coord_ : protocols::canonical_sampling::HamiltonianExchange
• max_cycle_ : protocols::antibody::ModelCDRH3
• max_cycle_close_trial_ : protocols::antibody::H3RefineCCD
• max_cycles() : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• max_cycles_ : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• 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_degrees_off_parallel_ : protocols::features::helixAssembly::HelixBundleFeatures
• max_dist_ : protocols::features::AtomAtomPairFeatures , protocols::simple_filters::ContactMapEvaluator
• max_dist_ndx_ : protocols::toolbox::KClusterElement
• max_dist_squared() : protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker
• max_dist_squared_ : protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker
• max_distance() : protocols::simple_moves::AddConstraintsToCurrentConformationMover , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerValueRange
• max_distance_ : protocols::hotspot_hashing::LSMSearchPattern , protocols::simple_moves::AddConstraintsToCurrentConformationMover , 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_E_in_extracted_sw_loop_ : protocols::features::strand_assembly::SandwichFeatures
• 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_frag_len() : protocols::frag_picker::FragmentPicker
• max_frag_size_ : protocols::farna::RNA_Relaxer , protocols::frag_picker::FragmentPicker
• 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_helix_fraction_ : protocols::simple_filters::AbinitioBaseFilter
• max_helix_length_ : protocols::fldsgn::filters::SecondaryStructureCountFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter , protocols::simple_filters::AbinitioBaseFilter
• 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_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() : protocols::relax::RelaxProtocolBase , protocols::simple_moves::MinMover
• max_iter_ : protocols::electron_density::BfactorFittingMover , 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::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_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_memory_pose_num_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• max_missing_weight() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• max_missing_weight_ : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions , protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• max_neighbors_ : protocols::match::NumNeighborsMPM
• max_noe_distance() : protocols::noesy_assign::CrossPeakInfo
• max_noe_distance_ : protocols::noesy_assign::CrossPeakInfo
• 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_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_outgoing_wu_mem() : protocols::wum2::EndPoint , protocols::wum2::StatusRequest
• max_output_poses_ : protocols::rosetta_scripts::MultiplePoseMover
• max_overlap_dis_ : protocols::match::output::UpstreamDownstreamCollisionFilter
• max_packet_size_ : protocols::moves::UDPSocketClient
• 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_pose_data_list_size_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• max_poses_ : protocols::rosetta_scripts::AdditionalOutputWrapper , protocols::rosetta_scripts::MultipleOutputWrapper
• 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 , protocols::hybridization::HybridizeSetup
• max_registry_shift_global_ : protocols::hybridization::ChunkTrialMover
• max_repeats_ : protocols::symmetric_docking::SymDockProtocol , protocols::ub_e2c::ubi_e2c_modeler
• 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_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::BundleGridSampler
• max_samples_ : protocols::helical_bundle::BundleGridSampler
• max_seglen_ : protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC , protocols::loops::loop_mover::refine::LoopMover_Refine_KIC
• 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_small_angle_ : protocols::simple_moves::oop::OopRandomSmallMover
• max_starting_loop_size_ : protocols::features::strand_assembly::SandwichFeatures
• 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_swap_buffer_size_ : protocols::wum::WorkUnitQueue_Swapped
• MAX_TARGETS : protocols::pockets::PocketGrid
• 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_trials_ : protocols::enzdes::DiversifyStoredRBConfs
• max_tries() : protocols::moves::FilterMover
• max_tries_ : protocols::moves::FilterMover , protocols::simple_moves::DME_FilterMover , protocols::stepwise::sampler::rna::RNA_KIC_Sampler
• max_tries_for_random_sugar_setup_ : protocols::stepwise::modeler::rna::sugar::StepWiseRNA_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_value() : protocols::simple_moves::PSSM2BfactorMover
• max_value_ : protocols::simple_moves::PSSM2BfactorMover
• max_volume_contribution() : protocols::noesy_assign::CrossPeak
• max_weight_ : protocols::optimize_weights::WeightRangeConstraint
• maxcycles() : protocols::moves::IteratedConvergenceMover
• maxcycles_ : protocols::moves::IteratedConvergenceMover
• maxfrac_ : protocols::mpi_refinement::WorkUnit_CombinePose
• maxfrac_crossover_ : protocols::simple_moves::CombinePoseMover
• maxiter_ : protocols::md::Rattle
• maxLen_ : protocols::pockets::PocketGrid
• maxPockSize_ : protocols::pockets::PocketGrid
• MaxSeqSepConstraintSet() : protocols::constraints_additional::MaxSeqSepConstraintSet
• maxtrials() : protocols::simple_moves::GenericMonteCarloMover
• maxtrials_ : protocols::simple_moves::GenericMonteCarloMover
• maxX : protocols::pockets::CCluster , protocols::pockets::PCluster
• maxY : protocols::pockets::CCluster , protocols::pockets::PCluster
• maxZ : protocols::pockets::CCluster , protocols::pockets::PCluster
• mc() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio , protocols::loops::loop_closure::ccd::LoopClosure , protocols::loops::loop_mover::refine::LoopRefineInnerCycle
• MC() : protocols::moves::DualMonteCarlo
• mc() : protocols::moves::TrialMover
• MC : protocols::sic_dock::Rose
• mc() : protocols::simple_moves::EnergyCutRotamerTrialsMover , protocols::simple_moves::symmetry::SymEnergyCutRotamerTrialsMover
• 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::AntibodyGraftDesignMover , protocols::antibody::GraftedStemOptimizer , protocols::antibody::H3PerturbCCD , protocols::antibody::H3RefineCCD , protocols::antibody::SnugDock , protocols::canonical_sampling::CanonicalSamplingMover , 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
• 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::EnergyCutRotamerTrialsMinMover , protocols::simple_moves::EnergyCutRotamerTrialsMover , protocols::simple_moves::rational_mc::RationalMonteCarlo , protocols::simple_moves::symmetry::SymEnergyCutRotamerTrialsMover , protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockingLowRes , protocols::symmetric_docking::SymDockProtocol
• mc_accepted() : protocols::moves::MonteCarlo
• mc_accepted_ : protocols::moves::MonteCarlo , protocols::simple_moves::GenericMonteCarloMover
• mc_accepted_string() : protocols::moves::MonteCarlo
• mc_accpeted() : protocols::simple_moves::GenericMonteCarloMover
• MC_Comb() : protocols::stepwise::sampler::MC_Comb
• mc_created : protocols::LoopRebuild
• mc_cycles_ : protocols::seeded_abinitio::SegmentHybridizer
• 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_kt_ : protocols::enzdes::BackboneSampler , protocols::protein_interface_design::movers::BackrubDDMover
• mc_kt_high_ : protocols::enzdes::EnzdesFlexBBProtocol
• mc_kt_low_ : protocols::enzdes::EnzdesFlexBBProtocol
• MC_mover_ : protocols::simple_moves::MonteCarloRecover , protocols::simple_moves::MonteCarloReset , protocols::simple_moves::MonteCarloTest
• MC_OneTorsion() : protocols::stepwise::sampler::MC_OneTorsion
• mc_ptr() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• mc_scorefxn_ : protocols::hybridization::CartesianSampler
• MC_StepWiseSampler() : protocols::stepwise::sampler::MC_StepWiseSampler
• mc_temp : protocols::simple_moves::ShakeStructureMover
• mc_temp_ : protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• mcfi() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList
• mcfi_ : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• mcfi_list() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• 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
• mcm_cycles : protocols::flexpep_docking::FlexPepDockingFlags
• MCR : protocols::sic_dock::Rose
• MCShowMover() : protocols::moves::MCShowMover
• md_energy_report_stepsize_ : protocols::md::MDBase
• md_report_stepsize_ : protocols::md::MDBase
• md_rsr_update_stepsize_ : protocols::md::MDBase
• MDBase() : protocols::md::MDBase
• mdsch_ : protocols::md::MDBase
• mean_ : protocols::ddg::ddGMover
• measure_bp_specificities() : protocols::dna::DnaInterfacePacker
• measure_rotamer_recovery() : protocols::optimize_weights::IterativeOptEDriver , protocols::rotamer_recovery::RRComparer , protocols::rotamer_recovery::RRComparerAutomorphicRMSD , protocols::rotamer_recovery::RRComparerChiDiff , protocols::rotamer_recovery::RRComparerElecDensDiff , protocols::rotamer_recovery::RRComparerRotBins , protocols::rotamer_recovery::RRProtocol
• measure_sequence_recovery() : protocols::optimize_weights::IterativeOptEDriver , protocols::toolbox::pose_metric_calculators::SequenceComparison
• measure_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_ : protocols::filters::ReplicateFilter
• median_rms_ : protocols::cluster::ClusterBase
• mem_center_ : protocols::membrane::TransformIntoMembraneMover
• mem_foot_print() : protocols::loophash::LoopHashLibrary , protocols::loophash::LoopHashMap , protocols::wum::WorkUnitManager , protocols::wum::WorkUnitQueue
• mem_footprint() : protocols::relax::SRelaxPose , protocols::wum::SilentStructStore , protocols::wum::WorkUnitBase
• mem_normal_ : protocols::membrane::TransformIntoMembraneMover
• mem_stats() : protocols::wum::WorkUnitQueue
• member : protocols::cluster::Cluster
• membrane_ : protocols::docking::DockingPrepackProtocol
• membrane_jumps_ : protocols::abinitio::AbrelaxApplication
• membrane_rsd_ : protocols::membrane::AddMembraneMover
• MembraneAbinitio() : protocols::abinitio::MembraneAbinitio
• MembraneCenterPerturbationMover() : protocols::rigid::MembraneCenterPerturbationMover
• MembraneEmbed_from_pose() : protocols::abinitio::MembraneAbinitio
• MembraneJump() : protocols::jumping::MembraneJump
• MembraneNormalPerturbationMover() : protocols::rigid::MembraneNormalPerturbationMover
• MembranePositionFromTopologyMover() : protocols::membrane::MembranePositionFromTopologyMover
• MembraneTopology() : protocols::simple_moves::MembraneTopology
• MembraneTopology_from_pose() : 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_offset_ : protocols::canonical_sampling::mc_convergence_checks::DataBuffer , protocols::canonical_sampling::mc_convergence_checks::TransferBuffer
• 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
• merge() : protocols::comparative_modeling::AlignmentCluster , protocols::loophash::LoopHashLibrary , protocols::wum::WorkUnitList
• merge_bbdb() : protocols::loophash::LoopHashLibrary
• merge_protein_surface_poses() : protocols::surface_docking::SurfaceDockingProtocol
• metal_site_ : protocols::metal_interface::ZincHeterodimerMover
• metal_to_mobile_ : protocols::metal_interface::ZincHeterodimerMover
• MetalloClaimer() : protocols::topology_broker::MetalloClaimer
• MetalSiteResidue() : protocols::metal_interface::MetalSiteResidue
• MetaPoseEvaluator() : protocols::evaluation::MetaPoseEvaluator
• method_ : protocols::mpi_refinement::Clusterer
• methodname() : protocols::mpi_refinement::Scheduler
• methodname_ : protocols::mpi_refinement::Scheduler
• methods_picked() : protocols::mpi_refinement::Scheduler
• methods_picked_ : protocols::mpi_refinement::Scheduler
• methyl_names_ : protocols::noesy_assign::MethylNameLibrary
• MethylNameLibrary() : protocols::noesy_assign::MethylNameLibrary
• MethylNames() : protocols::noesy_assign::MethylNames
• MethylNameTable : protocols::noesy_assign::MethylNameLibrary
• metric_ : protocols::simple_filters::PoseMetricEvaluator< T >
• 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::toolbox::pose_metric_calculators::MetricValueGetter
• metric_value_template_ : protocols::toolbox::pose_metric_calculators::MetricValueGetter
• MetricCalculatorFitnessFunction() : protocols::multistate_design::MetricCalculatorFitnessFunction
• MetricRecorder() : protocols::canonical_sampling::MetricRecorder
• MetricValueBase : protocols::fldsgn::NcontactsCalculator , protocols::toolbox::pose_metric_calculators::FragQualCalculator
• MetricValueGetter() : protocols::toolbox::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
• mh_ : protocols::sic_dock::scores::MotifHashRigidScore
• 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
• min_ : protocols::ddg::ddGMover , protocols::simple_filters::RepeatParameterFilter
• min_aa_probability_ : protocols::toolbox::task_operations::SeqprofConsensusOperation
• min_after_repack_ : protocols::loops::loop_mover::refine::LoopMover_Refine_KIC
• min_all_jumps_ : protocols::enzdes::EnzdesBaseProtocol
• min_angle() : protocols::simple_filters::AngleToVector
• min_angle_ : protocols::rigid::RollMover , protocols::simple_filters::AngleToVector
• min_atoms() : protocols::backrub::BackrubMover
• min_atoms_ : protocols::backrub::BackrubMover
• min_base_relax_ : protocols::antibody_legacy::CDRH3Modeler
• min_bb() : protocols::protein_interface_design::movers::PrepackMover , protocols::simple_moves::DesignRepackMover
• min_bb_ : protocols::enzdes::EnzRepackMinimize , protocols::protein_interface_design::movers::PrepackMover , protocols::simple_moves::DesignRepackMover , protocols::simple_moves::symmetry::TaskAwareSymMinMover
• min_bb_set() : protocols::simple_moves::DesignRepackMover
• min_bb_set_ : protocols::simple_moves::DesignRepackMover
• min_bbrms() : protocols::loophash::LoopHashMoverWrapper
• min_bbrms_ : protocols::loophash::LoopHashMoverWrapper , protocols::loophash::LoopHashSampler
• min_bin_ : protocols::scoring::methods::saxs::PDDFEnergy
• 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_CA_CA_dis_ : protocols::features::strand_assembly::SandwichFeatures
• min_chi_ : protocols::make_rot_lib::RotData , protocols::simple_moves::symmetry::TaskAwareSymMinMover
• min_client_rank() : protocols::jd2::MPIFileBufJobDistributor
• min_client_rank_ : protocols::jd2::MPIFileBufJobDistributor
• 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_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::seeded_abinitio::SegmentHybridizer
• min_decoys_for_statistics_ : protocols::jd2::archive::NormalizedEvaluatedArchive
• min_dist() : protocols::noesy_assign::FragsToAtomDist::DistanceRecord
• min_dist_ : protocols::features::AtomAtomPairFeatures , protocols::noesy_assign::FragsToAtomDist::DistanceRecord
• min_dist_squared_ : protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker
• min_diversity_list_ : protocols::abinitio::IterativeBase
• min_env_energy_ : protocols::flxbb::InterlockAroma
• min_epsilon_ : protocols::make_rot_lib::RotData
• min_fast_loops_ : protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure
• min_frag_length_ : protocols::simple_moves::ClassicFragmentMover
• min_good_loops_ : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• min_heap() : protocols::cluster::Exemplar
• min_helix_length_ : protocols::fldsgn::filters::SecondaryStructureCountFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter
• 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_interface_ : protocols::antibody::design::AntibodyDesignMoverGenerator
• min_intra_ss_bbrms() : protocols::loophash::LoopHashDiversifier
• min_intra_ss_bbrms_ : protocols::loophash::LoopHashDiversifier
• 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::protein_interface_design::movers::LoopFinder , protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• min_lig_ : protocols::enzdes::EnzRepackMinimize
• 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_map : protocols::cartesian::MolecularDynamics , protocols::normalmode::NormalModeMultifunc
• min_map_ : protocols::md::CartesianMD , protocols::normalmode::NormalModeMultifunc
• min_move() : protocols::abinitio::FoldConstraints
• min_move_ : protocols::abinitio::FoldConstraints
• min_movemap_ : protocols::dna::DnaInterfacePacker
• min_mover_ : 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_nb_ : protocols::simple_moves::AddCavitiesMover
• min_neighbor_sc() : protocols::antibody::design::CDRGraftDesignOptions
• min_neighbor_sc_ : protocols::antibody::design::CDRGraftDesignOptions
• min_neighbors_ : protocols::match::NumNeighborsMPM
• 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_omega_ : protocols::make_rot_lib::RotData
• min_only : protocols::flexpep_docking::FlexPepDockingFlags
• min_options() : protocols::simple_moves::MinMover , protocols::simple_moves::SaneMinMover
• min_options_ : protocols::loop_modeling::refiners::MinimizationRefiner , protocols::loops::loop_mover::refine::ShearMinCCDTrial , protocols::simple_moves::MinMover , protocols::simple_moves::SaneMinMover
• min_overlap_ : protocols::simple_moves::ClassicFragmentMover
• min_params : protocols::relax::CentroidRelax::parameters
• min_per_residue_fa_attr_ : protocols::features::helixAssembly::HelixBundleFeatures
• min_primary_seq_distance_diff_for_electrostatic_interactions_ : protocols::features::strand_assembly::SandwichFeatures
• min_rb() : protocols::antibody::design::CDRGraftDesignOptions , protocols::simple_moves::DesignRepackMover
• min_rb_ : protocols::antibody::design::CDRGraftDesignOptions , protocols::enzdes::EnzRepackMinimize , protocols::simple_moves::DesignRepackMover , protocols::simple_moves::symmetry::TaskAwareSymMinMover
• min_rb_set() : protocols::simple_moves::DesignRepackMover
• min_rb_set_ : protocols::simple_moves::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_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_sc() : protocols::antibody::design::CDRGraftDesignOptions , protocols::simple_moves::DesignRepackMover
• min_sc_ : protocols::antibody::design::AntibodyDesignMoverGenerator , protocols::antibody::design::CDRGraftDesignOptions , protocols::enzdes::EnzRepackMinimize , protocols::simple_moves::DesignRepackMover
• min_sc_set() : protocols::simple_moves::DesignRepackMover
• min_sc_set_ : protocols::simple_moves::DesignRepackMover
• min_scorefxn : protocols::simple_moves::ShakeStructureMover
• min_scorefxn_ : protocols::hybridization::CartesianHybridize , protocols::seeded_abinitio::SegmentHybridizer
• min_sep_ : protocols::simple_moves::AddCavitiesMover
• min_sep_d2_from_upstream_atoms_ : protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder
• min_seq_sep() : protocols::simple_moves::AddConstraintsToCurrentConformationMover
• min_seq_sep_ : protocols::frag_picker::nonlocal::NonlocalFrags , protocols::simple_moves::AddConstraintsToCurrentConformationMover
• min_seq_separation_ : protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator
• min_seq_separation_residue_assignment() : protocols::noesy_assign::CrossPeak
• min_seqsep_ : protocols::simple_filters::ContactMapEvaluator
• 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_size_ : protocols::simple_moves::AddCavitiesMover
• min_structures_for_acceptance_statistics_ : protocols::jd2::archive::ArchiveBase
• min_threshold_ : protocols::antibody::LHRepulsiveRampLegacy
• 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 : protocols::relax::ClassicRelax , protocols::relax::RelaxProtocolBase , protocols::simple_moves::MinMover , protocols::stepwise::options::StepWiseBasicOptions
• min_type_ : 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::farna::RNA_Minimizer , protocols::helical_bundle::FitSimpleHelix , protocols::relax::RelaxProtocolBase , protocols::simple_moves::symmetry::TaskAwareSymMinMover , protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer , protocols::stepwise::options::StepWiseBasicOptions , protocols::symmetric_docking::SymDockingHiRes , protocols::ub_e2c::ubi_e2c_modeler
• 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_weight_ : protocols::optimize_weights::WeightRangeConstraint
• minfrac_ : protocols::mpi_refinement::WorkUnit_CombinePose
• minfrac_crossover_ : protocols::simple_moves::CombinePoseMover
• mingap_ : protocols::protein_interface_design::movers::LoopFinder
• mini_pose() : protocols::farna::ChunkSet
• mini_pose_list() : protocols::farna::BasePairStepLibrary
• mini_pose_list_ : protocols::farna::ChunkSet
• mini_pose_lists_ : protocols::farna::BasePairStepLibrary
• MinimalistFlexbbEdge() : protocols::flexpack::interaction_graph::MinimalistFlexbbEdge
• MinimalistFlexbbInteractionGraph() : protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph
• MinimalistFlexbbNode() : protocols::flexpack::interaction_graph::MinimalistFlexbbNode
• MinimalRotamer() : protocols::simple_moves::MinimalRotamer
• 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_type_ : protocols::antibody::H3RefineCCD
• MinimizationRefiner() : protocols::loop_modeling::refiners::MinimizationRefiner
• minimize() : protocols::analysis::PeptideDeriverFilter , protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• minimize_ : protocols::dna::DnaInterfacePacker , protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch , protocols::mpi_refinement::StructAvrgMover , protocols::simple_moves::CyclizationMover , protocols::simple_moves::PeptideStapleMover
• minimize_after_delete() : protocols::stepwise::monte_carlo::mover::DeleteMover
• minimize_after_delete_ : protocols::stepwise::monte_carlo::mover::DeleteMover
• minimize_all() : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• minimize_all_ : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• minimize_all_ligand_torsions_ : protocols::enzdes::EnzdesBaseProtocol
• 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() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• minimize_backbone() : protocols::ligand_docking::MoveMapBuilder
• minimize_backbone_ : protocols::ligand_docking::LigandDockProtocol
• minimize_base_step() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• 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_cats_ : protocols::enzdes::EnzdesFlexBBProtocol
• minimize_cdrs() : protocols::antibody::design::AntibodyDesignModeler
• minimize_conformation() : protocols::vip::VIP_Mover
• minimize_dna_ : protocols::motifs::MotifDnaPacker
• minimize_flexible_region() : protocols::enzdes::EnzdesFlexBBProtocol
• minimize_in_stages() : protocols::enzdes::EnzRepackMinimize
• minimize_in_stages_ : protocols::enzdes::EnzRepackMinimize
• minimize_interface() : protocols::antibody::design::AntibodyDesignModeler
• minimize_jump_ : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• minimize_ligand_ : protocols::ligand_docking::LigandArea , protocols::ligand_docking::LigandDockProtocol
• minimize_ligand_torsions_ : protocols::enzdes::EnzdesBaseProtocol
• minimize_no_bb() : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• minimize_only() : protocols::flexpep_docking::FlexPepDockingProtocol
• minimize_options_ : protocols::dna::DnaInterfacePacker
• minimize_prepend_res() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• minimize_prot_jumps_ : protocols::enzdes::EnzRepackMinimize
• minimize_rebuild() : protocols::simple_moves::CyclizationMover
• minimize_region() : protocols::enzdes::EnzdesFlexibleRegion
• minimize_res_ : protocols::stepwise::monte_carlo::mover::TransientCutpointHandler
• minimize_rotamer() : protocols::make_rot_lib::MakeRotLibMover
• minimize_scorefxn_ : protocols::stepwise::modeler::StepWiseMinimizer
• 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::StepWiseMonteCarlo
• minimize_single_res_frequency() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• minimize_single_res_frequency_ : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• minimize_structure_ : protocols::farna::RNA_DeNovoProtocol
• minimize_sugar() : protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSampler
• minimize_sugar_sets_legacy() : protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator
• minimize_tensors_fix_from_PCS_data() : protocols::scoring::methods::pcs2::PcsEnergy
• minimize_tensors_from_PCS_data() : protocols::scoring::methods::pcs2::PcsEnergy , protocols::scoring::methods::pcs::PCS_Energy , protocols::scoring::methods::pcsTs1::PCS_Energy_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_Ts4
• minimize_tensors_from_PCS_data_with_svd() : protocols::scoring::methods::pcs2::PcsEnergy
• minimize_toward_stub() : protocols::protein_interface_design::movers::PlaceOnLoop
• minimize_toward_stub_ : protocols::protein_interface_design::movers::PlaceOnLoop
• minimize_trial_ : protocols::docking::DockMinMover
• minimize_water_ : protocols::ligand_docking::LigandDockProtocol , protocols::ligand_docking::MoveMapBuilder
• minimize_with_constraints() : protocols::ddg::ddGMover , protocols::simple_moves::ShakeStructureMover , protocols::simple_moves::symmetry::SymShakeStructureMover
• MinimizeBackbone() : protocols::ligand_docking::MinimizeBackbone
• minimized_pose_list() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer
• minimized_pose_list_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer
• MinimizeHotspots() : protocols::protein_interface_design::movers::MapHotspot
• MinimizeLigand() : protocols::ligand_docking::MinimizeLigand
• minimizer() : protocols::loops::loop_mover::refine::ShearMinCCDTrial , protocols::loops::loop_mover::refine::SmallMinCCDTrial
• minimizer_ : protocols::electron_density::BfactorFittingMover , 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 , protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• minimizer_dofs_after_minimization_ : protocols::optimize_weights::IterativeOptEDriver
• minimizer_dofs_before_minimization_ : protocols::optimize_weights::IterativeOptEDriver
• minimizer_dofs_mixed_ : protocols::optimize_weights::IterativeOptEDriver
• minimizer_options() : protocols::loops::loop_mover::refine::SmallMinCCDTrial
• minimizer_options_ : protocols::loops::loop_mover::refine::SmallMinCCDTrial , protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler , 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_ : protocols::farna::RNA_DeNovoProtocol
• MinimizerOptionsCOP : protocols::normalmode::NormalModeMinimizer , protocols::simple_moves::MinMover
• MinimizerOptionsOP : protocols::normalmode::NormalModeMinimizer , protocols::simple_moves::MinMover
• MinimizeStoredRBConfs() : protocols::enzdes::MinimizeStoredRBConfs
• minimum_peak_intensity() : protocols::noesy_assign::PeakFileFormat_Base
• minimum_peak_intensity_ : protocols::noesy_assign::PeakFileFormat_Base
• minimum_width_ : protocols::cluster::EnsembleConstraints_Simple
• miniPose_ : protocols::jumping::ResiduePairJump
• MiniRelax() : protocols::relax::MiniRelax
• minlen : protocols::hybridization::TMalign
• MinMover() : protocols::simple_moves::MinMover
• minmover_ : protocols::docking::SidechainMinMover , protocols::simple_moves::TaskAwareMinMover , protocols::symmetric_docking::SymSidechainMinMover
• minoption_ : protocols::normalmode::NormalModeRelaxMover
• MinPackMover() : protocols::simple_moves::MinPackMover
• minPockSize_ : protocols::pockets::PocketGrid
• mintype() : protocols::antibody::design::CDRGraftDesignOptions , protocols::grafting::AnchoredGraftMover
• mintype_ : protocols::antibody::design::CDRGraftDesignOptions , protocols::grafting::AnchoredGraftMover
• minX : protocols::pockets::CCluster , protocols::pockets::PCluster
• minY : protocols::pockets::CCluster , protocols::pockets::PCluster
• minZ : protocols::pockets::CCluster , protocols::pockets::PCluster
• missing_in_pose() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters , protocols::toolbox::match_enzdes_util::EnzdesCstParamCache
• missing_pt_ : protocols::pockets::DarcParticleSwarmMinimizer , protocols::pockets::FingerprintMultifunc
• missing_weight_ : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• missing_weight_interval_ : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• MissingDensityToJumpMover() : protocols::simple_moves::MissingDensityToJumpMover
• mixing_factor_ : protocols::optimize_weights::IterativeOptEDriver
• mkdir_pred() : protocols::sparta::Sparta::SpartaLib
• mm : protocols::cartesian::MolecularDynamics , protocols::protein_interface_design::movers::PrepackMover
• mm_ : protocols::cryst::SetCrystWeightMover , protocols::frags::TorsionFragmentMover , protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionSampler , protocols::normalmode::NormalModeRelaxMover , protocols::protein_interface_design::movers::PrepackMover , protocols::seeded_abinitio::SegmentHybridizer , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer
• mm_bondangle_library_ : protocols::branch_angle::BranchAngleOptimizer
• mman_ : protocols::simple_filters::MotifScoreFilter
• mmt_ : protocols::simple_moves::TorsionDOFMover
• mobile_label_ : protocols::rigid::UniformRigidBodyCM
• mobile_residues_ : protocols::environment::CoMTrackerCM
• mobile_selector_ : protocols::environment::CoMTrackerCM
• mod_segment_prod_ : protocols::fldsgn::MatchResidues
• mode() : protocols::matdes::SymUnsatHbondFilter , protocols::normalmode::NormalMode
• Mode : protocols::protein_interface_design::filters::AtomicContactCountFilter
• mode() : protocols::rosetta_scripts::ParsedProtocol , protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::toolbox::task_operations::StoreCompoundTaskMover
• mode1_1_packertask() : protocols::forge::remodel::RemodelDesignMover
• mode1_packertask() : protocols::forge::remodel::RemodelDesignMover
• mode2_packertask() : protocols::forge::remodel::RemodelDesignMover
• mode3_packertask() : protocols::forge::remodel::RemodelDesignMover
• mode4_packertask() : protocols::forge::remodel::RemodelDesignMover
• mode5_packertask() : protocols::forge::remodel::RemodelDesignMover
• mode6_packertask() : protocols::forge::remodel::RemodelDesignMover
• mode_ : protocols::enzdes::ValueEvaluator , protocols::ligand_docking::ComputeLigandRDF , protocols::matdes::SymUnsatHbondFilter , protocols::moves::MonteCarloUtil , protocols::normalmode::NormalMode , protocols::pose_reporters::RMSDReporter , protocols::rbsegment_relax::MakeStarTopologyMover , protocols::rosetta_scripts::ParsedProtocol , protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::toolbox::task_operations::SelectBySASAOperation , protocols::toolbox::task_operations::StoreCompoundTaskMover
• MODE_all_atom_rmsd : protocols::pose_reporters::RMSDReporter
• MODE_CA_rmsd : protocols::pose_reporters::RMSDReporter
• MODE_NONE : protocols::pose_reporters::RMSDReporter
• mode_scale_ : protocols::normalmode::NormalModeRelaxMover
• mode_using_ : protocols::normalmode::NormalModeRelaxMover
• Model : protocols::abinitio::PairingStatEntry , protocols::abinitio::PairingStatistics
• model_and_remove_capping_residues_ : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• model_cdrs_ : protocols::antibody::design::AntibodyDesignModeler , protocols::antibody::design::AntibodyDesignMoverGenerator
• model_count : protocols::boinc::BoincSharedMemory , protocols::canonical_sampling::TrajectoryRecorder
• model_count_ : protocols::canonical_sampling::TrajectoryRecorder
• model_h3() : protocols::antibody_legacy::CDRH3Modeler
• model_h3_ : protocols::antibody::AntibodyModelerProtocol , protocols::antibody_legacy::AntibodyModeler
• 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_post_design() : protocols::antibody::design::AntibodyDesignMover
• model_post_graft() : protocols::antibody::design::AntibodyDesignMover
• model_tag() : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• model_tag_ : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• model_weight_ : protocols::abinitio::PairingStatistics
• ModelCDRH3() : protocols::antibody::ModelCDRH3
• modeler_ : protocols::antibody::design::AntibodyDesignMover , protocols::antibody::design::AntibodyGraftDesignMover , protocols::antibody::design::AntibodySeqDesignMover
• modeler_scorefxn_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection
• modeler_sugar() : protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator
• modeler_sugar_at_chain_break() : protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator
• ModelFreq : protocols::abinitio::PairingStatistics
• ModelList : protocols::abinitio::PairingStatEntry
• models() : protocols::abinitio::PairingStatEntry
• models_ : protocols::abinitio::PairingStatEntry
• models_per_file_ : protocols::contact_map::ContactMap
• ModelWeight : protocols::abinitio::PairingStatistics
• modes_using_ : protocols::normalmode::NormalModeMinimizer , protocols::normalmode::NormalModeMultifunc
• modifiable() : protocols::moves::ResId
• modifiable_ : protocols::moves::ResId
• Modified2Original : protocols::forge::build::BuildManager
• modified2original_interval_endpoints() : protocols::forge::build::BuildManager
• modified2original_intervals() : protocols::forge::build::BuildManager
• modified_i2p_defined() : protocols::forge::build::BuildManager
• modified_i2p_new() : protocols::forge::build::BuildManager
• modified_i2p_preexisting() : protocols::forge::build::BuildManager
• modified_i2p_undefined() : protocols::forge::build::BuildManager
• modified_interval2movemap() : protocols::forge::build::BuildManager
• modified_match_positions() : protocols::match::AddAllPositionsMPM , protocols::match::BfactorMPM , protocols::match::MatchPositionModifier , protocols::match::NumNeighborsMPM , protocols::match::RemoveNorCTermMPM , protocols::match::SecondaryStructureMPM , protocols::match::TaskOperationMPM
• modified_task() : protocols::enzdes::EnzdesFlexBBProtocol
• modify() : protocols::forge::build::BuildInstruction , protocols::forge::build::BuildManager
• modify_after_jump() : protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• modify_after_jump_ : protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• modify_before_jump() : protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• modify_before_jump_ : protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• modify_impl() : protocols::forge::build::Bridge , protocols::forge::build::BuildInstruction , protocols::forge::build::ConnectRight , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::forge::build::RelativeConnectRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap
• modify_pose_build_resids_from_endes_input() : protocols::match::MatcherTask
• modify_relative_filters_pdb_names() : protocols::simple_filters::Operator
• modify_unselected_residues() : protocols::toolbox::task_operations::SelectResiduesWithinChainOperation
• modify_unselected_residues_ : protocols::toolbox::task_operations::SelectResiduesWithinChainOperation
• modify_was_successful() : protocols::forge::build::BuildInstruction
• modify_was_successful_ : protocols::forge::build::BuildManager
• ModifyAnnealer() : protocols::toolbox::task_operations::ModifyAnnealer
• ModifyStoredRBConfs() : protocols::enzdes::ModifyStoredRBConfs
• ModifyVariantTypeMover() : protocols::simple_moves::ModifyVariantTypeMover
• MolarMassFilter() : protocols::ligand_docking::MolarMassFilter
• MolecularDynamics() : protocols::cartesian::MolecularDynamics
• MolecularMassFilter() : protocols::ligand_docking::MolecularMassFilter
• MolecularWeightNormalization() : protocols::qsar::scoring_grid::MolecularWeightNormalization
• molName : protocols::pockets::SmallMol
• moltenres_2_flexseg_ : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• moltenres_2_resid() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• moltenres_2_resid_ : protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::flexpack::rotamer_set::FlexbbRotamerSets
• moltenres_for_rotamer() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• moltenres_for_rotamer_ : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• moltenres_part_of_flexsegment() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• moltenres_rotid_2_rotid() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• 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
• monte_carlo_ : protocols::canonical_sampling::MetropolisHastingsMover , protocols::canonical_sampling::TemperatureController , protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::RNA_DeNovoProtocol , protocols::loop_modeling::LoopProtocol , protocols::loop_modeling::utilities::AcceptanceCheck , protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::FullatomRelaxMover
• monte_carlo_cycles_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::RNA_DeNovoProtocol
• monte_carlo_cycles_max_default_ : protocols::farna::RNA_DeNovoProtocol
• MonteCarlo : protocols::forge::remodel::RemodelLoopMover , protocols::moves::MonteCarlo
• MonteCarloLoader() : protocols::jd2::parser::MonteCarloLoader
• MonteCarloRecover() : protocols::simple_moves::MonteCarloRecover
• MonteCarloReset() : protocols::simple_moves::MonteCarloReset
• MonteCarloTest() : protocols::simple_moves::MonteCarloTest
• MonteCarloUtil() : protocols::moves::MonteCarloUtil
• most_probable_bin() : protocols::frag_picker::quota::ABEGO_SS_Config
• Motif() : protocols::motifs::Motif
• motif_cuts : protocols::simple_filters::SymmetricMotifFilter
• 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_library() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• motif_library_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• motif_match_results_ : protocols::motif_grafting::movers::MotifGraftMover
• motif_search_ : protocols::enzdes::AddLigandMotifRotamers , protocols::motifs::MotifDnaPacker
• motif_sets_ : protocols::matdes::SchemePlaceMotifsMover
• motif_source_ : protocols::motifs::IRCollection
• motifAtomIDs : protocols::motifs::Motif
• motifcop() : protocols::motifs::MotifHit
• motifcop_ : protocols::motifs::MotifHit
• MotifDnaPacker() : protocols::motifs::MotifDnaPacker
• MotifGraftMover() : protocols::motif_grafting::movers::MotifGraftMover
• MotifHashRigidScore() : protocols::sic_dock::scores::MotifHashRigidScore
• motifHigh : protocols::motif_grafting::movers::motif2scaffold_indexes
• MotifHit() : protocols::motifs::MotifHit
• MotifLibrary() : protocols::motifs::MotifLibrary
• motifLow : protocols::motif_grafting::movers::motif2scaffold_indexes
• MotifMatch() : protocols::motif_grafting::movers::MotifMatch
• MotifScoreFilter() : protocols::simple_filters::MotifScoreFilter
• MotifSearch() : protocols::motifs::MotifSearch
• movable_ : protocols::nonlocal::BiasedFragmentMover , protocols::nonlocal::Chunk , protocols::nonlocal::SingleFragmentMover
• movable_jumps() : protocols::docking::DockingHighRes , protocols::docking::DockingProtocol , protocols::docking::DockMCMCycle , protocols::docking::RigidBodyInfo , protocols::docking::TemperedDocking , protocols::toolbox::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::symmetric_docking::SymDockProtocol , protocols::toolbox::task_operations::InterfaceTaskOperation
• move_ : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• move_all_inserted() : protocols::abinitio::MembraneAbinitio
• move_atoms_to_collcheck_begin() : protocols::toolbox::match_enzdes_util::LigandConformer
• move_distance : protocols::ligand_docking::Transform_info
• move_element() : protocols::stepwise::monte_carlo::SWA_Move
• move_element_ : protocols::stepwise::monte_carlo::SWA_Move
• move_first_rigid_body_ : protocols::farna::RNA_DeNovoProtocol , protocols::farna::RNA_Minimizer
• move_forward_to_next_model() : protocols::stepwise::setup::StepWiseMonteCarloJobDistributor
• 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_to_desired_centroid() : protocols::ligand_docking::LigandBaseProtocol
• move_map() : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::simple_moves::SaneMinMover
• move_map_ : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::simple_moves::CyclizationMover , protocols::simple_moves::RandomOmegaFlipMover , protocols::simple_moves::RandomTorsionMover , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer , protocols::surface_docking::FullatomRelaxMover
• move_pose_to_standard_orie() : protocols::pockets::PocketGrid
• move_side_chain() : protocols::stepwise::modeler::StepWiseMinimizer
• move_spans() : protocols::topology_broker::TMHTopologySamplerClaimer
• move_takeoff_torsions_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer
• move_type() : protocols::stepwise::monte_carlo::SWA_Move
• move_type_ : protocols::stepwise::monte_carlo::SWA_Move
• MoveBeforeFilter() : protocols::filters::MoveBeforeFilter
• moved_ : protocols::md::Rattle
• moveFromStubFrame() : protocols::hotspot_hashing::StubGenerator
• moveIntoStubFrame() : protocols::hotspot_hashing::StubGenerator
• movemap() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::KinematicControl , protocols::abinitio::MembraneAbinitio
• MoveMap : protocols::fldsgn::CircularPermutation , protocols::forge::build::Bridge
• movemap() : protocols::forge::build::Bridge
• MoveMap : protocols::forge::build::BuildInstruction
• movemap() : protocols::forge::build::BuildInstruction
• MoveMap : protocols::forge::build::BuildManager
• movemap() : protocols::forge::build::BuildManager , protocols::forge::build::ConnectRight
• MoveMap : protocols::forge::build::ConnectRight , protocols::forge::build::GrowLeft
• movemap() : protocols::forge::build::GrowLeft
• MoveMap : protocols::forge::build::GrowRight
• movemap() : protocols::forge::build::GrowRight
• MoveMap : protocols::forge::build::RelativeConnectRight
• movemap() : protocols::forge::build::SegmentInsert
• MoveMap : protocols::forge::build::SegmentInsert
• movemap() : protocols::forge::build::SegmentRebuild
• MoveMap : protocols::forge::build::SegmentRebuild
• movemap() : protocols::forge::build::SegmentSwap
• MoveMap : protocols::forge::build::SegmentSwap , protocols::forge::components::VarLengthBuild , protocols::forge::remodel::RemodelAccumulator , protocols::forge::remodel::RemodelDesignMover , protocols::forge::remodel::RemodelGlobalFrame , 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::CartesianMD , protocols::md::MDBase , protocols::moves::MoveMapMover , protocols::moves::NullMover , protocols::simple_moves::BackboneMover , protocols::simple_moves::BBGaussianMover , protocols::simple_moves::FragmentMover , protocols::simple_moves::MinMover , protocols::simple_moves::RingConformationMover
• movemap_ : protocols::abinitio::abscript::AbscriptLoopCloserCM , protocols::abinitio::ClassicAbinitio , protocols::abinitio::KinematicControl , protocols::abinitio::MembraneAbinitio , protocols::antibody::CloseOneCDRLoop , protocols::antibody::LHRepulsiveRamp , 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::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::kinematic_closure::KinematicPerturber , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::md::MDBase , protocols::normalmode::NormalModeMinimizer , protocols::rbsegment_relax::AutoRBMover , protocols::rbsegment_relax::CCDMoveWrapper , protocols::relax::CentroidRelax , protocols::relax::RelaxProtocolBase , protocols::seeded_abinitio::SeedSetupMover , protocols::simple_moves::BackboneMover , protocols::simple_moves::BBGaussianMover , protocols::simple_moves::DisulfideInsertionMover , protocols::simple_moves::FragmentMover , protocols::simple_moves::MinMover , protocols::simple_moves::RingConformationMover , protocols::simple_moves::SaneMinMover , protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockingLowRes , protocols::symmetric_docking::SymSidechainMinMover , protocols::toolbox::task_operations::RestrictToMoveMapChiOperation , protocols::topology_broker::FragmentClaimer
• movemap_as_OP() : protocols::forge::build::BuildManager
• movemap_builder_ : protocols::ligand_docking::FinalMinimizer , protocols::ligand_docking::HighResDocker
• 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_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_from_blueprint() : protocols::flxbb::FlxbbDesign
• movemap_from_blueprint_ : protocols::flxbb::FlxbbDesign
• movemap_lesstail_ : protocols::floppy_tail::FloppyTailMover
• movemap_minimizer_ : protocols::flexpep_docking::FlexPepDockingProtocol
• movemap_ptr() : protocols::abinitio::KinematicControl
• movemap_reset_ : protocols::docking::DockMCMProtocol
• movemap_set_ : protocols::toolbox::task_operations::RestrictToMoveMapChiOperation
• movemap_tag_ : protocols::relax::FastRelax
• MoveMapBuilder() : protocols::ligand_docking::MoveMapBuilder
• MoveMapBuilderLoader() : protocols::ligand_docking::MoveMapBuilderLoader
• MoveMapMover() : protocols::moves::MoveMapMover
• MoveMapOP : protocols::fldsgn::CircularPermutation , protocols::flxbb::FlxbbDesign , protocols::forge::build::BuildManager , protocols::jd2::parser::BluePrint , protocols::loops::loop_mover::LoopMover , protocols::nonlocal::Chunk , protocols::nonlocal::SingleFragmentMover
• MovePoseToMembraneCenterMover() : protocols::rigid::MovePoseToMembraneCenterMover
• mover() : protocols::abinitio::abscript::FragmentCM , protocols::abinitio::FragmentSampler , protocols::antibody::design::AntibodyDesignMoverGenerator
• Mover : protocols::fldsgn::MatchResidues , protocols::fldsgn::MatchResiduesMover
• mover() : protocols::flxbb::DesignTask
• Mover : protocols::jd2::Parser , protocols::moves::Mover
• mover() : protocols::moves::MoverApplyingMover , protocols::moves::TrialMover
• Mover : protocols::nonlocal::SingleFragmentMover
• mover() : protocols::simple_moves::ChangeAndResetFoldTreeMover , protocols::simple_moves::ContingentAcceptMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::rational_mc::RationalMonteCarlo , protocols::topology_broker::FragmentClaimer , protocols::topology_broker::TopologyBroker
• mover_ : protocols::abinitio::abscript::FragmentCM , protocols::antibody::design::AntibodyDesignMoverGenerator , protocols::comparative_modeling::RecoverSideChainsMover , protocols::enzdes::RemoveLigandFilter , protocols::flxbb::DesignTask , protocols::loop_modeling::samplers::LegacyKicSampler , protocols::loops::loop_mover::LoopCM , 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::rotamer_recovery::RRProtocolMover , protocols::simple_moves::ContingentAcceptMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::rational_mc::RationalMonteCarlo , protocols::topology_broker::FragmentClaimer
• mover_by_index() : protocols::canonical_sampling::MetropolisHastingsMover
• mover_creator_map_ : protocols::moves::MoverFactory
• mover_cycles_ : protocols::loop_modeling::LoopProtocol
• mover_generator_ : protocols::antibody::design::AntibodyGraftDesignMover
• mover_list_ : protocols::wum::MoverList
• Mover_LoopHashRefine() : protocols::loophash::Mover_LoopHashRefine
• mover_mc_trial_count : protocols::boinc::BoincSharedMemory
• mover_name() : protocols::abinitio::abscript::AbscriptLoopCloserCMCreator , protocols::abinitio::abscript::AbscriptMoverCreator , protocols::abinitio::abscript::ConstraintPreparerCreator , protocols::abinitio::abscript::FragmentCMCreator , protocols::abinitio::abscript::FragmentJumpCMCreator , protocols::abinitio::abscript::RigidChunkCMCreator , protocols::abinitio::abscript::StructPerturberCMCreator , protocols::abinitio::DomainAssemblyCreator , protocols::analysis::InterfaceAnalyzerMoverCreator , protocols::backrub::BackrubMoverCreator , protocols::backrub::BackrubSidechainMoverCreator , protocols::canonical_sampling::DbTrajectoryRecorderCreator , protocols::canonical_sampling::HamiltonianExchangeCreator , protocols::canonical_sampling::MetricRecorderCreator , protocols::canonical_sampling::MetropolisHastingsMoverCreator , protocols::canonical_sampling::ParallelTemperingCreator , protocols::canonical_sampling::PDBTrajectoryRecorderCreator , protocols::canonical_sampling::ProgressBarObserverCreator , protocols::canonical_sampling::SidechainMetropolisHastingsMoverCreator , protocols::canonical_sampling::SilentTrajectoryRecorderCreator , protocols::canonical_sampling::SimulatedTemperingCreator , protocols::canonical_sampling::TrialCounterObserverCreator , protocols::comparative_modeling::LoopRelaxMoverCreator , protocols::contact_map::ContactMapCreator , protocols::cryst::FitBfactorsMoverCreator , protocols::cryst::LoadDensityMapMoverCreator , protocols::cryst::RecomputeDensityMapMoverCreator , protocols::cryst::SetCrystWeightMoverCreator , protocols::cryst::SetRefinementOptionsMoverCreator , protocols::cryst::TagPoseWithRefinementStatsMoverCreator , protocols::cryst::UpdateSolventMoverCreator , protocols::cyclic_peptide::CreateAngleConstraintCreator , protocols::cyclic_peptide::CreateDistanceConstraintCreator , protocols::cyclic_peptide::CreateTorsionConstraintCreator , protocols::cyclic_peptide::DeclareBondCreator , protocols::cyclic_peptide::PeptideStubMoverCreator , protocols::design_opt::GreedyOptMutationMoverCreator , protocols::design_opt::ParetoOptMutationMoverCreator , protocols::dna::DesignProteinBackboneAroundDNACreator , protocols::dna::DnaInterfaceMinMoverCreator , protocols::dna::DnaInterfaceMultiStateDesignCreator , protocols::dna::DnaInterfacePackerCreator , protocols::dna::SeparateDnaFromNonDnaCreator , protocols::docking::ConformerSwitchMoverCreator , protocols::docking::DockingInitialPerturbationCreator , protocols::docking::DockingProtocolCreator , protocols::docking::DockSetupMoverCreator , protocols::docking::membrane::MPDockingMoverCreator , protocols::docking::membrane::MPDockingSetupMoverCreator , protocols::docking::TemperedDockingCreator , protocols::electron_density::BfactorFittingMoverCreator , protocols::electron_density::DensityMorphingMoverCreator , protocols::electron_density::ReportFSCCreator , protocols::electron_density::ScaleMapIntensitiesCreator , protocols::electron_density::SetupForDensityScoringMoverCreator , protocols::environment::CoMTrackerCMCreator , protocols::environment::EnvMoverCreator , protocols::environment::ScriptCMCreator , protocols::enzdes::AddOrRemoveMatchCstsCreator , protocols::enzdes::BackboneSamplerCreator , protocols::enzdes::EnzRepackMinimizeCreator , protocols::enzdes::PackRotamersMoverPartGreedyCreator , protocols::enzdes::PredesignPerturbMoverCreator , protocols::enzdes::UpdateEnzdesHeaderMoverCreator , protocols::features::ReportToDBCreator , protocols::features::TrajectoryReportToDBCreator , protocols::fldsgn::BluePrintBDRCreator , protocols::fldsgn::CircularPermutationCreator , protocols::fldsgn::potentials::SetAACompositionPotentialCreator , protocols::fldsgn::potentials::SetSecStructEnergiesCreator , protocols::fldsgn::SheetCstGeneratorCreator , protocols::flexpep_docking::FlexPepDockingProtocolCreator , protocols::flxbb::FlxbbDesignCreator , protocols::flxbb::InterlockAromaCreator , protocols::forge::constraints::ConstraintFileCstGeneratorCreator , protocols::forge::constraints::InverseRotamersCstGeneratorCreator , protocols::forge::constraints::InvrotTreeCstGeneratorCreator , protocols::forge::constraints::NtoCCstGeneratorCreator , protocols::forge::constraints::RemoveCstsCreator , protocols::forge::remodel::RemodelMoverCreator , protocols::forge::remodel::ResidueVicinityCstGeneratorCreator , protocols::generalized_kinematic_closure::GeneralizedKICCreator , protocols::grafting::AnchoredGraftMoverCreator , protocols::grafting::CCDEndsGraftMoverCreator , protocols::grafting::simple_movers::DeleteRegionMoverCreator , protocols::grafting::simple_movers::InsertPoseIntoPoseMoverCreator , protocols::grafting::simple_movers::KeepRegionMoverCreator , protocols::grafting::simple_movers::ReplaceRegionMoverCreator , protocols::helical_bundle::BundleGridSamplerCreator , protocols::helical_bundle::FitSimpleHelixCreator , protocols::helical_bundle::MakeBundleCreator , protocols::helical_bundle::MakeBundleHelixCreator , protocols::helical_bundle::PerturbBundleCreator , protocols::helical_bundle::PerturbBundleHelixCreator , protocols::hotspot_hashing::movers::PlaceSurfaceProbeCreator , protocols::hybridization::BackboneTorsionPerturbationCreator , protocols::hybridization::BackboneTorsionSamplerCreator , protocols::hybridization::CartesianHybridizeCreator , protocols::hybridization::CartesianSamplerCreator , protocols::hybridization::FoldTreeHybridizeCreator , protocols::hybridization::HybridizeProtocolCreator , protocols::hybridization::HybridizeSetupMoverCreator , protocols::idealize::IdealizeMoverCreator , protocols::ligand_docking::AddHydrogensCreator , protocols::ligand_docking::CompoundTranslateCreator , protocols::ligand_docking::ComputeLigandRDFCreator , protocols::ligand_docking::FinalMinimizerCreator , protocols::ligand_docking::GrowLigandCreator , protocols::ligand_docking::HighResDockerCreator , protocols::ligand_docking::InterfaceScoreCalculatorCreator , protocols::ligand_docking::LigandDesignCreator , protocols::ligand_docking::MinimizeBackboneCreator , protocols::ligand_docking::RandomConformersCreator , protocols::ligand_docking::RotateCreator , protocols::ligand_docking::RotatesCreator , protocols::ligand_docking::SlideTogetherCreator , protocols::ligand_docking::StartFromCreator , protocols::ligand_docking::TransformCreator , protocols::ligand_docking::TranslateCreator , protocols::ligand_docking::WriteLigandMolFileCreator , protocols::loophash::LoopHashDiversifierCreator , protocols::loophash::LoopHashMoverWrapperCreator , protocols::loops::FoldTreeFromLoopsCreator , protocols::loops::loop_closure::ccd::CCDLoopClosureMoverCreator , protocols::loops::loop_mover::LoopCMCreator , protocols::match::MatcherMoverCreator , protocols::matdes::ExtractSubposeMoverCreator , protocols::matdes::MatDesGreedyOptMutationMoverCreator , protocols::matdes::SchemePlaceMotifsMoverCreator , protocols::matdes::SymDofMoverCreator , protocols::md::CartesianMDCreator , protocols::membrane::AddMembraneMoverCreator , protocols::membrane::FlipMoverCreator , protocols::membrane::MembranePositionFromTopologyMoverCreator , protocols::membrane::RotationMoverCreator , protocols::membrane::SetMembraneCenterMoverCreator , protocols::membrane::SetMembraneNormalMoverCreator , protocols::membrane::SetMembranePositionMoverCreator , protocols::membrane::symmetry::SymmetricAddMembraneMoverCreator , protocols::membrane::TransformIntoMembraneMoverCreator , protocols::membrane::TranslationMoverCreator , protocols::membrane::TranslationRotationMoverCreator , protocols::membrane::visualize::VisualizeEmbeddingMoverCreator , protocols::membrane::visualize::VisualizeMembraneMoverCreator , protocols::motif_grafting::movers::MotifGraftCreator , protocols::motifs::MotifDnaPackerCreator , protocols::moves::DsspMoverCreator , protocols::moves::IfMoverCreator , protocols::moves::IteratedConvergenceMoverCreator , protocols::moves::PyMolMoverCreator , protocols::moves::RampingMoverCreator , protocols::moves::RandomMoverCreator , protocols::ncbb::NcbbDockDesignProtocolCreator , protocols::ncbb::oop::OopCreatorMoverCreator , protocols::ncbb::oop::OopDockDesignProtocolCreator , protocols::nonlocal::SingleFragmentMoverCreator , protocols::normalmode::NormalModeMinimizerCreator , protocols::pb_potential::SetupPoissonBoltzmannPotentialCreator , protocols::protein_interface_design::movers::AddChainBreakCreator , protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspotsCreator , protocols::protein_interface_design::movers::BackrubDDMoverCreator , protocols::protein_interface_design::movers::BestHotspotCstMoverCreator , protocols::protein_interface_design::movers::BuildAlaPoseCreator , protocols::protein_interface_design::movers::DesignMinimizeHbondsCreator , protocols::protein_interface_design::movers::DisulfideMoverCreator , protocols::protein_interface_design::movers::DockAndRetrieveSidechainsCreator , protocols::protein_interface_design::movers::DockWithHotspotMoverCreator , protocols::protein_interface_design::movers::FavorNativeResiduePreCycleCreator , protocols::protein_interface_design::movers::FavorNonNativeResiduePreCycleCreator , protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMoverCreator , protocols::protein_interface_design::movers::HotspotHasherMoverCreator , protocols::protein_interface_design::movers::InterfaceRecapitulationMoverCreator , protocols::protein_interface_design::movers::LoopFinderCreator , protocols::protein_interface_design::movers::LoopLengthChangeCreator , protocols::protein_interface_design::movers::LoopMoverFromCommandLineCreator , protocols::protein_interface_design::movers::LoopOverCreator , protocols::protein_interface_design::movers::LoopRemodelCreator , protocols::protein_interface_design::movers::MapHotspotCreator , protocols::protein_interface_design::movers::PatchdockTransformCreator , protocols::protein_interface_design::movers::PeptideStapleDesignMoverCreator , protocols::protein_interface_design::movers::PlacementAuctionMoverCreator , protocols::protein_interface_design::movers::PlacementMinimizationMoverCreator , protocols::protein_interface_design::movers::PlaceOnLoopCreator , protocols::protein_interface_design::movers::PlaceSimultaneouslyMoverCreator , protocols::protein_interface_design::movers::PlaceStubMoverCreator , protocols::protein_interface_design::movers::PrepackMoverCreator , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMoverCreator , protocols::protein_interface_design::movers::RandomMutationCreator , protocols::protein_interface_design::movers::RepackMinimizeCreator , protocols::protein_interface_design::movers::SaveAndRetrieveSidechainsCreator , protocols::protein_interface_design::movers::SetAtomTreeCreator , protocols::protein_interface_design::movers::SetTemperatureFactorCreator , protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMoverCreator , protocols::protein_interface_design::movers::SetupHotspotConstraintsMoverCreator , protocols::protein_interface_design::movers::ShoveResidueMoverCreator , protocols::protein_interface_design::movers::SpinMoverCreator , protocols::protein_interface_design::movers::SubroutineMoverCreator , protocols::protein_interface_design::movers::TaskAwareCstsCreator , protocols::protein_interface_design::movers::TopologyBrokerMoverCreator , protocols::protein_interface_design::movers::TryRotamersCreator , protocols::protein_interface_design::movers::VLBCreator , protocols::qsar::qsarCreator , protocols::qsar::RenderGridsToKinemageCreator , protocols::qsar::scoring_grid::GridInitMoverCreator , protocols::rbsegment_relax::IdealizeHelicesMoverCreator , protocols::rbsegment_relax::MakeStarTopologyMoverCreator , protocols::rbsegment_relax::OptimizeThreadingMoverCreator , protocols::relax::AtomCoordinateCstMoverCreator , protocols::relax::ClassicRelaxCreator , protocols::relax::FastRelaxCreator , protocols::relax::membrane::MPFastRelaxMoverCreator , protocols::rigid::RigidBodyPerturbNoCenterMoverCreator , protocols::rigid::RigidBodyTransMoverCreator , protocols::rigid::RollMoverCreator , protocols::rigid::UniformRigidBodyCMCreator , protocols::rigid::UniformRigidBodyMoverCreator , protocols::rosetta_scripts::AdditionalOutputWrapperCreator , protocols::rosetta_scripts::MultipleOutputWrapperCreator , protocols::rosetta_scripts::MultiplePoseMoverCreator , protocols::rosetta_scripts::ParsedProtocolCreator , protocols::rosetta_scripts::SavePoseMoverCreator , protocols::rotamer_recovery::RotamerRecoveryMoverCreator , protocols::seeded_abinitio::CAcstGeneratorCreator , protocols::seeded_abinitio::CloseFoldCreator , protocols::seeded_abinitio::CoordinateCstCreator , protocols::seeded_abinitio::DefineMovableLoopsCreator , protocols::seeded_abinitio::GrowPeptidesCreator , protocols::seeded_abinitio::SeedFoldTreeCreator , protocols::seeded_abinitio::SeedSetupMoverCreator , protocols::seeded_abinitio::SegmentHybridizerCreator , protocols::seeded_abinitio::SwapSegmentCreator , protocols::simple_moves::AddChainMoverCreator , protocols::simple_moves::AddConstraintsToCurrentConformationMoverCreator , protocols::simple_moves::AddJobPairDataCreator , protocols::simple_moves::AlignChainMoverCreator , protocols::simple_moves::BBGaussianMoverCreator , protocols::simple_moves::bin_transitions::InitializeByBinsCreator , protocols::simple_moves::bin_transitions::PerturbByBinsCreator , protocols::simple_moves::BoltzmannRotamerMoverCreator , protocols::simple_moves::ChangeAndResetFoldTreeMoverCreator , protocols::simple_moves::ClearConstraintsMoverCreator , protocols::simple_moves::ConsensusDesignMoverCreator , protocols::simple_moves::ConstraintSetMoverCreator , protocols::simple_moves::ContingentAcceptMoverCreator , protocols::simple_moves::CoupledMoverCreator , protocols::simple_moves::CutChainMoverCreator , protocols::simple_moves::ddGCreator , protocols::simple_moves::DumpPdbCreator , protocols::simple_moves::ExtendedPoseMoverCreator , protocols::simple_moves::FavorSequenceProfileCreator , protocols::simple_moves::FavorSymmetricSequenceCreator , protocols::simple_moves::FindConsensusSequenceCreator , protocols::simple_moves::ForceDisulfidesMoverCreator , protocols::simple_moves::GenericMonteCarloMoverCreator , protocols::simple_moves::LoadPDBMoverCreator , protocols::simple_moves::LoadUnboundRotMoverCreator , protocols::simple_moves::MakePolyXMoverCreator , protocols::simple_moves::MembraneTopologyCreator , protocols::simple_moves::MinMoverCreator , protocols::simple_moves::MinPackMoverCreator , protocols::simple_moves::MonteCarloRecoverCreator , protocols::simple_moves::MonteCarloResetCreator , protocols::simple_moves::MonteCarloTestCreator , protocols::simple_moves::MSDMoverCreator , protocols::simple_moves::MutateResidueCreator , protocols::simple_moves::PackRotamersMoverCreator , protocols::simple_moves::PackRotamersMoverLazyCreator , protocols::simple_moves::PDBReloadMoverCreator , protocols::simple_moves::PSSM2BfactorMoverCreator , protocols::simple_moves::RandomOmegaFlipMoverCreator , protocols::simple_moves::RandomTorsionMoverCreator , protocols::simple_moves::RepackSidechainsMoverCreator , protocols::simple_moves::RepeatPropagationMoverCreator , protocols::simple_moves::ReportEffectivePKACreator , protocols::simple_moves::ResetBaselineMoverCreator , protocols::simple_moves::ResidueTypeConstraintMoverCreator , protocols::simple_moves::RotamerTrialsMinMoverCreator , protocols::simple_moves::RotamerTrialsMoverCreator , protocols::simple_moves::SaneMinMoverCreator , protocols::simple_moves::ScoreMoverCreator , protocols::simple_moves::SequenceProfileMoverCreator , protocols::simple_moves::SetTorsionCreator , protocols::simple_moves::ShearMoverCreator , protocols::simple_moves::ShortBackrubMoverCreator , protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMoverCreator , protocols::simple_moves::sidechain_moves::PerturbChiSidechainMoverCreator , protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMoverCreator , protocols::simple_moves::sidechain_moves::SetChiMoverCreator , protocols::simple_moves::sidechain_moves::SidechainMCMoverCreator , protocols::simple_moves::sidechain_moves::SidechainMoverCreator , protocols::simple_moves::SmallMoverCreator , protocols::simple_moves::SuperimposeMoverCreator , protocols::simple_moves::SwitchChainOrderMoverCreator , protocols::simple_moves::SwitchResidueTypeSetMoverCreator , protocols::simple_moves::symmetry::DetectSymmetryMoverCreator , protocols::simple_moves::symmetry::ExtractAsymmetricPoseMoverCreator , protocols::simple_moves::symmetry::ExtractAsymmetricUnitMoverCreator , protocols::simple_moves::symmetry::SetupForSymmetryMoverCreator , protocols::simple_moves::symmetry::SetupNCSMoverCreator , protocols::simple_moves::symmetry::SymMinMoverCreator , protocols::simple_moves::symmetry::SymPackRotamersMoverCreator , protocols::simple_moves::symmetry::SymRotamerTrialsMoverCreator , protocols::simple_moves::symmetry::TaskAwareSymMinMoverCreator , protocols::simple_moves::TaskAwareMinMoverCreator , protocols::simple_moves::TumbleCreator , protocols::simple_moves::VirtualRootMoverCreator , protocols::symmetric_docking::membrane::MPSymDockMoverCreator , protocols::symmetric_docking::SymDockProtocolCreator , protocols::symmetric_docking::SymFoldandDockMoveRbJumpMoverCreator , protocols::symmetric_docking::SymFoldandDockRbTrialMoverCreator , protocols::symmetric_docking::SymFoldandDockSlideTrialMoverCreator , protocols::toolbox::task_operations::StoreCombinedStoredTasksMoverCreator , protocols::toolbox::task_operations::StoreCompoundTaskMoverCreator , protocols::toolbox::task_operations::StoreTaskMoverCreator
• mover_stopping_condition() : protocols::simple_moves::GenericMonteCarloMover
• mover_stopping_condition_ : protocols::simple_moves::GenericMonteCarloMover
• mover_tag() : protocols::topology_broker::FragmentClaimer
• mover_tag_ : protocols::rosetta_scripts::AdditionalOutputWrapper , protocols::rosetta_scripts::MultipleOutputWrapper , protocols::simple_moves::GenericMonteCarloMover , protocols::topology_broker::FragmentClaimer
• mover_type_text : protocols::boinc::BoincSharedMemory
• mover_weight() : protocols::topology_broker::TopologyClaimer
• 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 , protocols::rosetta_scripts::RosettaScriptsParser
• MoverFactoryOP : protocols::rosetta_scripts::RosettaScriptsParser
• MoverFilterPair() : protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair
• MoverFilterVector : protocols::rosetta_scripts::ParsedProtocol
• MoverForPoseList() : protocols::moves::MoverForPoseList
• 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::enzdes::RemoveLigandFilter , 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::RemodelLoopMover , protocols::forge::remodel::RemodelMover , protocols::jd2::Parser , protocols::match::MatcherMover , protocols::matdes::SymDofMover , protocols::moves::DsspMover , protocols::moves::FilterMover , protocols::nonlocal::SingleFragmentMover , protocols::simple_moves::BoltzmannRotamerMover , protocols::simple_moves::ConsensusDesignMover , protocols::simple_moves::CoupledMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::MakePolyXMover , protocols::simple_moves::MonteCarloRecover , protocols::simple_moves::MonteCarloReset , protocols::simple_moves::MonteCarloTest , protocols::simple_moves::RotamerTrialsMover , protocols::simple_moves::ShortBackrubMover
• 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
• movers_and_passes_ : protocols::environment::EnvClaimBroker
• Movers_map : protocols::fldsgn::BluePrintBDR , protocols::fldsgn::CircularPermutation , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::filters::FragQualFilter , protocols::fldsgn::filters::HelixKinkFilter , protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::filters::HSSTripletFilter , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::fldsgn::filters::NcontactsFilter , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter , protocols::fldsgn::filters::SecondaryStructureCountFilter , protocols::fldsgn::filters::SecondaryStructureFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter , protocols::fldsgn::filters::SheetTopologyFilter , protocols::fldsgn::MatchResidues , protocols::fldsgn::MatchResiduesMover , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::flxbb::FlxbbDesign , protocols::flxbb::InterlockAroma , protocols::forge::remodel::RemodelLoopMover , protocols::forge::remodel::RemodelMover , protocols::indexed_structure_store::filters::FragmentLookupFilter , protocols::match::MatcherMover , protocols::matdes::ClashCheckFilter , protocols::matdes::GetRBDOFValues , protocols::matdes::OligomericAverageDegreeFilter , protocols::matdes::SymDofMover , protocols::matdes::SymUnsatHbondFilter , protocols::moves::DsspMover , protocols::simple_filters::HolesFilter , protocols::simple_filters::InterRepeatContactFilter , protocols::simple_filters::IntraRepeatContactFilter , protocols::simple_filters::PackStatFilter , protocols::simple_filters::RangeFilter , protocols::simple_filters::SaveResfileToDiskFilter , protocols::simple_filters::ShapeComplementarityFilter , protocols::simple_filters::TaskAwareSASAFilter , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::MakePolyXMover , protocols::simple_moves::MonteCarloRecover , protocols::simple_moves::MonteCarloReset , protocols::simple_moves::MonteCarloTest , protocols::toolbox::pose_metric_calculators::FragQualCalculator
• MoverSet : protocols::abinitio::abscript::AbscriptMover , protocols::abinitio::abscript::AbscriptStageMover
• MoverStatistics() : protocols::moves::MoverStatistics
• movertype : protocols::mpi_refinement::MethodParams
• 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_ : protocols::electron_density::BfactorMultifunc
• moving_distance_ : protocols::normalmode::NormalModeRelaxMover
• 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::StepWiseRNA_VirtualSugarSampler
• moving_res : protocols::stepwise::modeler::rna::sugar::SugarModeling , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters , protocols::stepwise::monte_carlo::SWA_Move , 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::StepWiseRNA_VirtualSugarJustInTimeInstantiator , protocols::stepwise::modeler::rna::sugar::SugarInstantiateMover , protocols::stepwise::modeler::rna::sugar::SugarVirtualizeMover , 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::StepWiseRNA_VirtualSugarJustInTimeInstantiator
• moving_res_list_ : 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::NativeRMSD_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_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_suite_ : protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser , protocols::stepwise::sampler::rna::RNA_KIC_Sampler , protocols::stepwise::sampler::rna::RNA_KinematicCloser
• MPDockingMover() : protocols::docking::membrane::MPDockingMover
• MPDockingSetupMover() : protocols::docking::membrane::MPDockingSetupMover
• MPFastRelaxMover() : protocols::relax::membrane::MPFastRelaxMover
• 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_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
• MPIBPool_RMSD() : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD
• MpiFileBuffer() : protocols::jd2::MpiFileBuffer
• MPIFileBufJobDistributor() : protocols::jd2::MPIFileBufJobDistributor
• MPIHPool_RMSD() : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• MPIMultiCommJobDistributor() : protocols::jd2::MPIMultiCommJobDistributor
• MPIMultistateFitnessFunction() : protocols::pack_daemon::MPIMultistateFitnessFunction
• MPIPool_RMSD() : protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD
• MPIWorkPartitionJobDistributor() : protocols::jd2::MPIWorkPartitionJobDistributor
• MPIWorkPoolJobDistributor() : protocols::jd2::MPIWorkPoolJobDistributor
• MPSymDockMover() : protocols::symmetric_docking::membrane::MPSymDockMover
• mrlod_ : protocols::make_rot_lib::MakeRotLibJob , protocols::make_rot_lib::MakeRotLibJobInputter
• MRMover() : protocols::hybridization::MRMover
• ms_whenfail_ : protocols::moves::FilterMover , protocols::protein_interface_design::movers::LoopOver
• MSDMover() : protocols::simple_moves::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
• mulfactor_ : protocols::mpi_refinement::StructAvrgMover
• multi_fast_relax() : protocols::abinitio::AbrelaxApplication
• multi_origin_list() : protocols::pockets::FingerprintBase
• multi_origin_list_ : protocols::pockets::FingerprintBase
• multi_relative() : protocols::simple_filters::Operator
• multi_relative_ : protocols::simple_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
• 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
• multifunc_ : protocols::optimize_weights::WrappedOptEExpressionCreator , protocols::optimize_weights::WrapperOptEMultifunc
• MultiObjective() : protocols::mpi_refinement::MultiObjective
• MultiPhosphateSampler() : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• multiple_domain_mover_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• multiple_jumps_ : protocols::docking::DockingInitialPerturbation
• MultipleDomainMover() : protocols::farna::MultipleDomainMover
• MultipleOutputWrapper() : protocols::rosetta_scripts::MultipleOutputWrapper
• MultiplePoseMover() : protocols::rosetta_scripts::MultiplePoseMover
• MultipleSigmoids() : protocols::simple_filters::MultipleSigmoids
• multiplier_ : protocols::inputter::FastaInputter , protocols::inputter::PDBInputter , protocols::inputter::SilentFileInputter , protocols::optimize_weights::PNatLigPoseOptEData , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection
• multiply_over_all_ : protocols::inputter::FastaInputter , protocols::inputter::PDBInputter , protocols::inputter::SilentFileInputter
• 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< T >
• MultiStateFitnessFunction() : protocols::multistate_design::MultiStateFitnessFunction
• MultistateFitnessFunction() : protocols::pack_daemon::MultistateFitnessFunction
• MultiStatePacker() : protocols::multistate_design::MultiStatePacker
• MultiTemperatureTrialCounter() : protocols::canonical_sampling::MultiTemperatureTrialCounter
• MultiThreadingJob() : protocols::jd2::MultiThreadingJob
• MultiThreadingMover() : protocols::comparative_modeling::MultiThreadingMover
• Multivec : protocols::md::MDBase , protocols::optimize_weights::OptEData , protocols::optimize_weights::OptEMultifunc , protocols::optimize_weights::OptEPositionData , protocols::optimize_weights::WrapperOptEMultifunc
• multivec2poseBfacts() : protocols::electron_density::BfactorMultifunc
• 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_residue() : protocols::pmut_scan::MutationData
• mut_residue_ : protocols::pmut_scan::MutationData
• mut_to_gly() : protocols::analysis::InterfaceAnalyzerMover
• MUT_UNBOUNDS_LIST_FILE : protocols::optimize_weights::DDGBindOptEData
• mut_unfolded_energies_emap_ : protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData
• Mutant() : protocols::pmut_scan::Mutant , protocols::pmut_scan::MutationData
• mutant_complexes_ : protocols::optimize_weights::DDGBindOptEData
• mutant_components_ : protocols::ddg::ddGMover
• mutant_score_components() : protocols::ddg::ddGMover
• mutant_unbound_components_ : protocols::ddg::ddGMover
• mutant_unbounds_ : protocols::optimize_weights::DDGBindOptEData
• mutants_ : protocols::ddg::ddGMover
• 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() : protocols::genetic_algorithm::DiscreteRandomizer , protocols::genetic_algorithm::EntityRandomizer , protocols::genetic_algorithm::Mutate1Randomizer , protocols::genetic_algorithm::PositionSpecificRandomizer
• mutate_and_relax() : protocols::design_opt::PointMutationCalculator , protocols::matdes::MatDesPointMutationCalculator
• mutate_rate_ : protocols::dna::DnaInterfaceMultiStateDesign , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• mutate_to_glycine_ : protocols::simple_moves::RepulsiveOnlyMover
• MutateResidue() : protocols::simple_moves::MutateResidue
• mutation_label() : protocols::ddg::ddGMover
• mutation_rate() : protocols::genetic_algorithm::EntityRandomizer
• mutation_rate_ : protocols::genetic_algorithm::EntityRandomizer
• mutation_string() : protocols::pmut_scan::MutationData
• mutation_string_PDB_numbering() : protocols::pmut_scan::MutationData
• mutation_threshold() : protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::simple_filters::MutationsFilter
• 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
• MutationsFilter() : protocols::simple_filters::MutationsFilter
• muts_ : protocols::optimize_weights::DDGMutationOptEData
• my_constraints_ : protocols::ligand_docking::ResidueTorsionRestraints
• 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_hits_for_target_hit_map_ : protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• 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::jd2::MpiFileBuffer
• my_window_ : protocols::viewer::ConformationViewer
• MyAtom() : protocols::fldsgn::MyAtom
• myslaves_ : protocols::mpi_refinement::MPI_Refine_Master